Starting phenix.real_space_refine on Fri Dec 27 12:32:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tpj_26057/12_2024/7tpj_26057.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tpj_26057/12_2024/7tpj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7tpj_26057/12_2024/7tpj_26057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tpj_26057/12_2024/7tpj_26057.map" model { file = "/net/cci-nas-00/data/ceres_data/7tpj_26057/12_2024/7tpj_26057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tpj_26057/12_2024/7tpj_26057.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 3.23, per 1000 atoms: 0.68 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: 1.29 Conformation dependent library (CDL) restraints added in 614.4 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: 0.52 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: 1.32 Time building geometry restraints manager: 1.40 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: 1.080 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.070 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- 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 4870 Z= 0.291 Angle : 0.700 13.618 6625 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (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 TRP 0.051 0.002 TRP B 101 HIS 0.004 0.001 HIS B 294 PHE 0.016 0.001 PHE H 113 TYR 0.019 0.002 TYR B 73 ARG 0.008 0.001 ARG B 215 *********************** 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 : 0.522 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: 0.1602 time to fit residues: 24.2667 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 : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 35 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 overall best weight: 0.3580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4870 Z= 0.185 Angle : 0.553 7.102 6625 Z= 0.288 Chirality : 0.040 0.153 763 Planarity : 0.005 0.063 824 Dihedral : 4.152 17.219 682 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.00 % Allowed : 10.22 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.35), residues: 620 helix: 0.99 (0.31), residues: 300 sheet: 0.68 (0.52), residues: 94 loop : -1.01 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 101 HIS 0.002 0.000 HIS B 294 PHE 0.014 0.001 PHE B 80 TYR 0.009 0.001 TYR H 62 ARG 0.005 0.000 ARG B 215 *********************** 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 110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.6364 (mtt) cc_final: 0.6032 (mtm) REVERT: B 369 MET cc_start: 0.7411 (tpp) cc_final: 0.6626 (ttt) outliers start: 5 outliers final: 2 residues processed: 107 average time/residue: 0.1586 time to fit residues: 22.0080 Evaluate side-chains 100 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 30 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4870 Z= 0.165 Angle : 0.522 6.689 6625 Z= 0.269 Chirality : 0.039 0.149 763 Planarity : 0.004 0.051 824 Dihedral : 3.964 16.661 682 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.00 % Allowed : 13.43 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.35), residues: 620 helix: 1.27 (0.31), residues: 301 sheet: 0.76 (0.53), residues: 94 loop : -0.96 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 101 HIS 0.001 0.000 HIS B 171 PHE 0.022 0.001 PHE B 69 TYR 0.012 0.001 TYR H 53 ARG 0.003 0.000 ARG H 90 *********************** 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 : 0.447 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.6559 (mtt) cc_final: 0.6210 (mtm) REVERT: H 90 ARG cc_start: 0.7795 (ptp90) cc_final: 0.6994 (ptp90) outliers start: 5 outliers final: 4 residues processed: 100 average time/residue: 0.1680 time to fit residues: 21.5989 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 : 0.496 ------------------------------------------------------------------------------- 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 41 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4870 Z= 0.293 Angle : 0.628 6.904 6625 Z= 0.327 Chirality : 0.042 0.163 763 Planarity : 0.005 0.053 824 Dihedral : 4.550 19.783 682 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.61 % Allowed : 13.63 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.34), residues: 620 helix: 1.06 (0.31), residues: 299 sheet: 0.84 (0.54), residues: 90 loop : -1.20 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 101 HIS 0.005 0.001 HIS B 294 PHE 0.019 0.002 PHE B 69 TYR 0.019 0.002 TYR H 53 ARG 0.004 0.001 ARG B 215 *********************** 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 113 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.6669 (mtt) cc_final: 0.6391 (mtm) REVERT: H 90 ARG cc_start: 0.7662 (ptp90) cc_final: 0.7152 (ptp90) outliers start: 13 outliers final: 6 residues processed: 108 average time/residue: 0.1563 time to fit residues: 21.9266 Evaluate side-chains 101 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 33 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 ASN ** H 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN L 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4870 Z= 0.297 Angle : 0.624 7.326 6625 Z= 0.326 Chirality : 0.043 0.169 763 Planarity : 0.005 0.052 824 Dihedral : 4.692 19.855 682 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.34), residues: 620 helix: 0.97 (0.30), residues: 300 sheet: 1.02 (0.56), residues: 83 loop : -1.30 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 101 HIS 0.004 0.001 HIS B 294 PHE 0.029 0.002 PHE B 69 TYR 0.019 0.002 TYR H 53 ARG 0.003 0.001 ARG B 215 *********************** 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: 11 poor density : 103 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 MET cc_start: 0.6615 (mtt) cc_final: 0.6338 (mtm) REVERT: B 139 ARG cc_start: 0.7231 (mmp80) cc_final: 0.6936 (mmp80) REVERT: B 178 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6540 (mp) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.1643 time to fit residues: 23.0575 Evaluate side-chains 105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 53 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.0870 chunk 30 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4870 Z= 0.159 Angle : 0.527 7.665 6625 Z= 0.271 Chirality : 0.038 0.148 763 Planarity : 0.004 0.047 824 Dihedral : 4.175 16.486 682 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.00 % Allowed : 16.43 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.34), residues: 620 helix: 1.45 (0.31), residues: 298 sheet: 0.92 (0.56), residues: 84 loop : -1.29 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 101 HIS 0.003 0.001 HIS B 279 PHE 0.022 0.001 PHE B 69 TYR 0.012 0.001 TYR H 53 ARG 0.004 0.000 ARG H 90 *********************** 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 110 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.447 Fit side-chains REVERT: B 11 MET cc_start: 0.6395 (mtt) cc_final: 0.6081 (mtm) REVERT: B 55 TYR cc_start: 0.7942 (m-80) cc_final: 0.7702 (m-80) REVERT: B 139 ARG cc_start: 0.6881 (mmp80) cc_final: 0.6550 (mmp80) REVERT: B 178 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6588 (mp) REVERT: H 90 ARG cc_start: 0.7793 (ptp90) cc_final: 0.7313 (ptp90) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.1838 time to fit residues: 24.6337 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 : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 178 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.0060 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4870 Z= 0.170 Angle : 0.534 7.817 6625 Z= 0.273 Chirality : 0.039 0.151 763 Planarity : 0.004 0.046 824 Dihedral : 4.075 17.284 682 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.60 % Allowed : 17.03 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.34), residues: 620 helix: 1.53 (0.31), residues: 299 sheet: 1.10 (0.56), residues: 82 loop : -1.14 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 101 HIS 0.002 0.001 HIS B 294 PHE 0.020 0.001 PHE B 69 TYR 0.014 0.001 TYR H 33 ARG 0.005 0.000 ARG L 19 *********************** 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 108 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.6424 (mtt) cc_final: 0.6124 (mtm) REVERT: B 73 TYR cc_start: 0.7439 (OUTLIER) cc_final: 0.6578 (t80) REVERT: B 139 ARG cc_start: 0.6974 (mmp80) cc_final: 0.6531 (mmp80) REVERT: H 90 ARG cc_start: 0.7878 (ptp90) cc_final: 0.7545 (ptp90) outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 0.1624 time to fit residues: 21.6539 Evaluate side-chains 105 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 TYR 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 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 11 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.0770 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4870 Z= 0.171 Angle : 0.540 8.004 6625 Z= 0.275 Chirality : 0.039 0.150 763 Planarity : 0.004 0.044 824 Dihedral : 4.033 16.583 682 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.20 % Allowed : 17.64 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.34), residues: 620 helix: 1.54 (0.31), residues: 299 sheet: 1.16 (0.56), residues: 82 loop : -1.16 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 101 HIS 0.002 0.001 HIS B 406 PHE 0.019 0.001 PHE B 69 TYR 0.012 0.001 TYR H 53 ARG 0.005 0.000 ARG L 