Starting phenix.real_space_refine on Sat Apr 4 22:16:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpj_26057/04_2026/7tpj_26057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpj_26057/04_2026/7tpj_26057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tpj_26057/04_2026/7tpj_26057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpj_26057/04_2026/7tpj_26057.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tpj_26057/04_2026/7tpj_26057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpj_26057/04_2026/7tpj_26057.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 3071 2.51 5 N 816 2.21 5 O 839 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4758 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3053 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 16, 'TRANS': 386} Chain: "H" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 917 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 115} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Time building chain proxies: 1.12, per 1000 atoms: 0.24 Number of scatterers: 4758 At special positions: 0 Unit cell: (77.453, 79.575, 106.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 839 8.00 N 816 7.00 C 3071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 0.23 Conformation dependent library (CDL) restraints added in 268.6 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1138 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 52.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.876A pdb=" N SER B 9 " --> pdb=" O ASN B 5 " (cutoff:3.500A) Proline residue: B 20 - end of helix Processing helix chain 'B' and resid 28 through 42 removed outlier: 3.544A pdb=" N LEU B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 75 removed outlier: 3.606A pdb=" N THR B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) Proline residue: B 61 - end of helix removed outlier: 5.368A pdb=" N ALA B 65 " --> pdb=" O PRO B 61 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.521A pdb=" N ASP B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 89 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 94 through 106 removed outlier: 3.629A pdb=" N LEU B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 134 removed outlier: 4.255A pdb=" N TRP B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 162 removed outlier: 3.964A pdb=" N ALA B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 188 removed outlier: 3.524A pdb=" N LEU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.653A pdb=" N VAL B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 202 " --> pdb=" O LEU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 214 through 230 removed outlier: 4.552A pdb=" N ALA B 220 " --> pdb=" O MET B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 removed outlier: 4.058A pdb=" N VAL B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 254 Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.668A pdb=" N TYR B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.951A pdb=" N LEU B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 314 through 323 removed outlier: 3.984A pdb=" N ALA B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 352 removed outlier: 3.815A pdb=" N PHE B 335 " --> pdb=" O MET B 331 " (cutoff:3.500A) Proline residue: B 338 - end of helix removed outlier: 3.758A pdb=" N ALA B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 376 removed outlier: 3.597A pdb=" N VAL B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 407 removed outlier: 3.821A pdb=" N LEU B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.744A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.997A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 61 through 63 removed outlier: 3.672A pdb=" N TYR H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 51 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS H 99 " --> pdb=" O TRP H 116 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N TRP H 116 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG H 101 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 61 through 63 removed outlier: 3.672A pdb=" N TYR H 62 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL H 51 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 7 through 8 Processing sheet with id=AA5, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.626A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 266 hydrogen bonds defined for protein. 