Starting phenix.real_space_refine on Mon Feb 10 23:31:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x83_33054/02_2025/7x83_33054.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x83_33054/02_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_33054/02_2025/7x83_33054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x83_33054/02_2025/7x83_33054.map" model { file = "/net/cci-nas-00/data/ceres_data/7x83_33054/02_2025/7x83_33054.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x83_33054/02_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.84, per 1000 atoms: 0.87 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: 0.71 Conformation dependent library (CDL) restraints added in 369.4 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 14 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 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: 0.72 Time building geometry restraints manager: 0.84 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: 2.290 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: 0.030 Set scattering table: 0.020 Process input model: 12.520 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- 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 3312 Z= 0.585 Angle : 0.825 5.155 4503 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 *********************** 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 : 0.365 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: 0.2419 time to fit residues: 13.9499 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 : 0.400 ------------------------------------------------------------------------------- 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 = 96)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.225319 restraints weight = 3980.931| |-----------------------------------------------------------------------------| r_work (start): 0.4603 rms_B_bonded: 0.89 r_work: 0.4877 rms_B_bonded: 0.40 restraints_weight: 0.5000 r_work: 0.4854 rms_B_bonded: 0.70 restraints_weight: 0.2500 r_work: 0.4697 rms_B_bonded: 2.59 restraints_weight: 0.1250 r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 3312 Z= 0.265 Angle : 0.612 5.443 4503 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 *********************** 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 : 0.396 Fit side-chains REVERT: B 145 ASN cc_start: 0.8347 (p0) cc_final: 0.7908 (p0) REVERT: B 146 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8245 (pt) REVERT: B 178 LYS cc_start: 0.8306 (mttt) cc_final: 0.7785 (tptt) REVERT: B 215 THR cc_start: 0.7793 (t) cc_final: 0.7560 (t) REVERT: A 178 LYS cc_start: 0.8119 (mttt) cc_final: 0.7686 (tptt) REVERT: C 145 ASN cc_start: 0.8112 (p0) cc_final: 0.7613 (p0) REVERT: C 146 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7673 (pt) REVERT: C 178 LYS cc_start: 0.8011 (mttt) cc_final: 0.7561 (tptt) REVERT: C 215 THR cc_start: 0.7757 (t) cc_final: 0.7543 (t) outliers start: 14 outliers final: 6 residues processed: 55 average time/residue: 0.1813 time to fit residues: 12.0882 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 : 0.448 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 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: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.4672 r_free = 0.4672 target = 0.271741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.227649 restraints weight = 3950.061| |-----------------------------------------------------------------------------| r_work (start): 0.4620 rms_B_bonded: 0.85 r_work: 0.4893 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.4871 rms_B_bonded: 0.67 restraints_weight: 0.2500 r_work: 0.4717 rms_B_bonded: 2.61 restraints_weight: 0.1250 r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.003 0.031 3312 Z= 0.213 Angle : 0.582 5.982 4503 Z= 0.318 Chirality : 0.052 0.178 543 Planarity : 0.003 0.030 558 Dihedral : 6.159 16.580 447 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 3.97 % Allowed : 12.43 % Favored : 83.60 % 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: -5.30 (0.30), 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 0.002 HIS A 239 PHE 0.009 0.002 PHE A 237 TYR 0.015 0.001 TYR B 143 ARG 0.009 0.001 