Starting phenix.real_space_refine on Wed Jul 23 12:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x83_33054/07_2025/7x83_33054.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x83_33054/07_2025/7x83_33054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x83_33054/07_2025/7x83_33054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x83_33054/07_2025/7x83_33054.map" model { file = "/net/cci-nas-00/data/ceres_data/7x83_33054/07_2025/7x83_33054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x83_33054/07_2025/7x83_33054.cif" } resolution = 3.4 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= 0.001 sd= 0.003 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 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.86, per 1000 atoms: 1.80 Number of scatterers: 3258 At special positions: 0 Unit cell: (100.43, 100.43, 35.69, 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 507.7 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 14 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.705A 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: 6.653A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.302A 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: 6.553A pdb=" N TYR B 143 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 removed outlier: 6.958A pdb=" N LEU B 150 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 156 removed outlier: 6.509A pdb=" N ASN B 155 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 164 removed outlier: 6.916A pdb=" N GLU B 163 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.584A pdb=" N GLN B 168 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.541A pdb=" N THR B 185 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 192 removed outlier: 6.479A pdb=" N LEU B 190 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 213 removed outlier: 8.933A pdb=" N VAL B 202 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N GLU A 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA B 204 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N MET A 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU B 206 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR A 209 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER B 208 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N TYR A 211 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET B 210 " --> pdb=" O TYR A 211 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE A 213 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASP B 212 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 202 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE B 203 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA C 204 " --> pdb=" O ILE B 203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 216 through 219 removed outlier: 5.914A pdb=" N LEU B 216 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE C 219 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 222 through 230 removed outlier: 6.990A pdb=" N VAL B 230 " --> pdb=" O GLN A 229 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN B 223 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU C 226 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 225 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N MET C 228 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET B 227 " --> pdb=" O MET C 228 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N VAL C 230 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLN B 229 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.646A pdb=" N SER B 240 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ILE C 243 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN B 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 251 through 253 removed outlier: 6.458A pdb=" N ASP B 252 " --> pdb=" O CYS A 253 " (cutoff:3.500A) 41 hydrogen bonds defined for protein. 