753 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.66 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1505 1.34 - 1.46: 1202 1.46 - 1.58: 2107 1.58 - 1.70: 1 1.70 - 1.81: 55 Bond restraints: 4870 Sorted by residual: bond pdb=" CB PRO B 238 " pdb=" CG PRO B 238 " ideal model delta sigma weight residual 1.492 1.652 -0.160 5.00e-02 4.00e+02 1.02e+01 bond pdb=" CG PRO B 238 " pdb=" CD PRO B 238 " ideal model delta sigma weight residual 1.503 1.447 0.056 3.40e-02 8.65e+02 2.73e+00 bond pdb=" C VAL B 74 " pdb=" O VAL B 74 " ideal model delta sigma weight residual 1.241 1.228 0.013 1.03e-02 9.43e+03 1.62e+00 bond pdb=" N PRO B 238 " pdb=" CA PRO B 238 " ideal model delta sigma weight residual 1.469 1.453 0.015 1.28e-02 6.10e+03 1.42e+00 bond pdb=" C VAL B 337 " pdb=" N PRO B 338 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.36e-02 5.41e+03 1.38e+00 ... (remaining 4865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 6559 2.72 - 5.45: 58 5.45 - 8.17: 7 8.17 - 10.89: 0 10.89 - 13.62: 1 Bond angle restraints: 6625 Sorted by residual: angle pdb=" CA PRO B 238 " pdb=" N PRO B 238 " pdb=" CD PRO B 238 " ideal model delta sigma weight residual 112.00 98.38 13.62 1.40e+00 5.10e-01 9.46e+01 angle pdb=" N LEU B 62 " pdb=" CA LEU B 62 " pdb=" C LEU B 62 " ideal model delta sigma weight residual 114.75 107.20 7.55 1.26e+00 6.30e-01 3.59e+01 angle pdb=" N PRO B 238 " pdb=" CD PRO B 238 " pdb=" CG PRO B 238 " ideal model delta sigma weight residual 103.20 95.38 7.82 1.50e+00 4.44e-01 2.72e+01 angle pdb=" N LEU B 217 " pdb=" CA LEU B 217 " pdb=" C LEU B 217 " ideal model delta sigma weight residual 113.55 108.86 4.69 1.26e+00 6.30e-01 1.38e+01 angle pdb=" N PRO B 238 " pdb=" CA PRO B 238 " pdb=" CB PRO B 238 " ideal model delta sigma weight residual 103.25 99.64 3.61 1.05e+00 9.07e-01 1.18e+01 ... (remaining 6620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 2547 16.70 - 33.39: 219 33.39 - 50.09: 61 50.09 - 66.78: 12 66.78 - 83.48: 7 Dihedral angle restraints: 2846 sinusoidal: 1059 harmonic: 1787 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 151.79 -58.79 1 1.00e+01 1.00e-02 4.63e+01 dihedral pdb=" CA PHE B 80 " pdb=" C PHE B 80 " pdb=" N HIS B 81 " pdb=" CA HIS B 81 " ideal model delta harmonic sigma weight residual 180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA MET B 48 " pdb=" C MET B 48 " pdb=" N GLY B 49 " pdb=" CA GLY B 49 " ideal model delta harmonic sigma weight residual 180.00 162.62 17.38 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 458 0.031 - 0.062: 220 0.062 - 0.093: 61 0.093 - 0.124: 22 0.124 - 0.154: 2 Chirality restraints: 763 Sorted by residual: chirality pdb=" CA THR B 60 " pdb=" N THR B 60 " pdb=" C THR B 60 " pdb=" CB THR B 60 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA VAL B 26 " pdb=" N VAL B 26 " pdb=" C VAL B 26 " pdb=" CB VAL B 26 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA PRO B 90 " pdb=" N PRO B 90 " pdb=" C PRO B 90 " pdb=" CB PRO B 90 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 760 not shown) Planarity restraints: 824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 237 " -0.094 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO B 238 " 0.226 5.00e-02 4.00e+02 pdb=" CA PRO B 238 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 238 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 101 " -0.026 2.00e-02 2.50e+03 1.90e-02 9.05e+00 pdb=" CG TRP B 101 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 101 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 101 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 101 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 101 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 101 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 101 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 101 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 337 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO B 338 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 338 