Starting phenix.real_space_refine on Thu Jul 2 06:43:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dce_30636/07_2026/7dce_30636.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dce_30636/07_2026/7dce_30636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2026/7dce_30636.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2026/7dce_30636.cif" model { file = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2026/7dce_30636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2026/7dce_30636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2026/7dce_30636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dce_30636/07_2026/7dce_30636.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 28 5.16 5 C 4602 2.51 5 N 1161 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7102 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1032 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2837 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 17, 'TRANS': 336} Chain: "H" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1553 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1626 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 207} Chain: "X" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'DLP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.45, per 1000 atoms: 0.20 Number of scatterers: 7102 At special positions: 0 Unit cell: (113.295, 70.965, 117.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 1 15.00 O 1310 8.00 N 1161 7.00 C 4602 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 185 " distance=2.02 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 81 " - pdb=" SG CYS L 175 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 333.2 milliseconds 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1690 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 40.4% alpha, 28.9% 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 153 through 156 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 209 through 230 removed outlier: 3.713A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'X' and resid 8 through 41 Processing helix chain 'X' and resid 43 through 71 Processing helix chain 'X' and resid 83 through 91 Processing helix chain 'X' and resid 95 through 112 Processing helix chain 'X' and resid 116 through 141 removed outlier: 3.505A pdb=" N LEU X 120 " --> pdb=" O SER X 116 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA X 121 " --> pdb=" O GLU X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 157 Processing helix chain 'X' and resid 160 through 188 Processing helix chain 'X' and resid 195 through 225 Proline residue: X 213 - end of helix Processing helix chain 'X' and resid 228 through 247 Processing helix chain 'X' and resid 257 through 270 removed outlier: 4.160A pdb=" N TYR X 261 " --> pdb=" O SER X 257 " (cutoff:3.500A) Processing helix chain 'X' and resid 283 through 306 Processing helix chain 'X' and resid 315 through 340 removed outlier: 3.859A pdb=" N LEU X 320 " --> pdb=" O LEU X 316 " (cutoff:3.500A) Proline residue: X 321 - end of helix Processing helix chain 'X' and resid 348 through 358 removed outlier: 3.594A pdb=" N ASP X 352 " --> pdb=" O LYS X 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 63 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.603A pdb=" N THR H 87 " --> pdb=" O THR H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 185 through 190 removed outlier: 4.389A pdb=" N GLY H 189 " --> pdb=" O SER H 185 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 185 through 190' Processing helix chain 'H' and resid 200 through 203 Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 125 through 132 removed outlier: 3.514A pdb=" N LYS L 130 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 193 removed outlier: 3.593A pdb=" N HIS L 193 " --> pdb=" O ASP L 189 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 107 through 109 Processing sheet with id=AA2, first strand: chain 'B' and resid 113 through 117 removed outlier: 6.706A pdb=" N GLU B 114 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ARG B 203 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 116 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN B 182 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP B 136 " --> pdb=" O THR B 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 2 through 6 Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.811A pdb=" N ALA H 32 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N MET H 33 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE H 49 " --> pdb=" O MET H 33 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP H 35 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 4.221A pdb=" N ILE H 101 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 