Starting phenix.real_space_refine on Tue Aug 4 20:17:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0j_65506/08_2026/9w0j_65506.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0j_65506/08_2026/9w0j_65506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w0j_65506/08_2026/9w0j_65506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0j_65506/08_2026/9w0j_65506.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w0j_65506/08_2026/9w0j_65506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0j_65506/08_2026/9w0j_65506.map" } resolution = 2.09 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= 0.048 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 4128 2.51 5 N 1102 2.21 5 O 1232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s 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: 6503 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: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'GAL': 1, 'SIA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 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: 1.41, per 1000 atoms: 0.22 Number of scatterers: 6503 At special positions: 0 Unit cell: (105.203, 85.652, 84.721, 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 1232 8.00 N 1102 7.00 C 4128 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 BETA2-6 " GAL G 1 " - " SIA G 2 " ~> Even though SIA is an alpha isomer, a beta linkage is required... Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 366.8 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 16.3% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 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: 3.700A 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 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.654A 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: 4.159A 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 242 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 removed outlier: 3.501A pdb=" N THR A 57 " --> pdb=" O VAL A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.716A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.797A 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: 6.996A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.376A 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: 6.996A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.376A 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: 3.623A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.091A 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: 4.213A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.960A 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: 5.552A pdb=" N LEU A 68 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N MET A 241 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.960A 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: 6.887A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.759A 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 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 94 205 hydrogen bonds defined for protein. 492 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: 0.83 Time building geometry restraints manager: 0.51 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: 2112 1.34 - 1.46: 1540 1.46 - 1.58: 2944 1.58 - 1.70: 1 1.70 - 1.82: 68 Bond restraints: 6665 Sorted by residual: bond pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " ideal model delta sigma weight residual 1.334 1.471 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" CA GLN C 235 " pdb=" C GLN C 235 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.20e-02 6.94e+03 4.70e+00 bond pdb=" CA VAL A 295 " pdb=" C VAL A 295 " ideal model delta sigma weight residual 1.526 1.505 0.021 1.13e-02 7.83e+03 3.37e+00 bond pdb=" CA ILE A 294 " pdb=" C ILE A 294 " ideal model delta sigma weight residual 1.526 1.505 0.021 1.13e-02 7.83e+03 3.31e+00 bond pdb=" CA SER C 236 " pdb=" C SER C 236 " ideal model delta sigma weight residual 1.519 1.499 0.020 1.32e-02 5.74e+03 2.25e+00 ... (remaining 6660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 8958 1.89 - 3.78: 109 3.78 - 5.67: 6 5.67 - 7.56: 3 7.56 - 9.45: 2 Bond angle restraints: 9078 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 