123 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: 2.25 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1026 1.34 - 1.45: 538 1.45 - 1.57: 1712 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CA VAL B 230 " pdb=" C VAL B 230 " ideal model delta sigma weight residual 1.527 1.513 0.014 8.50e-03 1.38e+04 2.73e+00 bond pdb=" CA ARG B 247 " pdb=" C ARG B 247 " ideal model delta sigma weight residual 1.531 1.514 0.017 1.08e-02 8.57e+03 2.46e+00 bond pdb=" CA ARG A 247 " pdb=" C ARG A 247 " ideal model delta sigma weight residual 1.531 1.515 0.017 1.08e-02 8.57e+03 2.34e+00 bond pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 1.527 1.514 0.013 8.50e-03 1.38e+04 2.34e+00 bond pdb=" CA ARG C 247 " pdb=" C ARG C 247 " ideal model delta sigma weight residual 1.531 1.515 0.016 1.08e-02 8.57e+03 2.33e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 3790 1.03 - 2.06: 559 2.06 - 3.09: 121 3.09 - 4.12: 21 4.12 - 5.16: 12 Bond angle restraints: 4503 Sorted by residual: angle pdb=" C GLN C 245 " pdb=" N GLU C 246 " pdb=" CA GLU C 246 " ideal model delta sigma weight residual 122.11 117.17 4.94 1.59e+00 3.96e-01 9.66e+00 angle pdb=" C GLN B 245 " pdb=" N GLU B 246 " pdb=" CA GLU B 246 " ideal model delta sigma weight residual 122.11 117.17 4.94 1.59e+00 3.96e-01 9.66e+00 angle pdb=" C GLN A 245 " pdb=" N GLU A 246 " pdb=" CA GLU A 246 " ideal model delta sigma weight residual 122.11 117.21 4.90 1.59e+00 3.96e-01 9.50e+00 angle pdb=" C LEU A 144 " pdb=" N ASN A 145 " pdb=" CA ASN A 145 " ideal model delta sigma weight residual 121.54 126.70 -5.16 1.91e+00 2.74e-01 7.28e+00 angle pdb=" CA TYR C 143 " pdb=" CB TYR C 143 " pdb=" CG TYR C 143 " ideal model delta sigma weight residual 113.90 118.75 -4.85 1.80e+00 3.09e-01 7.27e+00 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 1788 16.36 - 32.72: 175 32.72 - 49.08: 17 49.08 - 65.43: 6 65.43 - 81.79: 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 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+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 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+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 180.00 158.00 22.00 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 1986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 255 0.035 - 0.071: 156 0.071 - 0.106: 88 0.106 - 0.142: 35 0.142 - 0.177: 9 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ASN A 145 " pdb=" N ASN A 145 " pdb=" C ASN A 145 " pdb=" CB ASN A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA ASN C 145 " pdb=" N ASN C 145 " pdb=" C ASN C 145 " pdb=" CB ASN C 145 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA ASN B 145 " pdb=" N ASN B 145 " pdb=" C ASN B 145 " pdb=" CB ASN B 145 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.018 2.00e-02 2.50e+03 1.14e-02 2.60e+00 pdb=" CG TYR A 143 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.018 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR C 143 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 143 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 143 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 143 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 143 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 143 " 0.018 2.00e-02 2.50e+03 1.12e-02 2.51e+00 pdb=" CG TYR B 143 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 143 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 143 " 0.003 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 " 0.004 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 30 2.60 - 3.18: 2875 3.18 - 3.75: 4567 3.75 - 4.33: 6568 4.33 - 4.90: 12143 Nonbonded interactions: 26183 Sorted by model distance: nonbonded pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " model vdw 2.027 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " model vdw 2.028 3.760 nonbonded pdb=" OH TYR B 236 " pdb=" OG SER B 240 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 236 " pdb=" OG SER A 240 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR C 236 " pdb=" OG SER C 240 " model vdw 2.218 3.040 ... (remaining 26178 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 110.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 22.220 Find NCS groups from input model: 0.060 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:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 0.058 3313 Z= 0.395 Angle : 0.825 5.155 4505 Z= 0.494 Chirality : 0.060 0.177 543 Planarity : 0.003 0.011 558 Dihedral : 13.347 81.792 1206 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % 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: -5.71 (0.28), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.35 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 222 PHE 0.010 0.003 PHE A 213 TYR 0.026 0.003 TYR A 143 ARG 0.003 0.001 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.12708 ( 41) hydrogen bonds : angle 7.06288 ( 123) SS BOND : bond 0.00389 ( 1) SS BOND : angle 1.78659 ( 2) covalent geometry : bond 0.00890 ( 3312) covalent geometry : angle 