119 through 123 removed outlier: 6.005A pdb=" N TYR H 175 " --> pdb=" O ASP H 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 119 through 123 removed outlier: 6.005A pdb=" N TYR H 175 " --> pdb=" O ASP H 143 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 176 " --> pdb=" O VAL H 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 150 through 153 Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.502A pdb=" N GLN L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 15 removed outlier: 6.452A pdb=" N VAL L 12 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS L 111 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA L 14 " --> pdb=" O LYS L 111 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 85 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.505A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 157 through 158 removed outlier: 3.621A pdb=" N LYS L 211 " --> pdb=" O CYS L 198 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1211 1.32 - 1.44: 2012 1.44 - 1.57: 4029 1.57 - 1.69: 2 1.69 - 1.82: 36 Bond restraints: 7290 Sorted by residual: bond pdb=" N PCA H 1 " pdb=" CD PCA H 1 " ideal model delta sigma weight residual 1.345 1.460 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C4 DLP X 501 " pdb=" O4P DLP X 501 " ideal model delta sigma weight residual 1.409 1.454 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" O4P DLP X 501 " pdb=" P DLP X 501 " ideal model delta sigma weight residual 1.649 1.605 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" CB VAL X 49 " pdb=" CG2 VAL X 49 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.52e+00 bond pdb=" CA ALA X 285 " pdb=" C ALA X 285 " ideal model delta sigma weight residual 1.524 1.498 0.027 1.29e-02 6.01e+03 4.25e+00 ... (remaining 7285 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 9618 2.94 - 5.88: 280 5.88 - 8.82: 34 8.82 - 11.76: 9 11.76 - 14.70: 3 Bond angle restraints: 9944 Sorted by residual: angle pdb=" N ALA X 285 " pdb=" CA ALA X 285 " pdb=" C ALA X 285 " ideal model delta sigma weight residual 111.40 103.05 8.35 1.22e+00 6.72e-01 4.68e+01 angle pdb=" N GLY H 98 " pdb=" CA GLY H 98 " pdb=" C GLY H 98 " ideal model delta sigma weight residual 112.37 100.25 12.12 1.84e+00 2.95e-01 4.34e+01 angle pdb=" N TRP X 340 " pdb=" CA TRP X 340 " pdb=" C TRP X 340 " ideal model delta sigma weight residual 111.24 118.00 -6.76 1.29e+00 6.01e-01 2.74e+01 angle pdb=" N ALA H 97 " pdb=" CA ALA H 97 " pdb=" C ALA H 97 " ideal model delta sigma weight residual 107.23 99.23 8.00 1.67e+00 3.59e-01 2.29e+01 angle pdb=" N GLU B 146 " pdb=" CA GLU B 146 " pdb=" C GLU B 146 " ideal model delta sigma weight residual 108.52 115.60 -7.08 1.52e+00 4.33e-01 2.17e+01 ... (remaining 9939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 4010 24.90 - 49.81: 218 49.81 - 74.71: 23 74.71 - 99.62: 9 99.62 - 124.52: 1 Dihedral angle restraints: 4261 sinusoidal: 1625 harmonic: 2636 Sorted by residual: dihedral pdb=" CB CYS L 81 " pdb=" SG CYS L 81 " pdb=" SG CYS L 175 " pdb=" CB CYS L 175 " ideal model delta sinusoidal sigma weight residual -86.00 -126.28 40.28 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" N DLP X 501 " pdb=" C4 DLP X 501 " pdb=" C5 DLP X 501 " pdb=" O4P DLP X 501 " ideal model delta sinusoidal sigma weight residual 288.95 164.43 124.52 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CB GLU L 199 " pdb=" CG GLU L 199 " pdb=" CD GLU L 199 " pdb=" OE1 GLU L 199 " ideal model delta sinusoidal sigma weight residual 0.00 86.84 -86.84 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 4258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 802 0.056 - 0.112: 253 0.112 - 0.168: 61 0.168 - 0.224: 12 0.224 - 0.280: 5 Chirality restraints: 1133 Sorted by residual: chirality pdb=" CA PRO X 253 " pdb=" N PRO X 253 " pdb=" C PRO X 253 " pdb=" CB PRO X 253 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA LEU X 236 " pdb=" N LEU X 236 " pdb=" C LEU X 236 " pdb=" CB LEU X 236 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA TRP X 212 " pdb=" N TRP X 212 " pdb=" C TRP X 212 " pdb=" CB TRP X 212 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1130 not shown) Planarity restraints: 1234 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C21 DLP X 501 " 0.062 2.00e-02 2.50e+03 1.21e-01 1.46e+02 pdb=" C22 DLP X 501 " -0.158 2.00e-02 2.50e+03 pdb=" C23 DLP X 501 " 0.159 2.00e-02 2.50e+03 pdb=" C24 DLP X 501 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG X 262 " 0.123 9.50e-02 1.11e+02 7.08e-02 2.67e+01 pdb=" NE ARG X 262 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG X 262 " 0.085 2.00e-02 2.50e+03 pdb=" NH1 ARG X 262 " -0.030 2.00e-02 2.50e+03 pdb=" NH2 ARG X 262 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C41 DLP X 501 " 0.044 