Starting phenix.real_space_refine on Tue Aug 4 20:30:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0k_65507/08_2026/9w0k_65507.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0k_65507/08_2026/9w0k_65507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w0k_65507/08_2026/9w0k_65507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0k_65507/08_2026/9w0k_65507.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w0k_65507/08_2026/9w0k_65507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0k_65507/08_2026/9w0k_65507.map" } resolution = 2.29 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= 0.008 sd= 0.051 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 41 5.16 5 C 4151 2.51 5 N 1103 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6543 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1880 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1901 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 297 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2299 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 278} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'SPH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.42, per 1000 atoms: 0.22 Number of scatterers: 6543 At special positions: 0 Unit cell: (105.203, 86.583, 83.79, 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 41 16.00 O 1248 8.00 N 1103 7.00 C 4151 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 354.2 milliseconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1550 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 16.0% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.663A pdb=" N ALA B 47 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.509A pdb=" N ILE B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.801A pdb=" N ARG B 151 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'C' and resid 42 through 48 removed outlier: 4.118A pdb=" N MET C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 50 through 55 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 57 Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.761A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.592A pdb=" N GLN A 164 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA2, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.989A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.989A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.589A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 40 removed outlier: 4.154A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 76 removed outlier: 5.591A pdb=" N LEU A 68 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N MET A 241 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.624A pdb=" N LEU C 80 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET C 196 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 82 " --> pdb=" O CYS C 194 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.296A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AB3, first strand: chain 'A' and resid 90 through 94 removed outlier: 4.166A pdb=" N ALA A 169 " --> pdb=" O PHE A 147 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 501 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: 0.71 Time building geometry restraints manager: 0.80 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: 2110 1.34 - 1.46: 1310 1.46 - 1.57: 3217 1.57 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 6705 Sorted by residual: bond pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " ideal model delta sigma weight residual 1.334 1.477 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" CA SER C 236 " pdb=" C SER C 236 " ideal model delta sigma weight residual 1.521 1.495 0.026 1.27e-02 6.20e+03 4.05e+00 bond pdb=" CA GLN C 235 " pdb=" C GLN C 235 " ideal model delta sigma weight residual 1.522 1.499 0.024 1.20e-02 6.94e+03 3.85e+00 bond pdb=" CA ASN C 237 " pdb=" C ASN C 237 " ideal model delta sigma weight residual 1.523 1.499 0.024 1.31e-02 5.83e+03 3.27e+00 bond pdb=" C3 SPH A 301 " pdb=" O3 SPH A 301 " ideal model delta sigma weight residual 1.438 1.407 0.031 2.00e-02 2.50e+03 2.43e+00 ... (remaining 6700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 8987 1.72 - 3.44: 124 3.44 - 5.15: 14 5.15 - 6.87: 4 6.87 - 8.59: 3 Bond angle restraints: 9132 Sorted by residual: angle