113.88 107.96 5.92 1.23e+00 6.61e-01 2.31e+01 angle pdb=" CB MET A 257 " pdb=" CG MET A 257 " pdb=" SD MET A 257 " ideal model delta sigma weight residual 112.70 122.15 -9.45 3.00e+00 1.11e-01 9.92e+00 angle pdb=" C ILE A 294 " pdb=" CA ILE A 294 " pdb=" CB ILE A 294 " ideal model delta sigma weight residual 111.23 108.19 3.04 1.08e+00 8.57e-01 7.94e+00 angle pdb=" C3 SPH A 301 " pdb=" C4 SPH A 301 " pdb=" C5 SPH A 301 " ideal model delta sigma weight residual 127.69 119.38 8.31 3.00e+00 1.11e-01 7.67e+00 angle pdb=" CB MET A 187 " pdb=" CG MET A 187 " pdb=" SD MET A 187 " ideal model delta sigma weight residual 112.70 120.11 -7.41 3.00e+00 1.11e-01 6.10e+00 ... (remaining 9073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 3560 17.78 - 35.57: 313 35.57 - 53.35: 86 53.35 - 71.14: 26 71.14 - 88.92: 12 Dihedral angle restraints: 3997 sinusoidal: 1597 harmonic: 2400 Sorted by residual: dihedral pdb=" CA ASN D 31 " pdb=" CB ASN D 31 " pdb=" CG ASN D 31 " pdb=" OD1 ASN D 31 " ideal model delta sinusoidal sigma weight residual -90.00 -164.17 74.17 2 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB GLU E 203 " pdb=" CG GLU E 203 " pdb=" CD GLU E 203 " pdb=" OE1 GLU E 203 " ideal model delta sinusoidal sigma weight residual 0.00 -88.92 88.92 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU A 15 " pdb=" CG GLU A 15 " pdb=" CD GLU A 15 " pdb=" OE1 GLU A 15 " ideal model delta sinusoidal sigma weight residual 0.00 -88.31 88.31 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 575 0.026 - 0.052: 263 0.052 - 0.078: 104 0.078 - 0.103: 58 0.103 - 0.129: 28 Chirality restraints: 1028 Sorted by residual: chirality pdb=" C2 SIA G 2 " pdb=" O6 GAL G 1 " pdb=" C1 SIA G 2 " pdb=" O6 SIA G 2 " both_signs ideal model delta sigma weight residual False -2.50 -2.43 -0.07 2.00e-02 2.50e+03 1.08e+01 chirality pdb=" CA ILE C 36 " pdb=" N ILE C 36 " pdb=" C ILE C 36 " pdb=" CB ILE C 36 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE B 127 " pdb=" N ILE B 127 " pdb=" C ILE B 127 " pdb=" CB ILE B 127 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 1025 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 SPH A 301 " 0.111 2.00e-02 2.50e+03 1.12e-01 1.26e+02 pdb=" C4 SPH A 301 " -0.107 2.00e-02 2.50e+03 pdb=" C5 SPH A 301 " -0.118 2.00e-02 2.50e+03 pdb=" C6 SPH A 301 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 102 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.27e+00 pdb=" CD GLN A 102 " 0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN A 102 " -0.007 2.00e-02 2.50e+03 pdb=" NE2 GLN A 102 " -0.007 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 2.77e-02 1.22e+00 pdb=" N PRO A 230 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.016 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 3526 3.01 - 3.48: 6132 3.48 - 3.96: 11150 3.96 - 4.43: 13232 4.43 - 4.90: 20621 Nonbonded interactions: 54661 Sorted by model distance: nonbonded pdb=" C6 GAL G 1 " pdb=" O6 SIA G 2 " model vdw 2.538 2.752 nonbonded pdb=" N ASP C 220 " pdb=" OD1 ASP C 220 " model vdw 2.547 3.120 nonbonded pdb=" O6 SIA G 2 " pdb=" O7 SIA G 2 " model vdw 2.584 2.432 nonbonded pdb=" N SER C 236 " pdb=" N ASN C 237 " model vdw 2.599 2.560 nonbonded pdb=" N ASN C 199 " pdb=" O ASN C 199 " model vdw 2.617 2.496 ... (remaining 54656 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: 0.880 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.800 Find NCS groups from input model: 0.020 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:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 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 0.137 6666 Z= 0.160 Angle : 0.518 9.447 9081 Z= 0.266 Chirality : 0.041 0.129 1028 Planarity : 0.005 0.112 1170 Dihedral : 16.151 88.924 2447 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.12 % Allowed : 18.46 % Favored : 80.42 % 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: -0.09 (0.29), residues: 819 helix: -1.37 (0.68), residues: 60 sheet: 0.60 (0.38), residues: 197 loop : -0.10 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 12 TYR 0.014 0.001 TYR B 31 PHE 0.007 0.001 PHE A 100 TRP 0.004 0.001 TRP A 249 HIS 0.002 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 6665) covalent