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 338 " -0.031 5.00e-02 4.00e+02 ... (remaining 821 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 116 2.71 - 3.26: 4826 3.26 - 3.80: 7535 3.80 - 4.35: 9121 4.35 - 4.90: 15628 Nonbonded interactions: 37226 Sorted by model distance: nonbonded pdb=" O SER B 56 " pdb=" OG1 THR B 60 " model vdw 2.159 3.040 nonbonded pdb=" O ASN H 31 " pdb=" OG SER H 34 " model vdw 2.188 3.040 nonbonded pdb=" OG SER H 55 " pdb=" OG SER H 60 " model vdw 2.228 3.040 nonbonded pdb=" OG SER L 10 " pdb=" OE1 GLN L 101 " model vdw 2.290 3.040 nonbonded pdb=" OD2 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.291 3.040 ... (remaining 37221 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.610 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.004 0.160 4873 Z= 0.164 Angle : 0.700 13.618 6631 Z= 0.402 Chirality : 0.040 0.154 763 Planarity : 0.006 0.131 824 Dihedral : 14.421 83.478 1699 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.35), residues: 620 helix: 0.70 (0.31), residues: 298 sheet: 0.41 (0.58), residues: 91 loop : -1.02 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 215 TYR 0.019 0.002 TYR B 73 PHE 0.016 0.001 PHE H 113 TRP 0.051 0.002 TRP B 101 HIS 0.004 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 4870) covalent geometry : angle 0.69974 ( 6625) SS BOND : bond 0.00338 ( 3) SS BOND : angle 1.06546 ( 6) hydrogen bonds : bond 0.16953 ( 257) hydrogen bonds : angle 6.30001 ( 753) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.176 Fit side-chains REVERT: B 95 LEU cc_start: 0.7684 (mm) cc_final: 0.7423 (mp) REVERT: H 90 ARG cc_start: 0.7822 (ptp90) cc_final: 0.7018 (ptp-170) REVERT: H 122 VAL cc_start: 0.6686 (m) cc_final: 0.6468 (p) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0618 time to fit residues: 9.3856 Evaluate side-chains 99 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 GLN H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.185766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164206 restraints weight = 6675.280| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.63 r_work: 0.3854 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3750 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4873 Z= 0.119 Angle : 0.560 6.964 6631 Z= 0.292 Chirality : 0.040 0.153 763 Planarity : 0.005 0.065 824 Dihedral : 4.177 17.559 682 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.00 % Allowed : 10.02 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.35), residues: 620 helix: 0.96 (0.31), residues: 301 sheet: 0.68 (0.53), residues: 94 loop : -0.97 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 215 TYR 0.008 0.001 TYR B 275 PHE 0.014 0.001 PHE B 80 TRP 0.028 0.001 TRP B 101 HIS 0.002 0.000 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 4870) covalent geometry : angle 0.55898 ( 6625) SS BOND : bond 0.00474 ( 3) SS BOND : angle 1.03583 ( 6) hydrogen bonds : bond 0.03449 ( 257) hydrogen bonds : angle 4.29607 ( 753) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.6890 (mtt) cc_final: 0.6510 (mtm) REVERT: B 98 LEU cc_start: 0.7289 (tp) cc_final: 0.7039 (mt) REVERT: B 369 MET cc_start: 0.7761 (tpp) cc_final: 0.7064 (ttt) outliers start: 5 outliers final: 2 residues processed: 106 average time/residue: 0.0630 time to fit residues: 8.6705 Evaluate side-chains 98 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain L residue 57 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.184506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.164571 restraints weight = 6659.262| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.49 r_work: 0.3827 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4873 Z= 0.115 Angle : 0.528 6.173 6631 Z= 0.272 Chirality : 0.039 0.155 763 Planarity : 0.004 0.040 824 Dihedral : 4.079 17.104 682 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.00 % Allowed : 13.63 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.35), residues: 620 helix: 1.28 (0.31), residues: 300 sheet: 0.57 (0.52), residues: 92 loop : -0.98 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 215 TYR 0.012 0.001 TYR H 53 PHE 0.025 0.001 PHE B 69 TRP 0.025 0.001 TRP B 101 HIS 0.002 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4870) covalent