19 *********************** 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 109 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: B 73 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6596 (t80) REVERT: B 139 ARG cc_start: 0.6956 (mmp80) cc_final: 0.6533 (mmp80) REVERT: H 90 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7479 (ptp90) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.1688 time to fit residues: 22.4120 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 : 0.596 ------------------------------------------------------------------------------- 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 91 SER 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 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 23 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 0.0670 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4870 Z= 0.239 Angle : 0.591 7.950 6625 Z= 0.302 Chirality : 0.041 0.158 763 Planarity : 0.004 0.045 824 Dihedral : 4.298 18.132 682 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.61 % Allowed : 17.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.34), residues: 620 helix: 1.44 (0.31), residues: 299 sheet: 1.07 (0.55), residues: 84 loop : -1.23 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 101 HIS 0.003 0.001 HIS B 294 PHE 0.018 0.001 PHE B 69 TYR 0.015 0.001 TYR H 53 ARG 0.004 0.000 ARG L 19 *********************** 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 109 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.6586 (mtt) cc_final: 0.6262 (mtm) REVERT: B 73 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6506 (t80) REVERT: B 139 ARG cc_start: 0.7067 (mmp80) cc_final: 0.6589 (mmp80) REVERT: B 216 MET cc_start: 0.4760 (OUTLIER) cc_final: 0.3838 (mtt) REVERT: H 90 ARG cc_start: 0.7878 (ptp90) cc_final: 0.7352 (ptp90) REVERT: H 105 LYS cc_start: 0.8233 (tppt) cc_final: 0.8027 (pttp) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.1732 time to fit residues: 22.3350 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 : 0.524 ------------------------------------------------------------------------------- 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 91 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 216 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4870 Z= 0.189 Angle : 0.567 8.181 6625 Z= 0.288 Chirality : 0.039 0.151 763 Planarity : 0.004 0.044 824 Dihedral : 4.168 17.018 682 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.20 % Allowed : 17.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.34), residues: 620 helix: 1.51 (0.31), residues: 299 sheet: 1.21 (0.55), residues: 82 loop : -1.17 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 101 HIS 0.002 0.001 HIS B 294 PHE 0.018 0.001 PHE B 69 TYR 0.012 0.001 TYR H 53 ARG 0.005 0.000 ARG L 19 ********************** 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 106 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: B 11 MET cc_start: 0.6472 (mtt) cc_final: 0.6143 (mtm) REVERT: B 73 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6454 (t80) REVERT: B 139 ARG cc_start: 0.7061 (mmp80) cc_final: 0.6598 (mmp80) REVERT: B 216 MET cc_start: 0.4613 (OUTLIER) cc_final: 0.3677 (mtt) REVERT: H 90 ARG cc_start: 0.7871 (ptp90) cc_final: 0.7360 (ptp90) REVERT: H 105 LYS cc_start: 0.8273 (tppt) cc_final: 0.8026 (pttp) outliers start: 11 outliers final: 9 residues processed: 100 average time/residue: 0.1703 time to fit residues: 22.2362 Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 91 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 216 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 20.0000 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 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 = 0.4147 r_free = 0.4147 target = 0.185219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163447 restraints weight = 6726.886| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.63 r_work: 0.3793 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4870 Z= 0.175 Angle : 0.550 8.180 6625 Z= 0.279 Chirality : 0.039 0.149 763 Planarity : 0.004 0.043 824 Dihedral : 4.020 17.010 682 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.00 % Allowed : 17.84 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.34), residues: 620 helix: 1.56 (0.31), residues: 301 sheet: 1.10 (0.54), residues: 84 loop : -1.16 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 101 HIS 0.003 0.001 HIS B 406 PHE 0.017 0.001 PHE B 69 TYR 0.012 0.001 TYR H 53 ARG 0.005 0.000 ARG L 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1377.61 seconds wall clock time: 25 minutes 46.50 seconds (1546.50 seconds total)