geometry : angle 0.51773 / 0.27 ( 9078) hydrogen bonds : bond 0.18864 / 12.21 ( 177) hydrogen bonds : angle 8.86039 / 6.15 ( 492) glycosidic custom : bond 0.00016 / 0.01 ( 1) glycosidic custom : angle 0.28939 / 0.16 ( 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 118 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.256 Fit side-chains REVERT: B 46 GLU cc_start: 0.9190 (pt0) cc_final: 0.8932 (pt0) REVERT: B 67 ARG cc_start: 0.8689 (mtp-110) cc_final: 0.8416 (mtp-110) REVERT: B 147 MET cc_start: 0.9269 (mmt) cc_final: 0.8928 (mmt) REVERT: B 150 GLU cc_start: 0.8808 (pp20) cc_final: 0.8224 (tm-30) REVERT: B 151 ARG cc_start: 0.8371 (tpt90) cc_final: 0.8007 (tpm170) REVERT: C 50 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8354 (mt-10) REVERT: C 86 LEU cc_start: 0.9456 (mt) cc_final: 0.9248 (mt) REVERT: C 114 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8402 (pp20) REVERT: A 14 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.9038 (p) REVERT: A 136 MET cc_start: 0.4950 (ttt) cc_final: 0.3733 (mtp) REVERT: A 182 MET cc_start: 0.9246 (ptp) cc_final: 0.8914 (ptt) REVERT: A 290 MET cc_start: 0.9320 (mmt) cc_final: 0.9101 (mmt) outliers start: 8 outliers final: 4 residues processed: 114 average time/residue: 0.6317 time to fit residues: 75.2661 Evaluate side-chains 112 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 272 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 ASN B 45 HIS B 55 GLN B 88 ASN B 97 GLN B 206 GLN B 240 ASN C 101 ASN C 160 GLN C 235 GLN D 31 ASN A 44 GLN A 102 GLN A 219 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.088248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.071201 restraints weight = 9296.066| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.01 r_work: 0.2725 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6666 Z= 0.180 Angle : 0.506 6.003 9081 Z= 0.264 Chirality : 0.043 0.137 1028 Planarity : 0.004 0.030 1170 Dihedral : 7.773 66.164 963 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.96 % Allowed : 16.22 % Favored : 81.82 % 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: -0.05 (0.29), residues: 819 helix: -1.50 (0.63), residues: 66 sheet: 0.75 (0.38), residues: 197 loop : -0.08 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 205 TYR 0.017 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.005 0.001 TRP B 177 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 6665) covalent geometry : angle 0.50581 / 0.26 ( 9078) hydrogen bonds : bond 0.04331 / 2.83 ( 177) hydrogen bonds : angle 6.61922 / 4.52 ( 492) glycosidic custom : bond 0.00048 / 0.03 ( 1) glycosidic custom : angle 0.77771 / 0.43 ( 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 118 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.212 Fit side-chains REVERT: B 46 GLU cc_start: 0.9275 (pt0) cc_final: 0.8975 (pt0) REVERT: B 147 MET cc_start: 0.9247 (mmt) cc_final: 0.8794 (mmt) REVERT: B 150 GLU cc_start: 0.8791 (pp20) cc_final: 0.8428 (pp20) REVERT: B 151 ARG cc_start: 0.8369 (tpt90) cc_final: 0.8135 (tpm170) REVERT: C 114 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8672 (pp20) REVERT: A 122 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9239 (tp) REVERT: A 136 MET cc_start: 0.5129 (ttt) cc_final: 0.3742 (mtp) REVERT: A 182 MET cc_start: 0.9340 (ptp) cc_final: 0.8980 (ptt) REVERT: A 241 MET cc_start: 0.9437 (ttp) cc_final: 0.9151 (ttm) outliers start: 14 outliers final: 7 residues processed: 114 average time/residue: 0.5729 time to fit residues: 68.4672 Evaluate side-chains 111 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 MET 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 122 LEU Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 66 optimal weight: 0.0980 chunk 12 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 ASN B 97 GLN C 160 GLN D 31 ASN A 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.087115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.070340 restraints weight = 9238.289| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.99 r_work: 0.2699 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6666 Z= 0.200 Angle : 0.528 8.978 9081 Z= 0.271 Chirality : 0.044 0.137 1028 Planarity : 0.004 0.032 1170 Dihedral : 7.615 64.925 961 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.96 % Allowed : 15.52 % Favored : 82.52 % 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: -0.04 (0.29), residues: 819 helix: -1.44 (0.63), residues: 66 sheet: 0.85 (0.38), residues: 189 loop : -0.11 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 205 TYR 0.018 0.002 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 ( 6665) covalent geometry : angle 0.52758 / 0.27 ( 9078) hydrogen bonds : bond 0.04020 / 2.62 ( 177) hydrogen bonds : angle 6.25965 / 4.26 ( 492) glycosidic custom : bond 0.00175 / 0.09 ( 1) glycosidic custom : angle 0.92013 / 0.51 ( 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 115 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.255 Fit side-chains REVERT: B 147 MET cc_start: 0.9209 (mmt) cc_final: 0.8838 (mmt) REVERT: B 151 ARG cc_start: 0.8341 (tpt90) cc_final: 0.8114 (tpm170) REVERT: C 114 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8587 (pp20) REVERT: D 55 GLU cc_start: 0.8884 (tt0) cc_final: 0.8666 (tt0) REVERT: A 136 MET cc_start: 0.5262 (ttt) cc_final: 0.3857 (mtp) REVERT: A 241 MET cc_start: 0.9505 (ttp) cc_final: 0.9210 (ttm) outliers start: 14 outliers final: 7 residues processed: 110 average time/residue: 0.6288 time to fit residues: 72.3905 Evaluate side-chains 110 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 272 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 0.0570 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 ASN C 160 GLN D 31 ASN A 102 GLN A 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.087266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.070427 restraints weight = 9343.108| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.01 r_work: 0.2710 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6666 Z= 0.187 Angle : 0.516 7.687 9081 Z= 0.266 Chirality : 0.043 0.138 1028 Planarity : 0.004 0.030 1170 Dihedral : 7.554 64.008 961 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.52 % Allowed : 14.55 % Favored : 82.94 % 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: -0.04 (0.29), residues: 819 helix: -1.42 (0.63), residues: 66 sheet: 0.87 (0.38), residues: 189 loop : -0.12 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 205 TYR 0.019 0.001 TYR B 31 PHE 0.011 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 ( 6665) covalent geometry : angle 0.51554 / 0.27 ( 9078) hydrogen bonds : bond 0.03777 / 2.46 ( 177) hydrogen bonds : angle 6.14325 / 4.19 ( 492) glycosidic custom : bond 0.00088 / 0.05 ( 1) glycosidic custom : angle 0.85839 / 0.47 ( 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 120 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.288 Fit side-chains REVERT: B 46 GLU cc_start: 0.9316 (pt0) cc_final: 0.9075 (pt0) REVERT: B 147 MET cc_start: 0.9187 (mmt) cc_final: 0.8825 (mmt) REVERT: B 151 ARG cc_start: 0.8345 (tpt90) cc_final: 0.8131 (tpm170) REVERT: C 114 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8649 (pp20) REVERT: D 55 GLU cc_start: 0.8874 (tt0) cc_final: 0.8652 (tt0) REVERT: A 122 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9260 (tp) REVERT: A 136 MET cc_start: 0.5245 (ttt) cc_final: 0.3837 (mtp) REVERT: A 241 MET cc_start: 0.9510 (ttp) cc_final: 0.9214 (ttm) outliers start: 18 outliers final: 10 residues processed: 114 average time/residue: 0.5666 time to fit residues: 67.6920 Evaluate side-chains 113 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 272 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 0.0070 chunk 19 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 4.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 ASN B 97 GLN C 160 GLN D 31 ASN A 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.087106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.070316 restraints weight = 9372.181| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.00 r_work: 0.2708 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6666 Z= 0.193 Angle : 0.524 7.046 9081 Z= 0.269 Chirality : 0.043 0.138 1028 Planarity : 0.004 0.032 1170 Dihedral : 7.500 62.993 961 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.24 % Allowed : 14.55 % Favored : 83.22 % 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: -0.04 (0.29), residues: 819 helix: -1.41 (0.63), residues: 66 sheet: 0.86 (0.38), residues: 189 loop : -0.12 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 205 TYR 0.019 0.001 TYR B 31 PHE 0.011 0.001 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 ( 6665) covalent geometry : angle 0.52418 / 0.27 ( 9078) hydrogen bonds : bond 0.03766 / 2.45 ( 177) hydrogen bonds : angle 6.08681 / 4.15 ( 492) glycosidic custom : bond 0.00066 / 0.03 ( 1) glycosidic custom : angle 0.86625 / 0.48 ( 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 117 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.189 Fit side-chains REVERT: B 46 GLU cc_start: 0.9327 (pt0) cc_final: 0.9003 (pt0) REVERT: B 147 MET cc_start: 0.9188 (mmt) cc_final: 0.8750 (mmt) REVERT: B 151 ARG cc_start: 0.8353 (tpt90) cc_final: 0.8147 (tpm170) REVERT: C 114 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8577 (pp20) REVERT: D 55 GLU cc_start: 0.8896 (tt0) cc_final: 0.8672 (tt0) REVERT: A 122 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9256 (tp) REVERT: A 136 MET cc_start: 0.5237 (ttt) cc_final: 0.3708 (mtp) REVERT: A 241 MET cc_start: 0.9526 (ttp) cc_final: 0.9248 (ttm) outliers start: 16 outliers final: 12 residues processed: 112 average time/residue: 0.6337 time to fit residues: 74.2081 Evaluate side-chains 114 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 272 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 ASN C 160 GLN D 31 ASN A 102 GLN A 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.088152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.071329 restraints weight = 9336.472| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.01 r_work: 0.2729 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6666 Z= 0.138 Angle : 0.496 8.474 9081 Z= 0.254 Chirality : 0.042 0.140 1028 Planarity : 0.004 0.029 1170 Dihedral : 7.383 60.722 961 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.10 % Allowed : 14.55 % Favored : 83.36 % 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: 0.01 (0.29), residues: 819 helix: -1.35 (0.64), residues: 66 sheet: 0.89 (0.38), residues: 189 loop : -0.09 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.017 0.001 TYR B 31 PHE 0.010 0.001 PHE A 100 TRP 0.005 0.001 TRP A 249 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 6665) covalent geometry : angle 0.49620 / 0.25 ( 9078) hydrogen bonds : bond 0.03425 / 2.22 ( 177) hydrogen bonds : angle 5.93569 / 4.05 ( 492) glycosidic custom : bond 0.00127 / 0.07 ( 1) glycosidic custom : angle 0.85350 / 0.47 ( 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 118 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.273 Fit side-chains REVERT: B 46 GLU cc_start: 0.9311 (pt0) cc_final: 0.9052 (pt0) REVERT: B 147 MET cc_start: 0.9168 (mmt) cc_final: 0.8782 (mmt) REVERT: C 114 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8545 (pp20) REVERT: D 55 GLU cc_start: 0.8887 (tt0) cc_final: 0.8659 (tt0) REVERT: A 122 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9236 (tp) REVERT: A 136 MET cc_start: 0.5239 (ttt) cc_final: 0.3717 (mtp) REVERT: A 241 MET cc_start: 0.9500 (ttp) cc_final: 0.9240 (ttm) outliers start: 15 outliers final: 11 residues processed: 114 average time/residue: 0.6099 time to fit residues: 72.9926 Evaluate side-chains 115 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 122 LEU 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 40 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 ASN B 97 GLN C 160 GLN D 31 ASN A 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.086457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.069710 restraints weight = 9290.383| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 1.98 r_work: 0.2705 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 6666 Z= 0.278 Angle : 0.575 8.802 9081 Z= 0.295 Chirality : 0.046 0.134 1028 Planarity : 0.004 0.046 1170 Dihedral : 7.613 61.678 961 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.24 % Allowed : 14.27 % Favored : 83.50 % 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: -0.07 (0.29), residues: 819 helix: -1.45 (0.63), residues: 66 sheet: 0.85 (0.38), residues: 189 loop : -0.15 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 