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C42 DLP X 501 " -0.047 2.00e-02 2.50e+03 pdb=" C43 DLP X 501 " -0.040 2.00e-02 2.50e+03 pdb=" C44 DLP X 501 " 0.043 2.00e-02 2.50e+03 ... (remaining 1231 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1158 2.76 - 3.29: 6879 3.29 - 3.83: 11876 3.83 - 4.36: 13450 4.36 - 4.90: 23314 Nonbonded interactions: 56677 Sorted by model distance: nonbonded pdb=" OG SER L 125 " pdb=" OE1 GLU L 127 " model vdw 2.220 3.040 nonbonded pdb=" NE2 HIS X 182 " pdb=" OH TYR X 337 " model vdw 2.222 3.120 nonbonded pdb=" NH2 ARG B 184 " pdb=" OE1 GLN B 195 " model vdw 2.256 3.120 nonbonded pdb=" OH TYR X 37 " pdb=" NE2 GLN X 163 " model vdw 2.263 3.120 nonbonded pdb=" OD1 ASP X 12 " pdb=" NH2 ARG X 183 " model vdw 2.287 3.120 ... (remaining 56672 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.300 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.009 0.115 7296 Z= 0.424 Angle : 1.213 14.698 9956 Z= 0.666 Chirality : 0.060 0.280 1133 Planarity : 0.009 0.121 1234 Dihedral : 14.945 124.523 2553 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.44 % Favored : 92.34 % Rotamer: Outliers : 3.27 % Allowed : 10.07 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % 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: -3.04 (0.24), residues: 901 helix: -2.75 (0.24), residues: 309 sheet: -0.59 (0.29), residues: 259 loop : -2.24 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.003 ARG X 262 TYR 0.028 0.003 TYR L 98 PHE 0.026 0.003 PHE L 102 TRP 0.053 0.004 TRP X 303 HIS 0.010 0.003 HIS X 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00945 / 0.42 ( 7290) covalent geometry : angle 1.21171 / 0.67 ( 9944) SS BOND : bond 0.00511 / 0.33 ( 6) SS BOND : angle 1.78943 / 1.89 ( 12) hydrogen bonds : bond 0.13483 / 8.84 ( 412) hydrogen bonds : angle 7.97139 / 5.63 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8162 (p0) REVERT: B 123 MET cc_start: 0.9056 (ttp) cc_final: 0.8611 (ttp) REVERT: B 160 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8861 (p) REVERT: B 173 ASN cc_start: 0.8943 (t0) cc_final: 0.8709 (t0) REVERT: B 227 PHE cc_start: 0.8523 (t80) cc_final: 0.8154 (t80) REVERT: X 43 TYR cc_start: 0.7301 (p90) cc_final: 0.6746 (p90) REVERT: X 66 LEU cc_start: 0.9346 (mm) cc_final: 0.9073 (mp) REVERT: X 103 LEU cc_start: 0.9204 (mt) cc_final: 0.8900 (mt) REVERT: X 132 MET cc_start: 0.9182 (mmm) cc_final: 0.8786 (mmp) REVERT: X 145 GLN cc_start: 0.8767 (tp40) cc_final: 0.8462 (tp40) REVERT: X 209 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8574 (mp) REVERT: X 233 PHE cc_start: 0.8576 (t80) cc_final: 0.8246 (t80) REVERT: X 259 TRP cc_start: 0.6462 (t60) cc_final: 0.6063 (t-100) REVERT: X 299 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8276 (mp) REVERT: X 326 CYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8510 (t) REVERT: H 28 LEU cc_start: 0.9142 (mt) cc_final: 0.8870 (mp) REVERT: H 33 MET cc_start: 0.8744 (mmm) cc_final: 0.8376 (mmt) REVERT: H 86 ASP cc_start: 0.8594 (m-30) cc_final: 0.8262 (m-30) REVERT: H 139 CYS cc_start: 0.6329 (m) cc_final: 0.6049 (m) REVERT: H 140 LEU cc_start: 0.9212 (tp) cc_final: 0.8795 (tt) REVERT: H 143 ASP cc_start: 0.7615 (m-30) cc_final: 0.7188 (m-30) REVERT: H 144 TYR cc_start: 0.8259 (p90) cc_final: 0.8026 (p90) REVERT: H 153 TRP cc_start: 0.7772 (m100) cc_final: 0.6836 (m100) REVERT: L 5 MET cc_start: 0.8958 (mmm) cc_final: 0.8101 (mmm) REVERT: L 91 SER cc_start: 0.9447 (t) cc_final: 0.9017 (m) REVERT: L 129 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7477 (mm) REVERT: L 180 SER cc_start: 0.7513 (p) cc_final: 0.7017 (p) REVERT: L 191 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8760 (mm-30) outliers start: 25 outliers final: 11 residues processed: 258 average time/residue: 0.0682 time to fit residues: 23.8323 Evaluate side-chains 183 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 220 LEU Chi-restraints excluded: chain X residue 263 VAL Chi-restraints excluded: chain X residue 299 LEU Chi-restraints excluded: chain X residue 326 CYS Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 24 CYS Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 129 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 ASN B 164 GLN B 170 HIS B 205 HIS ** X 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 306 HIS X 339 HIS H 163 HIS L 128 GLN L 142 ASN L 164 GLN L 214 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.147649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.111228 restraints weight = 12616.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110285 restraints weight = 9487.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111063 restraints weight = 9986.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112026 restraints weight = 6312.