0.82450 ( 4503) *********************** 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 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.364 Fit side-chains REVERT: B 140 ARG cc_start: 0.7649 (mtt180) cc_final: 0.7233 (ttm110) REVERT: B 178 LYS cc_start: 0.7339 (mttt) cc_final: 0.6399 (tptt) REVERT: B 215 THR cc_start: 0.7671 (t) cc_final: 0.7398 (t) REVERT: A 140 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7490 (ttm110) REVERT: A 178 LYS cc_start: 0.7850 (mttt) cc_final: 0.6991 (tptt) REVERT: C 140 ARG cc_start: 0.7745 (mtt180) cc_final: 0.7510 (ttm110) REVERT: C 178 LYS cc_start: 0.7310 (mttt) cc_final: 0.6486 (tptt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.5561 time to fit residues: 32.6125 Evaluate side-chains 37 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 1.534 ------------------------------------------------------------------------------- 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: 9.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 156 ASN B 223 ASN A 156 ASN A 223 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 223 ASN ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.270128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.225369 restraints weight = 3980.931| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 0.89 r_work: 0.4879 rms_B_bonded: 0.40 restraints_weight: 0.5000 r_work: 0.4850 rms_B_bonded: 0.70 restraints_weight: 0.2500 r_work: 0.4698 rms_B_bonded: 2.59 restraints_weight: 0.1250 r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3313 Z= 0.173 Angle : 0.612 5.443 4505 Z= 0.340 Chirality : 0.054 0.183 543 Planarity : 0.002 0.020 558 Dihedral : 6.646 19.261 447 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.03 % Favored : 86.97 % Rotamer: Outliers : 3.70 % Allowed : 12.17 % Favored : 84.13 % 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: -5.42 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.009 0.002 PHE A 237 TYR 0.019 0.002 TYR B 143 ARG 0.001 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.01833 ( 41) hydrogen bonds : angle 4.96274 ( 123) SS BOND : bond 0.00369 ( 1) SS BOND : angle 0.38048 ( 2) covalent geometry : bond 0.00406 ( 3312) covalent geometry : angle 0.61243 ( 4503) *********************** 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 60 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.407 Fit side-chains REVERT: B 145 ASN cc_start: 0.8347 (p0) cc_final: 0.7910 (p0) REVERT: B 146 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8246 (pt) REVERT: B 178 LYS cc_start: 0.8308 (mttt) cc_final: 0.7787 (tptt) REVERT: B 215 THR cc_start: 0.7794 (t) cc_final: 0.7560 (t) REVERT: A 178 LYS cc_start: 0.8119 (mttt) cc_final: 0.7687 (tptt) REVERT: C 145 ASN cc_start: 0.8114 (p0) cc_final: 0.7617 (p0) REVERT: C 146 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7675 (pt) REVERT: C 178 LYS cc_start: 0.8016 (mttt) cc_final: 0.7568 (tptt) REVERT: C 215 THR cc_start: 0.7757 (t) cc_final: 0.7542 (t) outliers start: 14 outliers final: 6 residues processed: 55 average time/residue: 0.3379 time to fit residues: 22.6087 Evaluate side-chains 46 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4637 r_free = 0.4637 target = 0.266727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.221188 restraints weight = 4001.107| |-----------------------------------------------------------------------------| r_work (start): 0.4581 rms_B_bonded: 0.85 r_work: 0.4854 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.4831 rms_B_bonded: 0.66 restraints_weight: 0.2500 r_work: 0.4679 rms_B_bonded: 2.57 restraints_weight: 0.1250 r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3313 Z= 0.201 Angle : 0.630 5.878 4505 Z= 0.347 Chirality : 0.054 0.182 543 Planarity : 0.003 0.027 558 Dihedral : 6.474 17.569 447 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 4.50 % Allowed : 12.17 % Favored : 83.33 % 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: -5.44 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.011 0.002 PHE A 237 TYR 0.019 0.002 TYR B 143 ARG 0.009 0.001 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.01783 ( 41) hydrogen bonds : angle 4.68306 ( 123) SS BOND : bond 0.00619 ( 1) SS BOND : angle 1.18211 ( 2) covalent geometry : bond 0.00477 ( 3312) covalent geometry : angle 0.62964 ( 4503) *********************** 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 61 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.688 Fit side-chains