12 TYR 0.019 0.002 TYR B 31 PHE 0.013 0.002 PHE A 100 TRP 0.008 0.001 TRP B 177 HIS 0.003 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.28 ( 6665) covalent geometry : angle 0.57445 / 0.30 ( 9078) hydrogen bonds : bond 0.04135 / 2.70 ( 177) hydrogen bonds : angle 6.13448 / 4.19 ( 492) glycosidic custom : bond 0.00151 / 0.08 ( 1) glycosidic custom : angle 0.88229 / 0.50 ( 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 118 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.254 Fit side-chains REVERT: B 46 GLU cc_start: 0.9305 (pt0) cc_final: 0.9059 (pt0) REVERT: B 147 MET cc_start: 0.9197 (mmt) cc_final: 0.8684 (mmt) REVERT: B 150 GLU cc_start: 0.8613 (pp20) cc_final: 0.8283 (pp20) REVERT: B 151 ARG cc_start: 0.8183 (tpm170) cc_final: 0.7945 (tpm170) REVERT: C 114 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8601 (pp20) REVERT: D 55 GLU cc_start: 0.8900 (tt0) cc_final: 0.8673 (tt0) REVERT: A 136 MET cc_start: 0.5338 (ttt) cc_final: 0.3773 (mtp) REVERT: A 241 MET cc_start: 0.9534 (ttp) cc_final: 0.9263 (ttm) outliers start: 16 outliers final: 9 residues processed: 113 average time/residue: 0.6329 time to fit residues: 74.8794 Evaluate side-chains 113 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 272 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 70 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN D 31 ASN A 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.087364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.070514 restraints weight = 9262.569| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.00 r_work: 0.2707 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6666 Z= 0.155 Angle : 0.517 9.249 9081 Z= 0.264 Chirality : 0.043 0.142 1028 Planarity : 0.004 0.031 1170 Dihedral : 7.430 59.508 961 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.54 % Allowed : 14.83 % Favored : 83.64 % 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: -0.02 (0.29), residues: 819 helix: -1.39 (0.63), residues: 66 sheet: 0.88 (0.38), residues: 189 loop : -0.11 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.017 0.001 TYR B 31 PHE 0.010 0.001 PHE A 100 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 6665) covalent geometry : angle 0.51705 / 0.26 ( 9078) hydrogen bonds : bond 0.03524 / 2.29 ( 177) hydrogen bonds : angle 5.96027 / 4.07 ( 492) glycosidic custom : bond 0.00113 / 0.06 ( 1) glycosidic custom : angle 0.87828 / 0.48 ( 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 113 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.313 Fit side-chains REVERT: B 46 GLU cc_start: 0.9300 (pt0) cc_final: 0.9031 (pt0) REVERT: B 147 MET cc_start: 0.9206 (mmt) cc_final: 0.8771 (mmt) REVERT: B 151 ARG cc_start: 0.8201 (tpm170) cc_final: 0.7952 (tpm170) REVERT: C 114 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8551 (pp20) REVERT: D 55 GLU cc_start: 0.8923 (tt0) cc_final: 0.8700 (tt0) REVERT: A 136 MET cc_start: 0.5300 (ttt) cc_final: 0.3734 (mtp) REVERT: A 241 MET cc_start: 0.9496 (ttp) cc_final: 0.9256 (ttm) outliers start: 11 outliers final: 10 residues processed: 109 average time/residue: 0.6387 time to fit residues: 72.9626 Evaluate side-chains 113 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 272 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 68 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 ASN B 97 GLN C 160 GLN D 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.087783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.070780 restraints weight = 9363.140| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.02 r_work: 0.2710 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6666 Z= 0.154 Angle : 0.517 9.709 9081 Z= 0.263 Chirality : 0.043 0.140 1028 Planarity : 0.004 0.029 1170 Dihedral : 7.343 57.185 961 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.96 % Allowed : 14.69 % Favored : 83.36 % 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: 0.02 (0.29), residues: 819 helix: -1.35 (0.63), residues: 66 sheet: 0.91 (0.38), residues: 189 loop : -0.08 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 12 TYR 0.017 0.001 TYR B 31 PHE 0.010 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 6665) covalent geometry : angle 0.51720 / 