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112978 restraints weight = 5426.052| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7296 Z= 0.173 Angle : 0.729 11.325 9956 Z= 0.362 Chirality : 0.044 0.154 1133 Planarity : 0.006 0.061 1234 Dihedral : 8.403 112.269 1043 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.31 % Allowed : 14.77 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.27), residues: 901 helix: 0.81 (0.28), residues: 315 sheet: 0.34 (0.31), residues: 252 loop : -1.67 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 184 TYR 0.029 0.002 TYR L 33 PHE 0.030 0.002 PHE L 213 TRP 0.017 0.002 TRP X 259 HIS 0.004 0.001 HIS H 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 ( 7290) covalent geometry : angle 0.72874 / 0.36 ( 9944) SS BOND : bond 0.00446 / 0.26 ( 6) SS BOND : angle 0.96896 / 1.02 ( 12) hydrogen bonds : bond 0.04566 / 3.06 ( 412) hydrogen bonds : angle 5.51991 / 3.89 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.8492 (p0) REVERT: B 173 ASN cc_start: 0.9027 (t0) cc_final: 0.8794 (t0) REVERT: B 227 PHE cc_start: 0.8583 (t80) cc_final: 0.8206 (t80) REVERT: X 154 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8474 (mp) REVERT: X 180 ASP cc_start: 0.8800 (m-30) cc_final: 0.8321 (m-30) REVERT: X 181 TYR cc_start: 0.9533 (t80) cc_final: 0.9140 (t80) REVERT: X 259 TRP cc_start: 0.6222 (t60) cc_final: 0.5895 (t-100) REVERT: H 28 LEU cc_start: 0.9043 (mt) cc_final: 0.8825 (mp) REVERT: H 86 ASP cc_start: 0.8539 (m-30) cc_final: 0.8270 (m-30) REVERT: H 141 VAL cc_start: 0.9511 (OUTLIER) cc_final: 0.9299 (p) REVERT: H 143 ASP cc_start: 0.7740 (m-30) cc_final: 0.7222 (t70) REVERT: H 144 TYR cc_start: 0.8445 (p90) cc_final: 0.8111 (p90) REVERT: H 153 TRP cc_start: 0.7928 (m100) cc_final: 0.7526 (m100) REVERT: L 196 TYR cc_start: 0.7772 (m-80) cc_final: 0.7544 (m-80) outliers start: 33 outliers final: 21 residues processed: 204 average time/residue: 0.0514 time to fit residues: 15.1175 Evaluate side-chains 183 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 170 SER Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain H residue 163 HIS Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 HIS ** X 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 288 HIS H 163 HIS L 23 ASN L 142 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108581 restraints weight = 12480.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108109 restraints weight = 10230.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.108390 restraints weight = 11667.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.109984 restraints weight = 6768.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110704 restraints weight = 5544.070| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 7296 Z= 0.242 Angle : 0.733 10.551 9956 Z= 0.362 Chirality : 0.044 0.210 1133 Planarity : 0.005 0.053 1234 Dihedral : 7.770 107.409 1021 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.75 % Allowed : 19.35 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.53 (0.28), residues: 901 helix: 1.70 (0.28), residues: 317 sheet: 0.69 (0.31), residues: 257 loop : -1.29 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 158 TYR 0.017 0.002 TYR X 122 PHE 0.017 0.002 PHE L 213 TRP 0.014 0.002 TRP X 110 HIS 0.005 0.001 HIS H 163 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 ( 7290) covalent geometry : angle 0.73091 / 0.36 ( 9944) SS BOND : bond 0.00675 / 0.53 ( 6) SS BOND : angle 1.72141 / 1.49 ( 12) hydrogen bonds : bond 0.04168 / 2.81 ( 412) hydrogen bonds : angle 5.14924 / 3.62 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 ASN cc_start: 0.8979 (OUTLIER) cc_final: 0.8472 (p0) REVERT: B 173 ASN cc_start: 0.9121 (t0) cc_final: 0.8918 (t0) REVERT: B 227 PHE cc_start: 0.8643 (t80) cc_final: 0.8257 (t80) REVERT: X 259 TRP cc_start: 0.6285 (t60) cc_final: 0.5931 (t-100) REVERT: H 28 LEU cc_start: 0.9225 (mt) cc_final: 0.8902 (mp) REVERT: H 86 ASP cc_start: 0.8628 (m-30) cc_final: 0.8249 (m-30) REVERT: H 141 VAL cc_start: 0.9547 (OUTLIER) cc_final: 0.9250 (p) REVERT: H 143 ASP cc_start: 0.7589 (m-30) cc_final: 0.6919 (t70) REVERT: H 153 TRP cc_start: 0.7829 (m100) cc_final: 0.7108 (m100) REVERT: L 141 ASN cc_start: 0.9098 (t0) cc_final: 0.8585 (t0) REVERT: L 149 LYS cc_start: 0.8422 (tptt) cc_final: 0.8203 (tptp) outliers start: 44 outliers final: 35 residues processed: 198 average time/residue: 0.0585 time to fit residues: 16.4483 Evaluate side-chains 195 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 64 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 GLN B 170 HIS X 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.143644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106871 restraints weight = 12649.