Starting phenix.real_space_refine on Fri Dec 27 06:49:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5h_38069/12_2024/8x5h_38069.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5h_38069/12_2024/8x5h_38069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5h_38069/12_2024/8x5h_38069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5h_38069/12_2024/8x5h_38069.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5h_38069/12_2024/8x5h_38069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5h_38069/12_2024/8x5h_38069.cif" } resolution = 3.47 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= 0.002 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 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3258 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1086 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Restraints were copied for chains: C, B Time building chain proxies: 2.53, per 1000 atoms: 0.78 Number of scatterers: 3258 At special positions: 0 Unit cell: (100.43, 97.94, 34.86, 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 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.02 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: 0.78 Conformation dependent library (CDL) restraints added in 398.4 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.664A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 137 removed outlier: 6.589A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 144 removed outlier: 6.536A pdb=" N ILE B 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 156 removed outlier: 6.564A pdb=" N ASN B 155 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 164 removed outlier: 6.985A pdb=" N GLU B 163 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.555A pdb=" N GLN B 168 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.495A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 190 through 192 removed outlier: 6.466A pdb=" N ASP B 191 " --> pdb=" O MET C 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 201 through 213 removed outlier: 8.949A pdb=" N VAL B 202 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N GLU A 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 204 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N MET A 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU B 206 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N TYR A 209 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER B 208 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR A 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET B 210 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE A 213 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ASP B 212 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 202 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 203 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA C 204 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 230 removed outlier: 7.012A pdb=" N VAL B 230 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASN B 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU C 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 242 through 244 removed outlier: 6.310A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253 removed outlier: 6.434A pdb=" N ASP B 252 " --> pdb=" O CYS A 253 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 108 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: 0.73 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1017 1.33 - 1.45: 426 1.45 - 1.57: 1833 1.57 - 1.68: 0 1.68 - 1.80: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CG LEU A 144 " pdb=" CD2 LEU A 144 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.27e+00 bond pdb=" CG LEU B 144 " pdb=" CD2 LEU B 144 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.26e+00 bond pdb=" CG LEU C 144 " pdb=" CD2 LEU C 144 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.18e+00 bond pdb=" CA ILE A 146 " pdb=" CB ILE A 146 " ideal model delta sigma weight residual 1.549 1.525 0.024 1.88e-02 2.83e+03 1.56e+00 bond pdb=" CA ILE C 146 " pdb=" CB ILE C 146 " ideal model delta sigma weight residual 1.549 1.525 0.023 1.88e-02 2.83e+03 1.56e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 4022 1.20 - 2.41: 412 2.41 - 3.61: 45 3.61 - 4.82: 19 4.82 - 6.02: 5 Bond angle restraints: 4503 Sorted by residual: angle pdb=" C LEU A 144 " pdb=" N ASN A 145 " pdb=" CA ASN A 145 " ideal model delta sigma weight residual 122.82 127.69 -4.87 1.42e+00 4.96e-01 1.17e+01 angle pdb=" C LEU C 144 " pdb=" N ASN C 145 " pdb=" CA ASN C 145 " ideal model delta sigma weight residual 122.82 127.65 -4.83 1.42e+00 4.96e-01 1.16e+01 angle pdb=" C LEU B 144 " pdb=" N ASN B 145 " pdb=" CA ASN B 145 " ideal model delta sigma weight residual 122.82 127.64 -4.82 1.42e+00 4.96e-01 1.15e+01 angle pdb=" C ARG A 140 " pdb=" CA ARG A 140 " pdb=" CB ARG A 140 " ideal model delta sigma weight residual 111.86 107.99 3.87 1.34e+00 5.57e-01 8.33e+00 angle pdb=" C ARG C 140 " pdb=" CA ARG C 140 " pdb=" CB ARG C 140 " ideal model delta sigma weight residual 111.86 108.01 3.85 1.34e+00 5.57e-01 8.25e+00 