pdb=" N SER C 236 " pdb=" CA SER C 236 " pdb=" C SER C 236 " ideal model delta sigma weight residual 113.97 108.08 5.89 1.28e+00 6.10e-01 2.12e+01 angle pdb=" CB LYS A 156 " pdb=" CG LYS A 156 " pdb=" CD LYS A 156 " ideal model delta sigma weight residual 111.30 119.55 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" N VAL C 189 " pdb=" CA VAL C 189 " pdb=" C VAL C 189 " ideal model delta sigma weight residual 112.96 109.60 3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " pdb=" C6 SPH A 301 " ideal model delta sigma weight residual 128.38 119.79 8.59 3.00e+00 1.11e-01 8.20e+00 angle pdb=" C3 SPH A 301 " pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " ideal model delta sigma weight residual 127.69 120.44 7.25 3.00e+00 1.11e-01 5.84e+00 ... (remaining 9127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.22: 3705 22.22 - 44.44: 273 44.44 - 66.66: 61 66.66 - 88.88: 15 88.88 - 111.10: 8 Dihedral angle restraints: 4062 sinusoidal: 1662 harmonic: 2400 Sorted by residual: dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" C5 MAN F 4 " ideal model delta sinusoidal sigma weight residual 54.75 -56.35 111.10 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O4 MAN F 4 " ideal model delta sinusoidal sigma weight residual 176.13 65.42 110.71 1 3.00e+01 1.11e-03 1.44e+01 dihedral pdb=" C5 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O3 MAN F 4 " ideal model delta sinusoidal sigma weight residual -174.53 -64.80 -109.73 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 4059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 867 0.053 - 0.106: 151 0.106 - 0.159: 27 0.159 - 0.211: 1 0.211 - 0.264: 1 Chirality restraints: 1047 Sorted by residual: chirality pdb=" C3 SPH A 301 " pdb=" C2 SPH A 301 " pdb=" C4 SPH A 301 " pdb=" O3 SPH A 301 " both_signs ideal model delta sigma weight residual False 2.42 2.16 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" O3 BMA F 3 " both_signs ideal model delta sigma weight residual False 2.41 2.23 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" C2 SPH A 301 " pdb=" C1 SPH A 301 " pdb=" C3 SPH A 301 " pdb=" N2 SPH A 301 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1044 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 SPH A 301 " 0.150 2.00e-02 2.50e+03 1.49e-01 2.21e+02 pdb=" C4 SPH A 301 " -0.153 2.00e-02 2.50e+03 pdb=" C5 SPH A 301 " -0.145 2.00e-02 2.50e+03 pdb=" C6 SPH A 301 " 0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 229 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO A 230 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 92 " -0.017 5.00e-02 4.00e+02 2.53e-02 1.02e+00 pdb=" N PRO C 93 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.014 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2453 2.89 - 3.39: 5752 3.39 - 3.89: 11352 3.89 - 4.40: 13536 4.40 - 4.90: 21725 Nonbonded interactions: 54818 Sorted by model distance: nonbonded pdb=" O5 MAN F 4 " pdb=" O6 MAN F 4 " model vdw 2.386 2.432 nonbonded pdb=" N2 SPH A 301 " pdb=" O1 SPH A 301 " model vdw 2.492 2.496 nonbonded pdb=" O5 BMA F 3 " pdb=" O6 BMA F 3 " model vdw 2.553 2.432 nonbonded pdb=" N SER C 236 " pdb=" N ASN C 237 " model vdw 2.581 2.560 nonbonded pdb=" C3 MAN F 4 " pdb=" O5 MAN F 4 " model vdw 2.594 2.776 ... (remaining 54813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.030 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 6710 Z= 0.162 Angle : 0.536 8.591 9147 Z= 0.272 Chirality : 0.042 0.264 1047 Planarity : 0.005 0.149 1170 Dihedral : 17.161 111.096 2512 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.10 % Allowed : 18.60 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.47 (0.28), residues: 819 helix: -1.57 (0.65), residues: 60 sheet: 0.43 (0.38), residues: 203 loop : -0.42 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.016 0.001 TYR B 31 PHE 0.008 0.001 PHE A 100 TRP 0.011 0.001 TRP A 93 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 6705) covalent geometry : angle 0.52977 / 0.27 ( 9132) hydrogen bonds : bond 0.19481 / 12.81 ( 177) hydrogen bonds : angle 8.91024 / 6.26 ( 501) link_ALPHA1-3 : bond 0.00443 / 0.23 ( 1) link_ALPHA1-3 : angle 3.04689 / 1.61 ( 3) link_ALPHA1-6 : bond 0.00567 / 0.30 ( 1) link_ALPHA1-6 : angle 1.32802 / 0.74 ( 3) link_BETA1-4 : bond 0.00060 / 0.03 ( 2) link_BETA1-4 : angle 2.12786 / 1.22 ( 6) link_BETA1-6 : bond 0.00395 / 0.21 ( 1) link_BETA1-6 : angle 1.11166 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.243 Fit side-chains REVERT: B 151 ARG cc_start: 0.8125 (mmt180) cc_final: 0.7815 (tpp-160) REVERT: C 52 MET cc_start: 0.9426 (mtm) cc_final: 0.8904 (mtm) REVERT: C 148 MET cc_start: 0.7536 (ppp) cc_final: 0.7264 (ptm) REVERT: C 183 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8585 (mttt) REVERT: C 226 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8921 (tt) REVERT: A 136 MET cc_start: 0.4647 (ttt) cc_final: 0.2638 (mmm) REVERT: A 157 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7990 (mt-10) outliers start: 15 outliers final: 9 residues processed: 119 average time/residue: 0.5477 time to fit residues: 68.0965 Evaluate side-chains 120 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 183 LYS Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.0470 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 45 HIS B 55 GLN B 206 GLN B 240 ASN C 74 GLN C 160 GLN C 179 ASN C 247 GLN A 44 GLN A 87 HIS A 102 GLN A 219 ASN A 278 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.081883 restraints weight = 9585.956| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.10 r_work: 0.2829 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6710 Z= 0.164 Angle : 0.536 8.118 9147 Z= 0.268 Chirality : 0.044 0.170 1047 Planarity : 0.004 0.029 1170 Dihedral : 9.862 62.579 1040 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.66 % Allowed : 17.48 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.44 (0.28), residues: 819 helix: -1.71 (0.62), residues: 66 sheet: 0.53 (0.38), residues: 203 loop : -0.40 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.016 0.001 TYR B 31 PHE 0.014 0.001 PHE A 100 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 6705) covalent geometry : angle 0.53045 / 0.27 ( 9132) hydrogen bonds : bond 0.04279 / 2.80 ( 177) hydrogen bonds : angle 6.66373 / 4.79 ( 501) link_ALPHA1-3 : bond 0.00627 / 0.33 ( 1) link_ALPHA1-3 : angle 2.30149 / 1.25 ( 3) link_ALPHA1-6 : bond 0.00400 / 0.21 ( 1) link_ALPHA1-6 : angle 1.42746 / 0.80 ( 3) link_BETA1-4 : bond 0.00113 / 0.06 ( 2) link_BETA1-4 : angle 2.14901 / 1.23 ( 6) link_BETA1-6 : bond 0.00411 / 0.22 ( 1) link_BETA1-6 : angle 1.16463 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.162 Fit side-chains REVERT: B 151 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7749 (tpp-160) REVERT: C 71 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8456 (pt) REVERT: C 148 MET cc_start: 0.7539 (ppp) cc_final: 0.7270 (ptm) REVERT: C 179 ASN cc_start: 0.7580 (OUTLIER) cc_final: 0.7343 (p0) REVERT: C 226 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8845 (tt) REVERT: D 43 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7941 (mtmp) REVERT: A 136 MET cc_start: 0.4829 (ttt) cc_final: 0.2674 (mmm) REVERT: A 157 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8034 (mp0) outliers start: 19 outliers final: 6 residues processed: 129 average time/residue: 0.4935 time to fit residues: 66.7986 Evaluate side-chains 120 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 237 ASN Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN B 206 GLN B 240 ASN C 160 GLN C 247 GLN A 87 HIS A 219 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.080996 restraints weight = 9497.155| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.10 r_work: 0.2815 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6710 Z= 0.197 Angle : 0.540 6.857 9147 Z= 0.272 Chirality : 0.044 0.142 1047 Planarity : 0.004 0.030 1170 Dihedral : 7.707 59.879 1029 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.38 % Allowed : 18.04 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.38 (0.28), residues: 819 helix: -1.65 (0.62), residues: 66 sheet: 0.61 (0.38), residues: 195 loop : -0.37 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 205 TYR 0.018 0.001 TYR B 31 PHE 0.013 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 6705) covalent geometry : angle 0.53406 / 0.27 ( 9132) hydrogen bonds : bond 0.04154 / 2.73 ( 177) hydrogen bonds : angle 6.38291 / 4.59 ( 501) link_ALPHA1-3 : bond 0.00324 / 0.17 ( 1) link_ALPHA1-3 : angle 2.76514 / 1.51 ( 3) link_ALPHA1-6 : bond 0.00392 / 0.21 ( 1) link_ALPHA1-6 : angle 1.46100 / 0.81 ( 3) link_BETA1-4 : bond 