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106915 restraints weight = 10949.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108476 restraints weight = 7724.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110427 restraints weight = 5940.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110793 restraints weight = 5364.677| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7296 Z= 0.215 Angle : 0.698 7.962 9956 Z= 0.345 Chirality : 0.043 0.143 1133 Planarity : 0.005 0.050 1234 Dihedral : 7.606 100.158 1021 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 6.54 % Allowed : 20.13 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.95 (0.28), residues: 901 helix: 2.07 (0.27), residues: 317 sheet: 0.92 (0.32), residues: 252 loop : -1.06 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 158 TYR 0.019 0.002 TYR H 144 PHE 0.019 0.002 PHE H 165 TRP 0.014 0.001 TRP B 210 HIS 0.002 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 ( 7290) covalent geometry : angle 0.69725 / 0.34 ( 9944) SS BOND : bond 0.00363 / 0.32 ( 6) SS BOND : angle 1.25146 / 1.02 ( 12) hydrogen bonds : bond 0.03810 / 2.58 ( 412) hydrogen bonds : angle 4.90254 / 3.43 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 PHE cc_start: 0.8636 (t80) cc_final: 0.8348 (t80) REVERT: X 114 GLU cc_start: 0.8938 (tp30) cc_final: 0.8489 (tp30) REVERT: X 181 TYR cc_start: 0.9528 (t80) cc_final: 0.9111 (t80) REVERT: X 242 LEU cc_start: 0.8762 (tt) cc_final: 0.8303 (mm) REVERT: X 259 TRP cc_start: 0.6240 (t60) cc_final: 0.5934 (t-100) REVERT: H 28 LEU cc_start: 0.9191 (mt) cc_final: 0.8863 (mp) REVERT: H 86 ASP cc_start: 0.8638 (m-30) cc_final: 0.8263 (m-30) REVERT: H 143 ASP cc_start: 0.7327 (m-30) cc_final: 0.6850 (t70) REVERT: L 7 GLN cc_start: 0.8885 (tt0) cc_final: 0.8648 (tt0) REVERT: L 141 ASN cc_start: 0.9140 (t0) cc_final: 0.8608 (t0) REVERT: L 149 LYS cc_start: 0.8438 (tptt) cc_final: 0.8219 (tptp) outliers start: 50 outliers final: 40 residues processed: 199 average time/residue: 0.0612 time to fit residues: 17.2484 Evaluate side-chains 199 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 59 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109109 restraints weight = 12680.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112918 restraints weight = 12385.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111744 restraints weight = 9744.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111922 restraints weight = 5662.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112571 restraints weight = 5011.834| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7296 Z= 0.181 Angle : 0.669 8.352 9956 Z= 0.329 Chirality : 0.042 0.159 1133 Planarity : 0.005 0.048 1234 Dihedral : 7.358 92.286 1019 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 6.14 % Allowed : 22.48 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.19 (0.28), residues: 901 helix: 2.20 (0.28), residues: 322 sheet: 1.17 (0.33), residues: 242 loop : -0.93 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 158 TYR 0.018 0.002 TYR H 144 PHE 0.018 0.002 PHE L 122 TRP 0.016 0.001 TRP X 347 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 7290) covalent geometry : angle 0.66807 / 0.33 ( 9944) SS BOND : bond 0.00320 / 0.29 ( 6) SS BOND : angle 1.09268 / 0.88 ( 12) hydrogen bonds : bond 0.03623 / 2.44 ( 412) hydrogen bonds : angle 4.69655 / 3.27 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8020 (mmm) REVERT: X 30 ASP cc_start: 0.8322 (t0) cc_final: 0.8122 (m-30) REVERT: X 85 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8612 (pp) REVERT: X 167 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7540 (mt) REVERT: X 180 ASP cc_start: 0.8808 (m-30) cc_final: 0.8494 (m-30) REVERT: X 181 TYR cc_start: 0.9378 (t80) cc_final: 0.9146 (t80) REVERT: X 242 LEU cc_start: 0.8734 (tt) cc_final: 0.8286 (mm) REVERT: X 259 TRP cc_start: 0.6074 (t60) cc_final: 0.5792 (t-100) REVERT: H 28 LEU cc_start: 0.9173 (mt) cc_final: 0.8812 (mp) REVERT: H 86 ASP cc_start: 0.8641 (m-30) cc_final: 0.8329 (m-30) REVERT: H 143 ASP cc_start: 0.7312 (m-30) cc_final: 0.6793 (t70) REVERT: L 141 ASN cc_start: 0.8992 (t0) cc_final: 0.8674 (t0) REVERT: L 149 LYS cc_start: 0.8500 (tptt) cc_final: 0.8275 (tptp) outliers start: 47 outliers final: 36 residues processed: 194 average time/residue: 0.0587 time to fit residues: 16.4125 Evaluate side-chains 195 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain X residue 85 LEU Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 30.0000 chunk 34 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 23 ASN L 71 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.145096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097902 restraints weight = 12603.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101453 restraints weight = 7276.