geometry : angle 0.52789 ( 6625) SS BOND : bond 0.00365 ( 3) SS BOND : angle 0.76322 ( 6) hydrogen bonds : bond 0.03008 ( 257) hydrogen bonds : angle 3.93396 ( 753) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.7021 (mtt) cc_final: 0.6635 (mtm) REVERT: B 55 TYR cc_start: 0.8250 (m-80) cc_final: 0.8039 (m-80) REVERT: B 98 LEU cc_start: 0.7345 (tp) cc_final: 0.7137 (mt) REVERT: H 86 MET cc_start: 0.8725 (mpp) cc_final: 0.8402 (mpp) REVERT: H 90 ARG cc_start: 0.7934 (ptp-170) cc_final: 0.7398 (ptp90) REVERT: L 80 GLN cc_start: 0.7946 (mp10) cc_final: 0.7664 (mp10) outliers start: 5 outliers final: 4 residues processed: 100 average time/residue: 0.0659 time to fit residues: 8.6529 Evaluate side-chains 99 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 53 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.182358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160195 restraints weight = 6669.278| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.64 r_work: 0.3774 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4873 Z= 0.147 Angle : 0.550 5.975 6631 Z= 0.284 Chirality : 0.040 0.157 763 Planarity : 0.004 0.040 824 Dihedral : 4.259 17.795 682 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.40 % Allowed : 15.03 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.34), residues: 620 helix: 1.31 (0.31), residues: 300 sheet: 1.19 (0.59), residues: 77 loop : -1.05 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 215 TYR 0.016 0.002 TYR H 53 PHE 0.018 0.001 PHE B 69 TRP 0.021 0.002 TRP B 101 HIS 0.003 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4870) covalent geometry : angle 0.54917 ( 6625) SS BOND : bond 0.00411 ( 3) SS BOND : angle 0.99207 ( 6) hydrogen bonds : bond 0.03250 ( 257) hydrogen bonds : angle 3.90534 ( 753) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.7202 (mtt) cc_final: 0.6831 (mtm) REVERT: H 105 LYS cc_start: 0.8440 (tppt) cc_final: 0.8168 (mmtt) REVERT: L 80 GLN cc_start: 0.7985 (mp10) cc_final: 0.7488 (mp10) outliers start: 7 outliers final: 5 residues processed: 104 average time/residue: 0.0685 time to fit residues: 9.1971 Evaluate side-chains 101 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 53 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 52 optimal weight: 0.0000 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.185288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.162945 restraints weight = 6758.236| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.67 r_work: 0.3815 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4873 Z= 0.105 Angle : 0.515 7.800 6631 Z= 0.265 Chirality : 0.039 0.150 763 Planarity : 0.004 0.036 824 Dihedral : 4.029 16.421 682 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.00 % Allowed : 15.43 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.35), residues: 620 helix: 1.51 (0.31), residues: 299 sheet: 1.51 (0.60), residues: 75 loop : -1.09 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 90 TYR 0.013 0.001 TYR H 53 PHE 0.015 0.001 PHE B 69 TRP 0.017 0.001 TRP B 101 HIS 0.001 0.000 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 4870) covalent geometry : angle 0.51506 ( 6625) SS BOND : bond 0.00373 ( 3) SS BOND : angle 0.81743 ( 6) hydrogen bonds : bond 0.02692 ( 257) hydrogen bonds : angle 3.70204 ( 753) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.7085 (mtt) cc_final: 0.6715 (mtm) REVERT: B 139 ARG cc_start: 0.7175 (mmp80) cc_final: 0.6804 (mmp80) REVERT: B 178 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6860 (mp) REVERT: B 188 ASN cc_start: 0.8912 (t0) cc_final: 0.8631 (t0) REVERT: H 86 MET cc_start: 0.8674 (mpp) cc_final: 0.8420 (mpp) REVERT: L 18 ASP cc_start: 0.6247 (p0) cc_final: 0.6037 (p0) outliers start: 10 outliers final: 4 residues processed: 110 average time/residue: 0.0634 time to fit residues: 9.0792 Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 53 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.184910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.162536 restraints weight = 6973.959| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.71 r_work: 0.3786 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4873 Z= 0.117 Angle : 0.532 7.800 6631 Z= 0.273 