REVERT: B 145 ASN cc_start: 0.8323 (p0) cc_final: 0.7858 (p0) REVERT: B 146 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8240 (pt) REVERT: B 178 LYS cc_start: 0.8431 (mttt) cc_final: 0.7922 (tptt) REVERT: B 215 THR cc_start: 0.7802 (t) cc_final: 0.7586 (t) REVERT: A 178 LYS cc_start: 0.8060 (mttt) cc_final: 0.7625 (tptt) REVERT: A 226 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7222 (tt) REVERT: C 145 ASN cc_start: 0.8177 (p0) cc_final: 0.7687 (p0) REVERT: C 146 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7685 (pt) REVERT: C 178 LYS cc_start: 0.8098 (mttt) cc_final: 0.7578 (tptt) outliers start: 17 outliers final: 12 residues processed: 59 average time/residue: 0.2455 time to fit residues: 18.3681 Evaluate side-chains 54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain C residue 134 SER 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 180 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 0.0970 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4660 r_free = 0.4660 target = 0.269530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4871 r_free = 0.4871 target = 0.224384 restraints weight = 4019.530| |-----------------------------------------------------------------------------| r_work (start): 0.4609 rms_B_bonded: 0.85 r_work: 0.4882 rms_B_bonded: 0.38 restraints_weight: 0.5000 r_work: 0.4859 rms_B_bonded: 0.65 restraints_weight: 0.2500 r_work: 0.4706 rms_B_bonded: 2.53 restraints_weight: 0.1250 r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3313 Z= 0.166 Angle : 0.598 6.108 4505 Z= 0.328 Chirality : 0.053 0.178 543 Planarity : 0.002 0.015 558 Dihedral : 6.210 16.238 447 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 4.50 % Allowed : 13.76 % 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: -5.29 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 239 PHE 0.010 0.002 PHE A 237 TYR 0.018 0.002 TYR B 143 ARG 0.005 0.001 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.01557 ( 41) hydrogen bonds : angle 4.55449 ( 123) SS BOND : bond 0.00512 ( 1) SS BOND : angle 0.99177 ( 2) covalent geometry : bond 0.00392 ( 3312) covalent geometry : angle 0.59804 ( 4503) *********************** 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 65 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.336 Fit side-chains REVERT: B 145 ASN cc_start: 0.8295 (p0) cc_final: 0.7836 (p0) REVERT: B 146 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8231 (pt) REVERT: B 178 LYS cc_start: 0.8399 (mttt) cc_final: 0.7888 (tptt) REVERT: B 215 THR cc_start: 0.7802 (t) cc_final: 0.7599 (t) REVERT: A 178 LYS cc_start: 0.8019 (mttt) cc_final: 0.7573 (tptt) REVERT: C 145 ASN cc_start: 0.8154 (p0) cc_final: 0.7683 (p0) REVERT: C 146 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7698 (pt) REVERT: C 178 LYS cc_start: 0.8105 (mttt) cc_final: 0.7593 (tptt) outliers start: 17 outliers final: 9 residues processed: 63 average time/residue: 0.1495 time to fit residues: 11.7519 Evaluate side-chains 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL 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 2 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** C 239 HIS ** 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 = 0.4685 r_free = 0.4685 target = 0.308045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.4977 r_free = 0.4977 target = 0.254278 restraints weight = 4363.664| |-----------------------------------------------------------------------------| r_work (start): 0.4504 rms_B_bonded: 0.86 r_work: 0.4430 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.4374 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 3313 Z= 0.315 Angle : 0.716 6.299 4505 Z= 0.398 Chirality : 0.058 0.192 543 Planarity : 0.003 0.013 558 Dihedral : 6.719 20.298 447 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.29 % Favored : 82.71 % Rotamer: Outliers : 5.82 % Allowed : 13.76 % Favored : 80.42 % 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: -5.43 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS B 222 PHE 0.017 0.003 PHE A 213 TYR 0.026 0.003 TYR A 143 ARG 0.003 0.001 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.01972 ( 41) hydrogen bonds : angle 4.55431 ( 123) SS BOND : bond 0.00826 ( 1) SS BOND : angle 1.36943 ( 2) covalent geometry : bond 0.00744 ( 3312) covalent geometry : angle 0.71527 ( 4503) *********************** 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 62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.374 