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103628 restraints weight = 5315.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105095 restraints weight = 4442.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.105636 restraints weight = 3995.985| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7296 Z= 0.163 Angle : 0.666 11.470 9956 Z= 0.324 Chirality : 0.042 0.297 1133 Planarity : 0.004 0.046 1234 Dihedral : 7.098 82.481 1018 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.75 % Allowed : 23.01 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.33 (0.28), residues: 901 helix: 2.33 (0.27), residues: 321 sheet: 1.23 (0.33), residues: 242 loop : -0.85 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 158 TYR 0.015 0.002 TYR H 57 PHE 0.016 0.002 PHE L 122 TRP 0.021 0.001 TRP X 347 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 7290) covalent geometry : angle 0.66547 / 0.32 ( 9944) SS BOND : bond 0.00319 / 0.30 ( 6) SS BOND : angle 1.00552 / 0.77 ( 12) hydrogen bonds : bond 0.03527 / 2.39 ( 412) hydrogen bonds : angle 4.60001 / 3.19 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 HIS cc_start: 0.8224 (OUTLIER) cc_final: 0.7640 (t70) REVERT: B 230 GLU cc_start: 0.7670 (mm-30) cc_final: 0.6866 (tt0) REVERT: X 114 GLU cc_start: 0.8888 (tp30) cc_final: 0.8452 (tp30) REVERT: X 167 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7422 (mt) REVERT: X 180 ASP cc_start: 0.8936 (m-30) cc_final: 0.8569 (m-30) REVERT: X 181 TYR cc_start: 0.9196 (t80) cc_final: 0.8983 (t80) REVERT: X 242 LEU cc_start: 0.8639 (tt) cc_final: 0.8169 (mm) REVERT: H 28 LEU cc_start: 0.9131 (mt) cc_final: 0.8742 (mp) REVERT: H 86 ASP cc_start: 0.8643 (m-30) cc_final: 0.8346 (m-30) REVERT: H 143 ASP cc_start: 0.7672 (m-30) cc_final: 0.6923 (t70) REVERT: L 141 ASN cc_start: 0.8957 (t0) cc_final: 0.8692 (t0) outliers start: 44 outliers final: 37 residues processed: 188 average time/residue: 0.0723 time to fit residues: 18.9898 Evaluate side-chains 187 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 37 optimal weight: 0.0670 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 87 optimal weight: 50.0000 chunk 18 optimal weight: 4.9990 overall best weight: 1.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 92 GLN L 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108456 restraints weight = 12537.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112508 restraints weight = 11950.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112319 restraints weight = 7982.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112241 restraints weight = 5624.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.112860 restraints weight = 5029.223| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7296 Z= 0.164 Angle : 0.676 12.760 9956 Z= 0.327 Chirality : 0.042 0.353 1133 Planarity : 0.005 0.047 1234 Dihedral : 6.980 75.942 1018 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.88 % Allowed : 23.40 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.45 (0.28), residues: 901 helix: 2.39 (0.27), residues: 321 sheet: 1.30 (0.32), residues: 256 loop : -0.84 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 158 TYR 0.027 0.002 TYR H 144 PHE 0.021 0.001 PHE L 122 TRP 0.018 0.001 TRP X 347 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 7290) covalent geometry : angle 0.67580 / 0.33 ( 9944) SS BOND : bond 0.00308 / 0.29 ( 6) SS BOND : angle 1.01220 / 0.78 ( 12) hydrogen bonds : bond 0.03440 / 2.31 ( 412) hydrogen bonds : angle 4.58238 / 3.17 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7643 (ttp80) REVERT: X 114 GLU cc_start: 0.8801 (tp30) cc_final: 0.8412 (tp30) REVERT: X 167 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7563 (mt) REVERT: X 180 ASP cc_start: 0.8801 (m-30) cc_final: 0.8469 (m-30) REVERT: X 242 LEU cc_start: 0.8695 (tt) cc_final: 0.8311 (mm) REVERT: H 28 LEU cc_start: 0.9123 (mt) cc_final: 0.8734 (mp) REVERT: H 86 ASP cc_start: 0.8666 (m-30) cc_final: 0.8328 (m-30) REVERT: H 143 ASP cc_start: 0.7323 (m-30) cc_final: 0.6890 (t70) REVERT: L 146 ARG cc_start: 0.8049 (tmm-80) cc_final: 0.7682 (tmm-80) outliers start: 45 outliers final: 37 residues processed: 186 average time/residue: 0.0611 time to fit residues: 15.9914 Evaluate side-chains 191 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 195 GLN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 2 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 86 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.096582 restraints weight = 12767.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099957 restraints weight = 7486.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102220 restraints weight = 5494.