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 1763 16.50 - 33.01: 199 33.01 - 49.51: 15 49.51 - 66.02: 9 66.02 - 82.52: 3 Dihedral angle restraints: 1989 sinusoidal: 771 harmonic: 1218 Sorted by residual: dihedral pdb=" CA GLN C 138 " pdb=" C GLN C 138 " pdb=" N LYS C 139 " pdb=" CA LYS C 139 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA GLN B 138 " pdb=" C GLN B 138 " pdb=" N LYS B 139 " pdb=" CA LYS B 139 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA GLN A 138 " pdb=" C GLN A 138 " pdb=" N LYS A 139 " pdb=" CA LYS A 139 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 1986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 376 0.053 - 0.107: 123 0.107 - 0.160: 38 0.160 - 0.213: 3 0.213 - 0.266: 3 Chirality restraints: 543 Sorted by residual: chirality pdb=" CB ILE A 186 " pdb=" CA ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CG2 ILE A 186 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE C 186 " pdb=" CA ILE C 186 " pdb=" CG1 ILE C 186 " pdb=" CG2 ILE C 186 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE B 186 " pdb=" CA ILE B 186 " pdb=" CG1 ILE B 186 " pdb=" CG2 ILE B 186 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.012 2.00e-02 2.50e+03 8.59e-03 1.48e+00 pdb=" CG TYR A 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 143 " 0.011 2.00e-02 2.50e+03 8.55e-03 1.46e+00 pdb=" CG TYR B 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 143 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 143 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 143 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.011 2.00e-02 2.50e+03 8.48e-03 1.44e+00 pdb=" CG TYR C 143 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.002 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 25 2.60 - 3.17: 2915 3.17 - 3.75: 4438 3.75 - 4.32: 6545 4.32 - 4.90: 12269 Nonbonded interactions: 26192 Sorted by model distance: nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " model vdw 2.023 3.760 nonbonded pdb=" OH TYR A 236 " pdb=" O HIS A 239 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR C 236 " pdb=" O HIS C 239 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR B 236 " pdb=" O HIS B 239 " model vdw 2.265 3.040 ... (remaining 26187 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.450 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 3312 Z= 0.584 Angle : 0.803 6.025 4503 Z= 0.472 Chirality : 0.059 0.266 543 Planarity : 0.003 0.009 558 Dihedral : 14.226 82.523 1206 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.99 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.56 (0.21), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 222 PHE 0.015 0.003 PHE C 213 TYR 0.021 0.003 TYR B 250 ARG 0.005 0.001 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.345 Fit side-chains REVERT: B 161 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8092 (mm-30) REVERT: B 192 MET cc_start: 0.8360 (mtt) cc_final: 0.8094 (mtp) REVERT: B 210 MET cc_start: 0.8090 (mtt) cc_final: 0.7831 (mtt) REVERT: B 220 LYS cc_start: 0.8308 (mttt) cc_final: 0.7985 (mtpt) REVERT: A 161 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 192 MET cc_start: 0.8610 (mtt) cc_final: 0.8296 (mtp) REVERT: A 207 MET cc_start: 0.6981 (ttm) cc_final: 0.6779 (ttm) REVERT: A 210 MET cc_start: 0.8415 (mtt) cc_final: 0.8180 (mtt) REVERT: C 161 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7157 (mm-30) REVERT: C 220 LYS cc_start: 0.8335 (mttt) cc_final: 0.7973 (mtpt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.2116 time to fit residues: 7.9716 Evaluate side-chains 30 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 35 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 223 ASN C 155 ASN C 223 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3312 Z= 0.145 Angle : 0.552 4.287 4503 Z= 0.314 Chirality : 0.052 0.151 543 Planarity : 0.002 0.020 558 Dihedral : 6.116 20.558 447 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.32 % Allowed : 12.96 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.57 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.24 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 239 PHE 0.004 0.001 PHE A 237 TYR 0.013 0.001 TYR B 250 ARG 0.001 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.383 Fit side-chains REVERT: B 210 MET cc_start: 0.8039 (mtt) cc_final: 0.7791 (mtt) REVERT: B 220 LYS cc_start: 0.8291 (mttt) cc_final: 0.7894 (mtpt) REVERT: A 180 ARG cc_start: 0.6932 (ptp-170) cc_final: 0.6661 (ptp90) REVERT: A 192 MET cc_start: 0.8437 (mtt) cc_final: 0.8153 (mtp) REVERT: A 207 MET cc_start: 0.6886 (ttm) cc_final: 0.6633 (ttm) REVERT: A 210 MET cc_start: 0.8300 (mtt) cc_final: 0.8023 (mtt) REVERT: C 220 LYS cc_start: 0.8355 (mttt) cc_final: 0.7981 (mtpt) outliers start: 5 outliers final: 2 residues processed: 41 average time/residue: 0.1937 time to fit residues: 9.6644 Evaluate side-chains 34 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3312 Z= 0.299 Angle : 0.605 3.823 4503 Z= 0.344 Chirality : 0.052 0.165 543 Planarity : 0.002 0.021 558 Dihedral : 6.263 20.372 447 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 