Chirality : 0.039 0.151 763 Planarity : 0.004 0.035 824 Dihedral : 4.017 16.597 682 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.20 % Allowed : 15.83 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.35), residues: 620 helix: 1.54 (0.31), residues: 299 sheet: 1.06 (0.56), residues: 84 loop : -1.16 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 215 TYR 0.013 0.001 TYR H 53 PHE 0.013 0.001 PHE B 69 TRP 0.016 0.001 TRP B 101 HIS 0.002 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4870) covalent geometry : angle 0.53144 ( 6625) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.83273 ( 6) hydrogen bonds : bond 0.02795 ( 257) hydrogen bonds : angle 3.68828 ( 753) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.7128 (mtt) cc_final: 0.6768 (mtm) REVERT: B 178 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.7024 (mp) REVERT: B 188 ASN cc_start: 0.8931 (t0) cc_final: 0.8683 (t0) REVERT: H 105 LYS cc_start: 0.8420 (tppt) cc_final: 0.7965 (pttp) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.0632 time to fit residues: 8.6023 Evaluate side-chains 102 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.184819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162733 restraints weight = 6870.800| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 1.70 r_work: 0.3783 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4873 Z= 0.117 Angle : 0.524 7.793 6631 Z= 0.270 Chirality : 0.039 0.151 763 Planarity : 0.004 0.040 824 Dihedral : 4.014 16.827 682 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.40 % Allowed : 15.83 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.34), residues: 620 helix: 1.56 (0.31), residues: 299 sheet: 1.05 (0.56), residues: 84 loop : -1.16 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 215 TYR 0.013 0.001 TYR H 53 PHE 0.013 0.001 PHE B 69 TRP 0.016 0.001 TRP B 101 HIS 0.002 0.001 HIS B 294 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4870) covalent geometry : angle 0.52342 ( 6625) SS BOND : bond 0.00361 ( 3) SS BOND : angle 0.89101 ( 6) hydrogen bonds : bond 0.02736 ( 257) hydrogen bonds : angle 3.68265 ( 753) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.7155 (mtt) cc_final: 0.6769 (mtm) REVERT: B 139 ARG cc_start: 0.7357 (mmp80) cc_final: 0.6905 (mmp80) REVERT: B 144 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8243 (mt) REVERT: H 86 MET cc_start: 0.8648 (mpp) cc_final: 0.8360 (mpp) REVERT: H 90 ARG cc_start: 0.7971 (ptp90) cc_final: 0.7471 (ptp90) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.0652 time to fit residues: 8.8832 Evaluate side-chains 106 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 10 optimal weight: 0.2980 chunk 43 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.186104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.165740 restraints weight = 6845.810| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.53 r_work: 0.3849 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4873 Z= 0.102 Angle : 0.523 8.051 6631 Z= 0.265 Chirality : 0.038 0.146 763 Planarity : 0.004 0.040 824 Dihedral : 3.886 16.316 682 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.80 % Allowed : 17.43 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.35), residues: 620 helix: 1.65 (0.31), residues: 298 sheet: 1.25 (0.56), residues: 82 loop : -1.12 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 90 TYR 0.012 0.001 TYR H 53 PHE 0.011 0.001 PHE B 69 TRP 0.013 0.001 TRP B 101 HIS 0.001 0.000 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4870) covalent geometry : angle 0.52313 ( 6625) SS BOND : bond 0.00335 ( 3) SS BOND : angle 0.74739 ( 6) hydrogen bonds : bond 0.02598 ( 257) hydrogen bonds : angle 3.59754 ( 753) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7172 (t80) REVERT: B 139 ARG cc_start: 0.7225 (mmp80) cc_final: 0.6759 (mmp80) REVERT: B 144 ILE cc_start: 0.8418 (pt) cc_final: 0.8173 (mt) REVERT: H 86 MET cc_start: 0.8602 (mpp) cc_final: 0.8297 (mpp) REVERT: H 105 LYS cc_start: 0.8414 (tppt) cc_final: 0.7965 (pttp) outliers start: 9 outliers final: 6 residues processed: 100 average time/residue: 0.0681 time to fit residues: 8.9604 Evaluate side-chains 101 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 