0.00232 / 0.12 ( 2) link_BETA1-4 : angle 2.25574 / 1.30 ( 6) link_BETA1-6 : bond 0.00099 / 0.05 ( 1) link_BETA1-6 : angle 1.21444 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.212 Fit side-chains REVERT: B 151 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7785 (tpp-160) REVERT: C 148 MET cc_start: 0.7566 (ppp) cc_final: 0.7306 (ptm) REVERT: C 226 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8925 (tt) REVERT: A 136 MET cc_start: 0.4814 (ttt) cc_final: 0.2664 (mmm) REVERT: A 157 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7967 (mp0) outliers start: 17 outliers final: 7 residues processed: 122 average time/residue: 0.5197 time to fit residues: 66.5419 Evaluate side-chains 117 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 GLN C 160 GLN C 247 GLN A 87 HIS A 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.082751 restraints weight = 9560.960| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.11 r_work: 0.2856 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6710 Z= 0.119 Angle : 0.489 6.275 9147 Z= 0.246 Chirality : 0.042 0.151 1047 Planarity : 0.003 0.027 1170 Dihedral : 7.135 59.718 1027 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.24 % Allowed : 17.90 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.33 (0.28), residues: 819 helix: -1.54 (0.62), residues: 66 sheet: 0.58 (0.37), residues: 203 loop : -0.33 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 66 TYR 0.018 0.001 TYR B 31 PHE 0.012 0.001 PHE A 100 TRP 0.005 0.001 TRP B 177 HIS 0.002 0.000 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6705) covalent geometry : angle 0.48138 / 0.24 ( 9132) hydrogen bonds : bond 0.03440 / 2.25 ( 177) hydrogen bonds : angle 6.08370 / 4.36 ( 501) link_ALPHA1-3 : bond 0.00133 / 0.07 ( 1) link_ALPHA1-3 : angle 3.42773 / 1.82 ( 3) link_ALPHA1-6 : bond 0.00389 / 0.20 ( 1) link_ALPHA1-6 : angle 1.41741 / 0.79 ( 3) link_BETA1-4 : bond 0.00104 / 0.05 ( 2) link_BETA1-4 : angle 2.02520 / 1.16 ( 6) link_BETA1-6 : bond 0.00457 / 0.24 ( 1) link_BETA1-6 : angle 1.04173 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.181 Fit side-chains REVERT: B 151 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7761 (tpp-160) REVERT: C 148 MET cc_start: 0.7516 (ppp) cc_final: 0.7291 (ptm) REVERT: C 226 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8874 (tt) REVERT: D 43 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7953 (mtmp) REVERT: E 203 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6481 (mt-10) REVERT: A 136 MET cc_start: 0.4768 (ttt) cc_final: 0.2665 (mmm) REVERT: A 157 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8017 (mp0) outliers start: 16 outliers final: 5 residues processed: 124 average time/residue: 0.5000 time to fit residues: 65.2942 Evaluate side-chains 119 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 39 optimal weight: 8.9990 chunk 31 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 52.6305 > 50:) chunk 8 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN B 206 GLN B 240 ASN C 160 GLN C 247 GLN A 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.095021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.079184 restraints weight = 9799.279| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.11 r_work: 0.2785 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 6710 Z= 0.287 Angle : 0.586 7.413 9147 Z= 0.296 Chirality : 0.046 0.155 1047 Planarity : 0.004 0.029 1170 Dihedral : 7.438 58.618 1026 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.80 % Allowed : 17.34 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.39 (0.28), residues: 819 helix: -1.65 (0.62), residues: 66 sheet: 0.71 (0.38), residues: 189 loop : -0.40 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 205 TYR 0.017 0.002 TYR B 31 PHE 0.015 0.002 PHE C 215 TRP 0.008 0.001 TRP B 177 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.29 ( 6705) covalent geometry : angle 0.58035 / 0.30 ( 9132) hydrogen bonds : bond 0.04242 / 2.79 ( 177) hydrogen bonds : angle 6.19272 / 4.45 ( 501) link_ALPHA1-3 : bond 0.00196 / 0.10 ( 1) link_ALPHA1-3 : angle 2.90039 / 1.55 ( 3) link_ALPHA1-6 : bond 0.00288 / 0.15 ( 1) link_ALPHA1-6 : angle 1.39824 / 0.78 ( 3) link_BETA1-4 : bond 0.00281 / 0.15 ( 2) link_BETA1-4 : angle 2.26848 / 1.30 ( 6) link_BETA1-6 : bond 0.00123 / 