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103433 restraints weight = 4599.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.103904 restraints weight = 4160.637| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7296 Z= 0.205 Angle : 0.727 12.698 9956 Z= 0.347 Chirality : 0.044 0.363 1133 Planarity : 0.005 0.047 1234 Dihedral : 7.022 72.589 1018 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.27 % Allowed : 23.66 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.43 (0.28), residues: 901 helix: 2.34 (0.27), residues: 321 sheet: 1.43 (0.33), residues: 234 loop : -0.79 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 201 TYR 0.027 0.002 TYR L 98 PHE 0.020 0.002 PHE L 122 TRP 0.020 0.001 TRP X 347 HIS 0.003 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 ( 7290) covalent geometry : angle 0.72675 / 0.35 ( 9944) SS BOND : bond 0.00351 / 0.31 ( 6) SS BOND : angle 1.12767 / 1.00 ( 12) hydrogen bonds : bond 0.03564 / 2.40 ( 412) hydrogen bonds : angle 4.67419 / 3.24 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7578 (ttp80) REVERT: X 242 LEU cc_start: 0.8655 (tt) cc_final: 0.8259 (mm) REVERT: X 286 ILE cc_start: 0.8511 (pt) cc_final: 0.8120 (mm) REVERT: H 28 LEU cc_start: 0.9166 (mt) cc_final: 0.8732 (mp) REVERT: H 86 ASP cc_start: 0.8693 (m-30) cc_final: 0.8370 (m-30) REVERT: H 143 ASP cc_start: 0.7669 (m-30) cc_final: 0.6940 (t70) REVERT: L 146 ARG cc_start: 0.8136 (tmm-80) cc_final: 0.7782 (tmm-80) REVERT: L 190 TYR cc_start: 0.7944 (t80) cc_final: 0.7732 (t80) outliers start: 48 outliers final: 43 residues processed: 180 average time/residue: 0.0633 time to fit residues: 15.9814 Evaluate side-chains 190 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 260 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 335 LEU Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 8.9990 chunk 23 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.096496 restraints weight = 12682.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.099961 restraints weight = 7394.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102278 restraints weight = 5435.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103409 restraints weight = 4538.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104224 restraints weight = 4097.867| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7296 Z= 0.194 Angle : 0.730 12.344 9956 Z= 0.348 Chirality : 0.044 0.349 1133 Planarity : 0.005 0.047 1234 Dihedral : 6.995 69.392 1018 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 6.67 % Allowed : 23.40 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.43 (0.28), residues: 901 helix: 2.37 (0.27), residues: 321 sheet: 1.26 (0.32), residues: 250 loop : -0.77 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 262 TYR 0.027 0.002 TYR H 144 PHE 0.019 0.002 PHE L 122 TRP 0.029 0.002 TRP X 259 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 ( 7290) covalent geometry : angle 0.72941 / 0.35 ( 9944) SS BOND : bond 0.00340 / 0.31 ( 6) SS BOND : angle 1.08465 / 0.90 ( 12) hydrogen bonds : bond 0.03539 / 2.38 ( 412) hydrogen bonds : angle 4.67776 / 3.24 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7559 (ttp80) REVERT: B 184 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7706 (ttm-80) REVERT: B 230 GLU cc_start: 0.7669 (mm-30) cc_final: 0.6857 (tt0) REVERT: X 167 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7427 (mt) REVERT: X 242 LEU cc_start: 0.8638 (tt) cc_final: 0.8237 (mm) REVERT: X 259 TRP cc_start: 0.6200 (m-90) cc_final: 0.5706 (t-100) REVERT: X 286 ILE cc_start: 0.8516 (pt) cc_final: 0.8154 (mm) REVERT: H 28 LEU cc_start: 0.9163 (mt) cc_final: 0.8737 (mp) REVERT: H 86 ASP cc_start: 0.8715 (m-30) cc_final: 0.8395 (m-30) REVERT: H 143 ASP cc_start: 0.7715 (m-30) cc_final: 0.6975 (t70) REVERT: L 146 ARG cc_start: 0.8195 (tmm-80) cc_final: 0.7870 (tmm-80) REVERT: L 190 TYR cc_start: 0.8032 (t80) cc_final: 0.7770 (t80) outliers start: 51 outliers final: 48 residues processed: 184 average time/residue: 0.0622 time to fit residues: 16.0415 Evaluate side-chains 198 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 149 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 133 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 287 ILE Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 335 LEU Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 167 VAL Chi-restraints excluded: chain L residue 171 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... X 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.107824 restraints weight = 12661.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109175 restraints weight = 11697.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108966 restraints weight = 11404.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110594 restraints weight = 6456.