8 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.0020 chunk 9 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.184311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162637 restraints weight = 6759.334| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.62 r_work: 0.3821 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4873 Z= 0.111 Angle : 0.536 8.063 6631 Z= 0.272 Chirality : 0.039 0.148 763 Planarity : 0.004 0.042 824 Dihedral : 3.943 16.820 682 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.60 % Allowed : 17.84 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.35), residues: 620 helix: 1.62 (0.31), residues: 299 sheet: 1.13 (0.56), residues: 84 loop : -1.11 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 215 TYR 0.012 0.001 TYR H 53 PHE 0.011 0.001 PHE B 69 TRP 0.014 0.001 TRP B 101 HIS 0.002 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4870) covalent geometry : angle 0.53515 ( 6625) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.84863 ( 6) hydrogen bonds : bond 0.02708 ( 257) hydrogen bonds : angle 3.63000 ( 753) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.7158 (mtt) cc_final: 0.6754 (mtm) REVERT: B 73 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7182 (t80) REVERT: B 139 ARG cc_start: 0.7362 (mmp80) cc_final: 0.6904 (mmp80) REVERT: B 144 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8161 (mt) REVERT: H 90 ARG cc_start: 0.8069 (ptp90) cc_final: 0.7498 (ptp90) outliers start: 8 outliers final: 6 residues processed: 99 average time/residue: 0.0710 time to fit residues: 9.0640 Evaluate side-chains 101 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 50 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.183113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.161163 restraints weight = 6708.514| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.58 r_work: 0.3805 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4873 Z= 0.128 Angle : 0.570 8.994 6631 Z= 0.286 Chirality : 0.040 0.149 763 Planarity : 0.004 0.042 824 Dihedral : 4.082 16.834 682 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.80 % Allowed : 17.84 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.34), residues: 620 helix: 1.53 (0.31), residues: 299 sheet: 1.17 (0.56), residues: 84 loop : -1.13 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 46 TYR 0.014 0.001 TYR H 53 PHE 0.011 0.001 PHE B 69 TRP 0.013 0.001 TRP B 101 HIS 0.002 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4870) covalent geometry : angle 0.56966 ( 6625) SS BOND : bond 0.00349 ( 3) SS BOND : angle 0.93217 ( 6) hydrogen bonds : bond 0.02909 ( 257) hydrogen bonds : angle 3.70462 ( 753) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7107 (t80) REVERT: B 141 SER cc_start: 0.8415 (t) cc_final: 0.8023 (p) REVERT: H 90 ARG cc_start: 0.8075 (ptp90) cc_final: 0.7496 (ptp90) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 0.0605 time to fit residues: 7.7576 Evaluate side-chains 101 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 TYR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 53 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.184505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164251 restraints weight = 6773.718| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.41 r_work: 0.3812 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4873 Z= 0.125 Angle : 0.573 8.160 6631 Z= 0.289 Chirality : 0.039 0.149 763 Planarity : 0.004 0.043 824 Dihedral : 4.087 16.807 682 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.80 % Allowed : 18.64 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.34), residues: 620 helix: 1.54 (0.31), residues: 299 sheet: 1.16 (0.55), residues: 84 loop : -1.20 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 215 TYR 0.013 0.001 TYR H 53 PHE 0.011 0.001 PHE B 69 TRP 0.013 0.001 TRP B 101 HIS 0.002 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4870) covalent geometry : angle 0.57270 ( 6625) SS BOND : bond 0.00353 ( 3) SS BOND : angle 0.90058 ( 6) hydrogen bonds : bond 0.02838 ( 257) hydrogen bonds : angle 3.69785 ( 753) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.75 seconds wall clock time: 24 minutes 1.44 seconds (1441.44 seconds total)