Fit side-chains REVERT: B 141 THR cc_start: 0.9040 (OUTLIER) cc_final: 0.8744 (t) REVERT: B 145 ASN cc_start: 0.7618 (p0) cc_final: 0.7163 (p0) REVERT: B 178 LYS cc_start: 0.7659 (mttt) cc_final: 0.6684 (tptt) REVERT: A 178 LYS cc_start: 0.7698 (mttt) cc_final: 0.6924 (tptt) REVERT: A 226 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7528 (tt) REVERT: C 145 ASN cc_start: 0.7846 (p0) cc_final: 0.7433 (p0) REVERT: C 178 LYS cc_start: 0.7421 (mttt) cc_final: 0.6527 (tptt) outliers start: 22 outliers final: 17 residues processed: 60 average time/residue: 0.1291 time to fit residues: 9.8912 Evaluate side-chains 55 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL 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 176 ILE Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4724 r_free = 0.4724 target = 0.313075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.5014 r_free = 0.5014 target = 0.260478 restraints weight = 4448.804| |-----------------------------------------------------------------------------| r_work (start): 0.4595 rms_B_bonded: 0.87 r_work: 0.4866 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.4842 rms_B_bonded: 0.66 restraints_weight: 0.2500 r_work: 0.4693 rms_B_bonded: 2.53 restraints_weight: 0.1250 r_work (final): 0.4693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3313 Z= 0.208 Angle : 0.630 5.405 4505 Z= 0.350 Chirality : 0.055 0.204 543 Planarity : 0.002 0.009 558 Dihedral : 6.441 17.408 447 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 6.08 % Allowed : 14.55 % 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: -5.34 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.014 0.002 PHE A 213 TYR 0.021 0.002 TYR A 143 ARG 0.003 0.001 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.01632 ( 41) hydrogen bonds : angle 4.44379 ( 123) SS BOND : bond 0.00597 ( 1) SS BOND : angle 1.02026 ( 2) covalent geometry : bond 0.00491 ( 3312) covalent geometry : angle 0.63024 ( 4503) *********************** 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 62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 39 time to evaluate : 0.369 Fit side-chains REVERT: B 141 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8586 (t) REVERT: B 145 ASN cc_start: 0.8268 (p0) cc_final: 0.7841 (p0) REVERT: B 146 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8256 (pt) REVERT: B 178 LYS cc_start: 0.8398 (mttt) cc_final: 0.7922 (tptt) REVERT: A 178 LYS cc_start: 0.8067 (mttt) cc_final: 0.7674 (tptt) REVERT: A 226 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7204 (tt) REVERT: C 145 ASN cc_start: 0.8152 (p0) cc_final: 0.7643 (p0) REVERT: C 146 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7709 (pt) REVERT: C 178 LYS cc_start: 0.8138 (mttt) cc_final: 0.7622 (tptt) outliers start: 23 outliers final: 18 residues processed: 59 average time/residue: 0.1394 time to fit residues: 10.4400 Evaluate side-chains 57 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 35 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR 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 176 ILE Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 186 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4672 r_free = 0.4672 target = 0.305874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.252766 restraints weight = 4375.439| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 1.17 r_work: 0.4366 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.4292 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 3313 Z= 0.344 Angle : 0.740 6.029 4505 Z= 0.416 Chirality : 0.060 0.207 543 Planarity : 0.003 0.013 558 Dihedral : 6.850 21.295 447 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.55 % Favored : 80.45 % Rotamer: Outliers : 6.88 % Allowed : 14.81 % Favored : 78.31 % 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: -5.49 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS B 222 PHE 0.016 0.003 PHE A 237 TYR 0.029 0.003 TYR A 143 ARG 0.002 0.000 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.02093 ( 41) hydrogen bonds : angle 4.53024 ( 123) SS BOND : bond 0.00816 ( 1) SS BOND : angle 1.22751 ( 2) covalent geometry : bond 0.00813 ( 3312) covalent geometry : angle 0.73965 ( 4503) *********************** 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 62 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 36 time to evaluate : 0.378 Fit side-chains REVERT: B 141 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8686 (t) REVERT: B 145 ASN cc_start: 0.7593 (p0) cc_final: 0.7153 (p0) REVERT: B 178 LYS cc_start: 0.7491 (mttt) cc_final: 0.6507 (tptt) REVERT: A 178 LYS cc_start: 0.7636 (mttt) cc_final: 0.6805 (tptt) REVERT: A 226 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7617 (tt) REVERT: C 145 ASN cc_start: 0.7924 (p0) cc_final: 0.7488 (p0) REVERT: C 178 LYS cc_start: 0.7280 (mttt) cc_final: 0.6353 (tptt) outliers start: 26 outliers final: 19 residues processed: 58 average time/residue: 0.1190 time to fit residues: 8.9517 Evaluate side-chains 56 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 35 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR 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 176 ILE Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4644 r_free = 0.4644 target = 0.265119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 104)---------------| | r_work = 0.4861 r_free = 0.4861 target = 0.219008 restraints weight = 4017.935| |-----------------------------------------------------------------------------| r_work (start): 0.4596 rms_B_bonded: 0.83 r_work: 0.4870 rms_B_bonded: 0.38 restraints_weight: 0.5000 r_work: 0.4850 rms_B_bonded: 0.63 restraints_weight: 0.2500 r_work: 0.4696 rms_B_bonded: 2.48 restraints_weight: 0.1250 r_work (final): 0.4696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3313 Z= 0.201 Angle : 0.635 5.419 4505 Z= 0.352 Chirality : 0.055 0.221 543 Planarity : 0.002 0.012 558 Dihedral : 6.466 17.641 447 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 5.56 % Allowed : 16.14 % Favored : 78.31 % 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: -5.40 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.11 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.012 0.002 PHE A 213 TYR 0.024 0.002 TYR A 143 ARG 0.002 0.001 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.01573 ( 41) hydrogen bonds : angle 4.41657 ( 123) SS BOND : bond 0.00556 ( 1) SS BOND : angle 0.86675 ( 2) covalent geometry : bond 0.00473 ( 3312) covalent geometry : angle 0.63466 ( 4503) *********************** 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 60 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 39 time to evaluate : 0.392 Fit side-chains REVERT: B 141 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8630 (t) REVERT: B 145 ASN cc_start: 0.8324 (p0) cc_final: 0.7900 (p0) REVERT: B 146 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8223 (pt) REVERT: B 178 LYS cc_start: 0.8421 (mttt) cc_final: 0.7981 (tptt) REVERT: A 178 LYS cc_start: 0.8052 (mttt) cc_final: 0.7650 (tptt) REVERT: A 226 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7210 (tt) REVERT: C 145 ASN cc_start: 0.8093 (p0) cc_final: 0.7627 (p0) REVERT: C 146 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7747 (pt) REVERT: C 178 LYS cc_start: 0.8151 (mttt) cc_final: 0.7609 (tptt) outliers start: 21 outliers final: 17 residues processed: 57 average time/residue: 0.1135 time to fit residues: 8.3433 Evaluate side-chains 59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 38 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR 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 176 ILE Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4671 r_free = 0.4671 target = 0.270060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.223293 restraints weight = 4050.129| |-----------------------------------------------------------------------------| r_work (start): 0.4623 rms_B_bonded: 0.85 r_work: 0.4896 rms_B_bonded: 0.40 restraints_weight: 0.5000 r_work: 0.4875 rms_B_bonded: 0.67 restraints_weight: 0.2500 r_work: 0.4727 rms_B_bonded: 2.55 restraints_weight: 0.1250 r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3313 Z= 0.152 Angle : 0.599 5.537 4505 Z= 0.331 Chirality : 0.053 0.202 543 Planarity : 0.002 0.010 558 Dihedral : 6.137 17.050 447 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 6.08 % Allowed : 16.14 % Favored : 77.78 % 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: -5.28 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.011 0.002 PHE A 213 TYR 0.019 0.002 TYR A 143 ARG 0.002 0.001 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.01427 ( 41) hydrogen bonds : angle 4.34004 ( 123) SS BOND : bond 0.00461 ( 1) SS BOND : angle 0.69705 ( 2) covalent geometry : bond 0.00357 ( 3312) covalent geometry : angle 0.59850 ( 4503) *********************** 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 67 