2.38 % Allowed : 14.81 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.47 (0.29), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 222 PHE 0.009 0.002 PHE B 171 TYR 0.021 0.002 TYR A 143 ARG 0.001 0.000 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.412 Fit side-chains REVERT: B 210 MET cc_start: 0.8141 (mtt) cc_final: 0.7846 (mtt) REVERT: B 220 LYS cc_start: 0.8286 (mttt) cc_final: 0.7864 (mtpt) REVERT: A 180 ARG cc_start: 0.7113 (ptp-170) cc_final: 0.6734 (ptp90) REVERT: A 192 MET cc_start: 0.8483 (mtt) cc_final: 0.8222 (mtp) REVERT: A 207 MET cc_start: 0.7127 (ttm) cc_final: 0.6916 (ttm) REVERT: A 210 MET cc_start: 0.8312 (mtt) cc_final: 0.8044 (mtm) REVERT: C 220 LYS cc_start: 0.8374 (mttt) cc_final: 0.7971 (mtpt) outliers start: 9 outliers final: 7 residues processed: 40 average time/residue: 0.1734 time to fit residues: 8.5455 Evaluate side-chains 38 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 244 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.0020 chunk 3 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3312 Z= 0.139 Angle : 0.506 3.663 4503 Z= 0.288 Chirality : 0.051 0.153 543 Planarity : 0.002 0.021 558 Dihedral : 5.628 17.204 447 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.65 % Allowed : 15.61 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.25 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.006 0.001 PHE A 237 TYR 0.009 0.001 TYR B 236 ARG 0.001 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.380 Fit side-chains REVERT: B 146 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8459 (pt) REVERT: B 210 MET cc_start: 0.8129 (mtt) cc_final: 0.7741 (mtt) REVERT: B 220 LYS cc_start: 0.8252 (mttt) cc_final: 0.7859 (mtpt) REVERT: A 180 ARG cc_start: 0.6843 (ptp-170) cc_final: 0.6517 (ptp90) REVERT: A 192 MET cc_start: 0.8372 (mtt) cc_final: 0.8125 (mtp) REVERT: A 207 MET cc_start: 0.7033 (ttm) cc_final: 0.6809 (ttm) REVERT: A 210 MET cc_start: 0.8253 (mtt) cc_final: 0.7987 (mtt) REVERT: C 146 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8471 (pt) REVERT: C 220 LYS cc_start: 0.8358 (mttt) cc_final: 0.7959 (mtpt) outliers start: 10 outliers final: 5 residues processed: 38 average time/residue: 0.2036 time to fit residues: 9.3744 Evaluate side-chains 37 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3312 Z= 0.318 Angle : 0.600 4.019 4503 Z= 0.343 Chirality : 0.052 0.169 543 Planarity : 0.002 0.018 558 Dihedral : 6.114 20.484 447 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 4.23 % Allowed : 15.61 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.21 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 222 PHE 0.010 0.002 PHE A 237 TYR 0.023 0.002 TYR A 143 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.345 Fit side-chains REVERT: B 146 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8477 (pt) REVERT: B 210 MET cc_start: 0.8134 (mtt) cc_final: 0.7717 (mtt) REVERT: A 192 MET cc_start: 0.8457 (mtt) cc_final: 0.8254 (mtm) REVERT: A 210 MET cc_start: 0.8345 (mtt) cc_final: 0.8000 (mtt) REVERT: C 146 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8503 (pt) REVERT: C 220 LYS cc_start: 0.8375 (mttt) cc_final: 0.7931 (mtpt) outliers start: 16 outliers final: 11 residues processed: 45 average time/residue: 0.1782 time to fit residues: 9.8423 Evaluate side-chains 45 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 244 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3312 Z= 0.353 Angle : 0.617 4.083 4503 Z= 0.353 Chirality : 0.053 0.177 543 Planarity : 0.002 0.018 558 Dihedral : 6.297 20.823 447 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 4.76 % Allowed : 15.34 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.27 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 222 PHE 0.010 0.002 PHE A 237 TYR 0.024 0.002 TYR A 143 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 30 time to evaluate : 0.381 Fit side-chains REVERT: B 146 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8416 (pt) REVERT: B 210 MET cc_start: 0.8178 (mtt) cc_final: 0.7749 (mtt) REVERT: A 146 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8720 (pt) REVERT: A 210 MET cc_start: 0.8304 (mtt) cc_final: 0.7999 (mtt) REVERT: C 146 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8517 (pt) REVERT: C 220 LYS cc_start: 0.8387 (mttt) cc_final: 0.7972 (mtpt) outliers start: 18 outliers final: 14 residues processed: 46 average time/residue: 0.1877 time to fit residues: 10.5643 Evaluate side-chains 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 30 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 244 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 15 optimal weight: 0.0570 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3312 Z= 0.161 Angle : 0.522 3.967 4503 Z= 0.298 Chirality : 0.051 0.161 543 Planarity : 0.002 0.020 558 Dihedral : 5.726 17.681 447 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.23 % Allowed : 16.40 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.18 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 239 PHE 0.006 0.001 PHE A 237 TYR 0.013 0.001 TYR A 143 