0.26 ( 9078) hydrogen bonds : bond 0.03493 / 2.26 ( 177) hydrogen bonds : angle 5.91328 / 4.05 ( 492) glycosidic custom : bond 0.00084 / 0.04 ( 1) glycosidic custom : angle 0.90868 / 0.50 ( 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 118 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.284 Fit side-chains REVERT: B 46 GLU cc_start: 0.9289 (pt0) cc_final: 0.9024 (pt0) REVERT: B 147 MET cc_start: 0.9185 (mmt) cc_final: 0.8816 (mmt) REVERT: B 151 ARG cc_start: 0.8257 (tpm170) cc_final: 0.8009 (tpm170) REVERT: C 114 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8567 (pp20) REVERT: D 55 GLU cc_start: 0.8916 (tt0) cc_final: 0.8690 (tt0) REVERT: A 136 MET cc_start: 0.5304 (ttt) cc_final: 0.3739 (mtp) REVERT: A 241 MET cc_start: 0.9487 (ttp) cc_final: 0.9258 (ttm) outliers start: 14 outliers final: 11 residues processed: 113 average time/residue: 0.6336 time to fit residues: 74.9962 Evaluate side-chains 115 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 ASN B 97 GLN C 160 GLN D 31 ASN A 102 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.086919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.070082 restraints weight = 9249.439| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.00 r_work: 0.2699 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6666 Z= 0.187 Angle : 0.538 9.403 9081 Z= 0.275 Chirality : 0.043 0.138 1028 Planarity : 0.004 0.035 1170 Dihedral : 7.391 56.714 961 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.68 % Allowed : 14.83 % Favored : 83.50 % 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: -0.01 (0.29), residues: 819 helix: -1.37 (0.63), residues: 66 sheet: 0.89 (0.38), residues: 189 loop : -0.11 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.018 0.001 TYR B 31 PHE 0.011 0.001 PHE A 100 TRP 0.007 0.001 TRP B 177 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 ( 6665) covalent geometry : angle 0.53820 / 0.27 ( 9078) hydrogen bonds : bond 0.03685 / 2.39 ( 177) hydrogen bonds : angle 5.97093 / 4.09 ( 492) glycosidic custom : bond 0.00047 / 0.02 ( 1) glycosidic custom : angle 0.94932 / 0.53 ( 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 115 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.288 Fit side-chains REVERT: B 46 GLU cc_start: 0.9298 (pt0) cc_final: 0.9034 (pt0) REVERT: B 147 MET cc_start: 0.9187 (mmt) cc_final: 0.8826 (mmt) REVERT: B 151 ARG cc_start: 0.8294 (tpm170) cc_final: 0.8054 (tpm170) REVERT: C 114 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8585 (pp20) REVERT: D 55 GLU cc_start: 0.8921 (tt0) cc_final: 0.8692 (tt0) REVERT: A 136 MET cc_start: 0.5333 (ttt) cc_final: 0.3745 (mtp) REVERT: A 241 MET cc_start: 0.9498 (ttp) cc_final: 0.9266 (ttm) outliers start: 12 outliers final: 11 residues processed: 111 average time/residue: 0.6533 time to fit residues: 76.0109 Evaluate side-chains 114 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 114 GLU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 44 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 40 ASN C 160 GLN D 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.088117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.071163 restraints weight = 9228.331| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 2.01 r_work: 0.2719 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6666 Z= 0.141 Angle : 0.515 9.943 9081 Z= 0.262 Chirality : 0.042 0.140 1028 Planarity : 0.004 0.029 1170 Dihedral : 7.280 57.571 961 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.68 % Allowed : 15.10 % Favored : 83.22 % 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: 0.04 (0.29), residues: 819 helix: -1.32 (0.64), residues: 66 sheet: 0.92 (0.38), residues: 189 loop : -0.07 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.017 0.001 TYR B 31 PHE 0.010 0.001 PHE C 215 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6665) covalent geometry : angle 0.51445 / 0.26 ( 9078) hydrogen bonds : bond 0.03392 / 2.20 ( 177) hydrogen bonds : angle 5.86599 / 4.02 ( 492) glycosidic custom : bond 0.00133 / 0.07 ( 1) glycosidic custom : angle 0.93916 / 0.52 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3190.58 seconds wall clock time: 55 minutes 5.33 seconds (3305.33 seconds total)