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 44 time to evaluate : 0.439 Fit side-chains REVERT: B 141 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8652 (t) REVERT: B 145 ASN cc_start: 0.8351 (p0) cc_final: 0.7945 (p0) REVERT: B 146 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8145 (pt) REVERT: B 178 LYS cc_start: 0.8384 (mttt) cc_final: 0.7920 (tptt) REVERT: A 178 LYS cc_start: 0.8007 (mttt) cc_final: 0.7579 (tptt) REVERT: C 145 ASN cc_start: 0.8137 (p0) cc_final: 0.7594 (p0) REVERT: C 146 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7710 (pt) REVERT: C 178 LYS cc_start: 0.8126 (mttt) cc_final: 0.7610 (tptt) outliers start: 23 outliers final: 17 residues processed: 64 average time/residue: 0.1356 time to fit residues: 11.1020 Evaluate side-chains 58 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 141 THR 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 176 ILE Chi-restraints excluded: chain C residue 180 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.0010 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4736 r_free = 0.4736 target = 0.279970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4975 r_free = 0.4975 target = 0.233399 restraints weight = 3937.798| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 0.85 r_work: 0.4982 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.4962 rms_B_bonded: 0.65 restraints_weight: 0.2500 r_work: 0.4810 rms_B_bonded: 2.56 restraints_weight: 0.1250 r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3313 Z= 0.111 Angle : 0.560 5.856 4505 Z= 0.307 Chirality : 0.052 0.185 543 Planarity : 0.002 0.011 558 Dihedral : 5.685 14.978 447 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.76 % Allowed : 17.46 % Favored : 77.78 % 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: -5.07 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.86 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.009 0.001 PHE A 213 TYR 0.015 0.001 TYR A 143 ARG 0.002 0.001 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.01296 ( 41) hydrogen bonds : angle 4.21847 ( 123) SS BOND : bond 0.00324 ( 1) SS BOND : angle 0.68534 ( 2) covalent geometry : bond 0.00251 ( 3312) covalent geometry : angle 0.56026 ( 4503) ********************** 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 70 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.354 Fit side-chains REVERT: B 141 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8671 (t) REVERT: B 145 ASN cc_start: 0.8401 (p0) cc_final: 0.8150 (p0) REVERT: B 146 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8167 (pt) REVERT: B 178 LYS cc_start: 0.8242 (mttt) cc_final: 0.7817 (tptt) REVERT: A 178 LYS cc_start: 0.7857 (mttt) cc_final: 0.7487 (tptt) REVERT: C 145 ASN cc_start: 0.8000 (p0) cc_final: 0.7481 (t0) REVERT: C 146 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7649 (pt) REVERT: C 178 LYS cc_start: 0.8026 (mttt) cc_final: 0.7538 (tptt) outliers start: 18 outliers final: 13 residues processed: 67 average time/residue: 0.1635 time to fit residues: 13.3978 Evaluate side-chains 56 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4664 r_free = 0.4664 target = 0.268350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.220408 restraints weight = 4091.612| |-----------------------------------------------------------------------------| r_work (start): 0.4612 rms_B_bonded: 0.89 r_work: 0.4889 rms_B_bonded: 0.40 restraints_weight: 0.5000 r_work: 0.4870 rms_B_bonded: 0.67 restraints_weight: 0.2500 r_work: 0.4717 rms_B_bonded: 2.55 restraints_weight: 0.1250 r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3313 Z= 0.199 Angle : 0.642 5.898 4505 Z= 0.354 Chirality : 0.054 0.206 543 Planarity : 0.003 0.057 558 Dihedral : 6.099 17.701 447 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.53 % Favored : 86.47 % Rotamer: Outliers : 4.23 % Allowed : 19.05 % Favored : 76.72 % 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: -5.13 (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 0.006 0.003 HIS A 239 PHE 0.010 0.002 PHE A 237 TYR 0.021 0.002 TYR A 143 ARG 0.014 0.001 ARG A 140 Details of bonding type rmsd hydrogen bonds : bond 0.01532 ( 41) hydrogen bonds : angle 4.14825 ( 123) SS BOND : bond 0.00571 ( 1) SS BOND : angle 1.21785 ( 2) covalent geometry : bond 0.00471 ( 3312) covalent geometry : angle 0.64211 ( 4503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2813.67 seconds wall clock time: 51 minutes 6.35 seconds (3066.35 seconds total)