ARG 0.000 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.353 Fit side-chains REVERT: B 146 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8382 (pt) REVERT: B 180 ARG cc_start: 0.7091 (ptp-170) cc_final: 0.6677 (ptm160) REVERT: B 210 MET cc_start: 0.8128 (mtt) cc_final: 0.7741 (mtt) REVERT: A 146 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8627 (pt) REVERT: A 210 MET cc_start: 0.8293 (mtt) cc_final: 0.8027 (mtt) REVERT: C 146 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8443 (pt) REVERT: C 220 LYS cc_start: 0.8375 (mttt) cc_final: 0.7949 (mtpt) outliers start: 16 outliers final: 6 residues processed: 45 average time/residue: 0.1865 time to fit residues: 10.1880 Evaluate side-chains 39 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3312 Z= 0.178 Angle : 0.537 4.834 4503 Z= 0.307 Chirality : 0.051 0.167 543 Planarity : 0.002 0.020 558 Dihedral : 5.672 18.230 447 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.70 % Allowed : 16.67 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.05 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.008 0.001 PHE A 237 TYR 0.014 0.001 TYR A 143 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.347 Fit side-chains REVERT: B 146 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8422 (pt) REVERT: B 180 ARG cc_start: 0.7114 (ptp-170) cc_final: 0.6688 (ptm160) REVERT: B 210 MET cc_start: 0.8162 (mtt) cc_final: 0.7757 (mtt) REVERT: A 210 MET cc_start: 0.8285 (mtt) cc_final: 0.8033 (mtt) REVERT: C 146 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8422 (pt) REVERT: C 220 LYS cc_start: 0.8367 (mttt) cc_final: 0.7915 (mtpt) outliers start: 14 outliers final: 7 residues processed: 41 average time/residue: 0.1919 time to fit residues: 9.4687 Evaluate side-chains 39 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3312 Z= 0.378 Angle : 0.644 5.417 4503 Z= 0.366 Chirality : 0.054 0.172 543 Planarity : 0.003 0.018 558 Dihedral : 6.190 21.450 447 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 4.23 % Allowed : 16.67 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.12 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 222 PHE 0.012 0.003 PHE A 237 TYR 0.027 0.003 TYR A 143 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.376 Fit side-chains REVERT: B 144 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7671 (mp) REVERT: B 146 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8412 (pt) REVERT: B 180 ARG cc_start: 0.7188 (ptp-170) cc_final: 0.6744 (ptm160) REVERT: B 210 MET cc_start: 0.8176 (mtt) cc_final: 0.7764 (mtt) REVERT: A 146 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8725 (pt) REVERT: A 210 MET cc_start: 0.8330 (mtt) cc_final: 0.8112 (mtt) REVERT: C 146 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8475 (pt) REVERT: C 220 LYS cc_start: 0.8382 (mttt) cc_final: 0.7969 (mtpt) outliers start: 16 outliers final: 9 residues processed: 45 average time/residue: 0.2058 time to fit residues: 11.1004 Evaluate side-chains 44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3312 Z= 0.205 Angle : 0.572 6.954 4503 Z= 0.322 Chirality : 0.052 0.162 543 Planarity : 0.002 0.019 558 Dihedral : 5.869 19.213 447 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.97 % Allowed : 16.67 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.10 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.008 0.002 PHE A 237 TYR 0.017 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.452 Fit side-chains REVERT: B 146 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8319 (pt) REVERT: B 180 ARG cc_start: 0.7299 (ptp-170) cc_final: 0.6892 (ptp90) REVERT: B 210 MET cc_start: 0.8167 (mtt) cc_final: 0.7763 (mtt) REVERT: A 146 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8678 (pt) REVERT: A 210 MET cc_start: 0.8287 (mtt) cc_final: 0.8015 (mtt) REVERT: C 146 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8408 (pt) REVERT: C 220 LYS cc_start: 0.8377 (mttt) cc_final: 0.7945 (mtpt) outliers start: 15 outliers final: 10 residues processed: 44 average time/residue: 0.2329 time to fit residues: 12.1776 Evaluate side-chains 44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 HIS ** 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 = 0.4326 r_free = 0.4326 target = 0.151425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.134117 restraints weight = 3678.705| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.45 r_work: 0.4108 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3992 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3312 Z= 0.360 Angle : 0.656 7.231 4503 Z= 0.370 Chirality : 0.054 0.172 543 Planarity : 0.002 0.019 558 Dihedral : 6.232 22.015 447 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.53 % Favored : 87.47 % Rotamer: Outliers : 3.70 % Allowed : 16.93 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.16 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 222 PHE 0.011 0.002 PHE A 237 TYR 0.027 0.002 TYR A 143 ARG 0.001 0.000 ARG A 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.83 seconds wall clock time: 24 minutes 13.88 seconds (1453.88 seconds total)