0.06 ( 1) link_BETA1-6 : angle 1.35485 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.171 Fit side-chains REVERT: C 148 MET cc_start: 0.7601 (ppp) cc_final: 0.7386 (ptm) REVERT: C 226 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8976 (tt) REVERT: D 43 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7915 (mtmp) REVERT: A 136 MET cc_start: 0.4902 (ttt) cc_final: 0.2669 (mmm) REVERT: A 157 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7981 (mp0) outliers start: 20 outliers final: 11 residues processed: 121 average time/residue: 0.4763 time to fit residues: 60.4735 Evaluate side-chains 119 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 GLN B 240 ASN C 160 GLN C 247 GLN A 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.098802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.082885 restraints weight = 9478.392| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.13 r_work: 0.2848 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6710 Z= 0.106 Angle : 0.490 6.153 9147 Z= 0.246 Chirality : 0.041 0.157 1047 Planarity : 0.003 0.026 1170 Dihedral : 7.164 59.945 1026 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.52 % Allowed : 17.62 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.33 (0.28), residues: 819 helix: -1.49 (0.62), residues: 66 sheet: 0.62 (0.38), residues: 195 loop : -0.34 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.015 0.001 TYR B 31 PHE 0.011 0.001 PHE A 100 TRP 0.004 0.001 TRP B 177 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 6705) covalent geometry : angle 0.48354 / 0.24 ( 9132) hydrogen bonds : bond 0.03259 / 2.13 ( 177) hydrogen bonds : angle 5.92613 / 4.24 ( 501) link_ALPHA1-3 : bond 0.00232 / 0.12 ( 1) link_ALPHA1-3 : angle 3.30176 / 1.75 ( 3) link_ALPHA1-6 : bond 0.00491 / 0.26 ( 1) link_ALPHA1-6 : angle 1.40475 / 0.79 ( 3) link_BETA1-4 : bond 0.00203 / 0.10 ( 2) link_BETA1-4 : angle 1.93854 / 1.11 ( 6) link_BETA1-6 : bond 0.00523 / 0.28 ( 1) link_BETA1-6 : angle 1.03513 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.236 Fit side-chains REVERT: B 151 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7712 (tpp-160) REVERT: C 148 MET cc_start: 0.7512 (ppp) cc_final: 0.7289 (ptm) REVERT: C 226 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8859 (tt) REVERT: D 43 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7920 (mtmp) REVERT: E 203 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6569 (mt-10) REVERT: A 136 MET cc_start: 0.4651 (ttt) cc_final: 0.2611 (mmm) REVERT: A 157 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7975 (mp0) outliers start: 18 outliers final: 7 residues processed: 127 average time/residue: 0.5126 time to fit residues: 68.0789 Evaluate side-chains 121 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN B 206 GLN B 240 ASN C 160 GLN C 247 GLN A 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.082601 restraints weight = 9543.488| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.10 r_work: 0.2843 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6710 Z= 0.136 Angle : 0.502 5.909 9147 Z= 0.252 Chirality : 0.042 0.160 1047 Planarity : 0.003 0.027 1170 Dihedral : 7.140 59.645 1026 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.24 % Allowed : 17.90 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.32 (0.28), residues: 819 helix: -1.45 (0.62), residues: 66 sheet: 0.61 (0.37), residues: 195 loop : -0.32 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 151 TYR 0.015 0.001 TYR B 31 PHE 0.013 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 6705) covalent geometry : angle 0.49499 / 0.25 ( 9132) hydrogen bonds : bond 0.03414 / 2.23 ( 177) hydrogen bonds : angle 5.84879 / 4.18 ( 501) link_ALPHA1-3 : bond 0.00215 / 0.11 ( 1) link_ALPHA1-3 : angle 3.12915 / 1.66 ( 3) link_ALPHA1-6 : bond 0.00456 / 0.24 ( 1) link_ALPHA1-6 : angle 1.38916 / 0.78 ( 3) link_BETA1-4 : bond 0.00154 / 0.08 ( 2) link_BETA1-4 : angle 2.00716 / 1.15 ( 6) link_BETA1-6 : bond 0.00342 / 0.18 ( 1) link_BETA1-6 : angle 1.20953 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.176 Fit side-chains REVERT: B 151 ARG cc_start: 0.8079 (mmt180) cc_final: 0.7734 (tpp-160) REVERT: C 65 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8721 (mt-10) REVERT: C 148 MET cc_start: 0.7549 (ppp) cc_final: 0.7335 (ptm) REVERT: C 226 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8896 (tt) REVERT: D 43 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7951 (mtmp) REVERT: E 203 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6600 (mt-10) REVERT: E 205 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7826 (ttt-90) REVERT: A 136 MET cc_start: 0.4798 (ttt) cc_final: 0.2664 (mmm) REVERT: A 157 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7985 (mp0) outliers start: 16 outliers final: 9 residues processed: 117 average time/residue: 0.5223 time to fit residues: 63.9401 Evaluate side-chains 120 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 74 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN B 206 GLN B 240 ASN C 160 GLN C 247 GLN A 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.080464 restraints weight = 9653.321| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.10 r_work: 0.2810 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6710 Z= 0.207 Angle : 0.549 6.624 9147 Z= 0.276 Chirality : 0.044 0.162 1047 Planarity : 0.004 0.028 1170 Dihedral : 7.325 59.848 1026 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.38 % Allowed : 17.76 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.35 (0.28), residues: 819 helix: -1.51 (0.62), residues: 66 sheet: 0.62 (0.36), residues: 204 loop : -0.37 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 205 TYR 0.016 0.001 TYR B 31 PHE 0.014 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 ( 6705) covalent geometry : angle 0.54313 / 0.27 ( 9132) hydrogen bonds : bond 0.03821 / 2.50 ( 177) hydrogen bonds : angle 5.96320 / 4.28 ( 501) link_ALPHA1-3 : bond 0.00224 / 0.12 ( 1) link_ALPHA1-3 : angle 3.03315 / 1.61 ( 3) link_ALPHA1-6 : bond 0.00434 / 0.23 ( 1) link_ALPHA1-6 : angle 1.37393 / 0.77 ( 3) link_BETA1-4 : bond 0.00185 / 0.09 ( 2) link_BETA1-4 : angle 2.11659 / 1.21 ( 6) link_BETA1-6 : bond 0.00300 / 0.16 ( 1) link_BETA1-6 : angle 1.15633 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.189 Fit side-chains REVERT: B 151 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7761 (tpp-160) REVERT: C 148 MET cc_start: 0.7601 (ppp) cc_final: 0.7369 (ptm) REVERT: C 226 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8919 (tt) REVERT: D 43 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7923 (mtmp) REVERT: E 203 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6683 (mt-10) REVERT: E 205 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7849 (tmt170) REVERT: A 136 MET cc_start: 0.4858 (ttt) cc_final: 0.2637 (mmm) REVERT: A 157 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7952 (mp0) outliers start: 17 outliers final: 10 residues processed: 117 average time/residue: 0.5181 time to fit residues: 63.5756 Evaluate side-chains 120 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 GLN B 240 ASN C 160 GLN C 247 GLN A 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.081536 restraints weight = 9656.265| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.11 r_work: 0.2826 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6710 Z= 0.161 Angle : 0.528 6.381 9147 Z= 0.264 Chirality : 0.043 0.165 1047 Planarity : 0.004 0.028 1170 Dihedral : 7.471 59.769 1026 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.38 % Allowed : 17.76 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.34 (0.28), residues: 819 helix: -1.47 (0.62), residues: 66 sheet: 0.62 (0.36), residues: 204 loop : -0.37 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 205 TYR 0.016 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 6705) covalent geometry : angle 0.52154 / 0.26 ( 9132) hydrogen bonds : bond 0.03556 / 2.32 ( 177) hydrogen bonds : angle 5.90423 / 4.23 ( 501) link_ALPHA1-3 : bond 0.00176 / 0.09 ( 1) link_ALPHA1-3 : angle 3.14471 / 1.67 ( 3) link_ALPHA1-6 : bond 0.00473 / 0.25 ( 1) link_ALPHA1-6 : angle 1.38183 / 0.77 ( 3) link_BETA1-4 : bond 0.00171 / 0.08 ( 2) link_BETA1-4 : angle 2.08386 / 1.19 ( 6) link_BETA1-6 : bond 0.00388 / 0.20 ( 1) link_BETA1-6 : angle 1.12136 / 0.