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111137 restraints weight = 5223.387| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7296 Z= 0.175 Angle : 0.720 11.992 9956 Z= 0.341 Chirality : 0.044 0.343 1133 Planarity : 0.005 0.047 1234 Dihedral : 6.921 65.256 1018 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 6.27 % Allowed : 24.18 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.48 (0.28), residues: 901 helix: 2.42 (0.27), residues: 321 sheet: 1.37 (0.33), residues: 239 loop : -0.76 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG X 262 TYR 0.026 0.002 TYR H 144 PHE 0.020 0.001 PHE L 122 TRP 0.020 0.001 TRP X 110 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 7290) covalent geometry : angle 0.71954 / 0.34 ( 9944) SS BOND : bond 0.00329 / 0.30 ( 6) SS BOND : angle 1.02635 / 0.84 ( 12) hydrogen bonds : bond 0.03460 / 2.30 ( 412) hydrogen bonds : angle 4.65713 / 3.22 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7629 (ttp80) REVERT: B 184 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7695 (ttm-80) REVERT: B 230 GLU cc_start: 0.7681 (mm-30) cc_final: 0.6855 (tt0) REVERT: X 167 ILE cc_start: 0.7760 (OUTLIER) cc_final: 0.7502 (mt) REVERT: X 182 HIS cc_start: 0.9289 (t-90) cc_final: 0.8199 (t-90) REVERT: X 242 LEU cc_start: 0.8723 (tt) cc_final: 0.8347 (mm) REVERT: X 286 ILE cc_start: 0.8493 (pt) cc_final: 0.8142 (mm) REVERT: H 28 LEU cc_start: 0.9133 (mt) cc_final: 0.8707 (mp) REVERT: H 86 ASP cc_start: 0.8733 (m-30) cc_final: 0.8390 (m-30) REVERT: H 143 ASP cc_start: 0.7358 (m-30) cc_final: 0.6734 (t70) REVERT: L 146 ARG cc_start: 0.8123 (tmm-80) cc_final: 0.7827 (tmm-80) REVERT: L 190 TYR cc_start: 0.7934 (t80) cc_final: 0.7619 (t80) outliers start: 48 outliers final: 44 residues processed: 187 average time/residue: 0.0581 time to fit residues: 15.5801 Evaluate side-chains 196 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 151 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain X residue 30 ASP Chi-restraints excluded: chain X residue 91 LEU Chi-restraints excluded: chain X residue 138 THR Chi-restraints excluded: chain X residue 147 THR Chi-restraints excluded: chain X residue 167 ILE Chi-restraints excluded: chain X residue 171 PHE Chi-restraints excluded: chain X residue 174 ILE Chi-restraints excluded: chain X residue 204 PHE Chi-restraints excluded: chain X residue 209 LEU Chi-restraints excluded: chain X residue 229 VAL Chi-restraints excluded: chain X residue 236 LEU Chi-restraints excluded: chain X residue 272 SER Chi-restraints excluded: chain X residue 294 SER Chi-restraints excluded: chain X residue 297 ILE Chi-restraints excluded: chain X residue 302 THR Chi-restraints excluded: chain X residue 314 ILE Chi-restraints excluded: chain X residue 335 LEU Chi-restraints excluded: chain X residue 338 TYR Chi-restraints excluded: chain H residue 21 CYS Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain H residue 109 THR Chi-restraints excluded: chain H residue 120 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 66 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 113 THR Chi-restraints excluded: chain L residue 167 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.0770 chunk 84 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 ASN B 182 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.147094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.100575 restraints weight = 12626.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104111 restraints weight = 7307.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.106507 restraints weight = 5324.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107836 restraints weight = 4413.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108394 restraints weight = 3959.659| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7296 Z= 0.130 Angle : 0.703 11.656 9956 Z= 0.329 Chirality : 0.043 0.331 1133 Planarity : 0.005 0.048 1234 Dihedral : 6.702 59.438 1018 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.05 % Allowed : 26.80 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 1.66 (0.29), residues: 901 helix: 2.56 (0.28), residues: 321 sheet: 1.54 (0.33), residues: 239 loop : -0.72 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 262 TYR 0.025 0.002 TYR H 144 PHE 0.013 0.001 PHE L 213 TRP 0.020 0.001 TRP X 259 HIS 0.003 0.001 HIS X 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7290) covalent geometry : angle 0.70230 / 0.33 ( 9944) SS BOND : bond 0.00280 / 0.29 ( 6) SS BOND : angle 0.86891 / 0.67 ( 12) hydrogen bonds : bond 0.03266 / 2.17 ( 412) hydrogen bonds : angle 4.51736 / 3.12 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1082.94 seconds wall clock time: 19 minutes 25.59 seconds (1165.59 seconds total)