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.253 Fit side-chains REVERT: B 151 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7764 (tpp-160) REVERT: C 148 MET cc_start: 0.7578 (ppp) cc_final: 0.7352 (ptm) REVERT: C 226 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8884 (tt) REVERT: D 43 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7944 (mtmp) REVERT: E 203 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6678 (mt-10) REVERT: E 205 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7810 (tmt170) REVERT: A 136 MET cc_start: 0.4832 (ttt) cc_final: 0.2623 (mmm) REVERT: A 157 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7965 (mp0) outliers start: 17 outliers final: 10 residues processed: 119 average time/residue: 0.4953 time to fit residues: 61.8512 Evaluate side-chains 123 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN B 206 GLN B 240 ASN C 160 GLN C 247 GLN A 87 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.096847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.081116 restraints weight = 9590.686| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.11 r_work: 0.2825 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6710 Z= 0.166 Angle : 0.537 8.109 9147 Z= 0.268 Chirality : 0.043 0.165 1047 Planarity : 0.004 0.028 1170 Dihedral : 7.418 59.725 1026 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.24 % Allowed : 17.76 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.34 (0.28), residues: 819 helix: -1.49 (0.62), residues: 66 sheet: 0.60 (0.36), residues: 204 loop : -0.35 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 205 TYR 0.017 0.001 TYR B 31 PHE 0.013 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 6705) covalent geometry : angle 0.53102 / 0.27 ( 9132) hydrogen bonds : bond 0.03582 / 2.33 ( 177) hydrogen bonds : angle 5.89043 / 4.22 ( 501) link_ALPHA1-3 : bond 0.00120 / 0.06 ( 1) link_ALPHA1-3 : angle 3.10693 / 1.65 ( 3) link_ALPHA1-6 : bond 0.00485 / 0.26 ( 1) link_ALPHA1-6 : angle 1.36960 / 0.77 ( 3) link_BETA1-4 : bond 0.00194 / 0.10 ( 2) link_BETA1-4 : angle 2.11557 / 1.21 ( 6) link_BETA1-6 : bond 0.00284 / 0.15 ( 1) link_BETA1-6 : angle 1.21182 / 0.67 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.247 Fit side-chains REVERT: B 151 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7767 (tpp-160) REVERT: C 148 MET cc_start: 0.7553 (ppp) cc_final: 0.7325 (ptm) REVERT: C 226 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8901 (tt) REVERT: D 43 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7964 (mtmp) REVERT: E 203 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6697 (mt-10) REVERT: E 205 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7839 (ttt-90) REVERT: A 136 MET cc_start: 0.4855 (ttt) cc_final: 0.2650 (mmm) REVERT: A 157 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7969 (mp0) outliers start: 16 outliers final: 10 residues processed: 118 average time/residue: 0.4743 time to fit residues: 58.6586 Evaluate side-chains 122 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain E residue 205 ARG Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 206 GLN B 240 ASN C 160 GLN C 247 GLN A 87 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.083654 restraints weight = 9417.704| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.10 r_work: 0.2861 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6710 Z= 0.108 Angle : 0.499 8.186 9147 Z= 0.248 Chirality : 0.041 0.169 1047 Planarity : 0.003 0.027 1170 Dihedral : 7.389 59.939 1026 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.24 % Allowed : 17.90 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 are not related in a simple way. whole: -0.33 (0.28), residues: 819 helix: -1.38 (0.62), residues: 66 sheet: 0.45 (0.37), residues: 203 loop : -0.29 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 205 TYR 0.014 0.001 TYR B 31 PHE 0.010 0.001 PHE C 215 TRP 0.005 0.001 TRP B 177 HIS 0.002 0.000 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6705) covalent geometry : angle 0.49222 / 0.25 ( 9132) hydrogen bonds : bond 0.03171 / 2.06 ( 177) hydrogen bonds : angle 5.78451 / 4.13 ( 501) link_ALPHA1-3 : bond 0.00190 / 0.10 ( 1) link_ALPHA1-3 : angle 3.24680 / 1.72 ( 3) link_ALPHA1-6 : bond 0.00556 / 0.29 ( 1) link_ALPHA1-6 : angle 1.38211 / 0.77 ( 3) link_BETA1-4 : bond 0.00220 / 0.10 ( 2) link_BETA1-4 : angle 1.97507 / 1.12 ( 6) link_BETA1-6 : bond 0.00449 / 0.24 ( 1) link_BETA1-6 : angle 1.05800 / 0.59 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2530.99 seconds wall clock time: 43 minutes 40.33 seconds (2620.33 seconds total)