ARG A 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 54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.406 Fit side-chains REVERT: B 145 ASN cc_start: 0.8326 (p0) cc_final: 0.7984 (p0) REVERT: B 146 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8221 (pt) REVERT: B 178 LYS cc_start: 0.8263 (mttt) cc_final: 0.7734 (tptt) REVERT: A 178 LYS cc_start: 0.7979 (mttt) cc_final: 0.7538 (tptt) REVERT: C 145 ASN cc_start: 0.8168 (p0) cc_final: 0.7675 (p0) REVERT: C 146 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7659 (pt) REVERT: C 178 LYS cc_start: 0.7976 (mttt) cc_final: 0.7506 (tptt) outliers start: 15 outliers final: 8 residues processed: 53 average time/residue: 0.1424 time to fit residues: 9.8373 Evaluate side-chains 44 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.4697 r_free = 0.4697 target = 0.275251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.4916 r_free = 0.4916 target = 0.231252 restraints weight = 3978.303| |-----------------------------------------------------------------------------| r_work (start): 0.4650 rms_B_bonded: 0.85 r_work: 0.4927 rms_B_bonded: 0.38 restraints_weight: 0.5000 r_work: 0.4907 rms_B_bonded: 0.65 restraints_weight: 0.2500 r_work: 0.4744 rms_B_bonded: 2.64 restraints_weight: 0.1250 r_work (final): 0.4744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3312 Z= 0.189 Angle : 0.553 6.051 4503 Z= 0.302 Chirality : 0.052 0.173 543 Planarity : 0.002 0.017 558 Dihedral : 5.855 15.453 447 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 5.29 % Allowed : 12.96 % 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: -5.12 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.24), 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 237 TYR 0.014 0.001 TYR B 143 ARG 0.005 0.001 ARG B 140 *********************** 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 64 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.400 Fit side-chains REVERT: B 145 ASN cc_start: 0.8301 (p0) cc_final: 0.7857 (p0) REVERT: B 146 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8195 (pt) REVERT: B 178 LYS cc_start: 0.8224 (mttt) cc_final: 0.7690 (tptt) REVERT: A 138 GLN cc_start: 0.8418 (pt0) cc_final: 0.8074 (pt0) REVERT: A 178 LYS cc_start: 0.7921 (mttt) cc_final: 0.7523 (tptt) REVERT: C 145 ASN cc_start: 0.8201 (p0) cc_final: 0.7694 (p0) REVERT: C 146 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7630 (pt) REVERT: C 178 LYS cc_start: 0.7937 (mttt) cc_final: 0.7451 (tptt) outliers start: 20 outliers final: 12 residues processed: 62 average time/residue: 0.1471 time to fit residues: 11.4405 Evaluate side-chains 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4674 r_free = 0.4674 target = 0.271473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.225998 restraints weight = 3994.121| |-----------------------------------------------------------------------------| r_work (start): 0.4629 rms_B_bonded: 0.83 r_work: 0.4913 rms_B_bonded: 0.37 restraints_weight: 0.5000 r_work: 0.4880 rms_B_bonded: 0.65 restraints_weight: 0.2500 r_work: 0.4726 rms_B_bonded: 2.53 restraints_weight: 0.1250 r_work (final): 0.4726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3312 Z= 0.242 Angle : 0.582 6.418 4503 Z= 0.320 Chirality : 0.053 0.176 543 Planarity : 0.002 0.012 558 Dihedral : 5.881 15.765 447 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 5.56 % Allowed : 13.23 % Favored : 81.22 % 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: -5.04 (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 0.015 0.002 PHE A 213 TYR 0.017 0.002 TYR B 143 ARG 0.003 0.001 ARG A 140 *********************** 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: 21 poor density : 41 time to evaluate : 0.396 Fit side-chains REVERT: B 141 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8765 (t) REVERT: B 145 ASN cc_start: 0.8305 (p0) cc_final: 0.7935 (p0) REVERT: B 146 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8228 (pt) REVERT: B 178 LYS cc_start: 0.8213 (mttt) cc_final: 0.7710 (tptt) REVERT: A 178 LYS cc_start: 0.7963 (mttt) cc_final: 0.7572 (tptt) REVERT: C 145 ASN cc_start: 0.8237 (p0) cc_final: 0.7719 (p0) REVERT: C 146 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7674 (pt) REVERT: C 178 LYS cc_start: 0.7984 (mttt) cc_final: 0.7471 (tptt) outliers start: 21 outliers final: 13 residues processed: 60 average time/residue: 0.1347 time to fit residues: 10.2537 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 : 0.426 ------------------------------------------------------------------------------- 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 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 180 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4617 r_free = 0.4617 target = 0.263032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.4823 r_free = 0.4823 target = 0.216196 restraints weight = 4171.212| |-----------------------------------------------------------------------------| r_work (start): 0.4564 rms_B_bonded: 0.85 r_work: 0.4832 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.4807 rms_B_bonded: 0.66 restraints_weight: 0.2500 r_work: 0.4663 rms_B_bonded: 2.45 restraints_weight: 0.1250 r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3312 Z= 0.426 Angle : 0.680 6.915 4503 Z= 0.377 Chirality : 0.057 0.193 543 Planarity : 0.003 0.016 558 Dihedral : 6.378 18.438 447 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Rotamer: Outliers : 5.56 % Allowed : 12.70 % 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: -5.19 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.004 HIS A 239 PHE 0.014 0.003 PHE A 237 TYR 0.025 0.002 TYR A 143 ARG 0.003 0.001 ARG A 140 *********************** 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: 21 poor density : 41 time to evaluate : 0.394 Fit side-chains REVERT: B 141 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8634 (t) REVERT: B 145 ASN cc_start: 0.8355 (p0) cc_final: 0.7796 (p0) REVERT: B 178 LYS cc_start: 0.8403 (mttt) cc_final: 0.7892 (tptt) REVERT: B 209 TYR cc_start: 0.7471 (m-80) cc_final: 0.7262 (m-80) REVERT: A 141 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8559 (t) REVERT: A 145 ASN cc_start: 0.8160 (p0) cc_final: 0.7893 (p0) REVERT: A 178 LYS cc_start: 0.8077 (mttt) cc_final: 0.7644 (tptt) REVERT: C 145 ASN cc_start: 0.8244 (p0) cc_final: 0.7745 (p0) REVERT: C 178 LYS cc_start: 0.8157 (mttt) cc_final: 0.7625 (tptt) outliers start: 21 outliers final: 16 residues processed: 61 average time/residue: 0.1256 time to fit residues: 9.8991 Evaluate side-chains 58 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 141 THR 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 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 180 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 31 optimal weight: 0.0970 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 = 0.4649 r_free = 0.4649 target = 0.267049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.220342 restraints weight = 4016.864| |-----------------------------------------------------------------------------| r_work (start): 0.4595 rms_B_bonded: 0.85 r_work: 0.4874 rms_B_bonded: 0.37 restraints_weight: 0.5000 r_work: 0.4843 rms_B_bonded: 0.67 restraints_weight: 0.2500 r_work: 0.4706 rms_B_bonded: 2.40 restraints_weight: 0.1250 r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3312 Z= 0.324 Angle : 0.638 6.689 4503 Z= 0.353 Chirality : 0.055 0.183 543 Planarity : 0.002 0.012 558 Dihedral : 6.287 17.548 447 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 5.29 % Allowed : 14.29 % 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: -5.17 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.017 0.003 PHE C 213 TYR 0.022 0.002 TYR A 143 ARG 0.002 0.001 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 57 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 37 time to evaluate : 0.386 Fit side-chains REVERT: B 141 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8673 (t) REVERT: B 145 ASN cc_start: 0.8316 (p0) cc_final: 0.7773 (p0) REVERT: B 146 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8267 (pt) REVERT: B 178 LYS cc_start: 0.8368 (mttt) cc_final: 0.7915 (tptt) REVERT: A 141 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8556 (t) REVERT: A 145 ASN cc_start: 0.8106 (p0) cc_final: 0.7832 (p0) REVERT: A 178 LYS cc_start: 0.8044 (mttt) cc_final: 0.7662 (tptt) REVERT: C 145 ASN cc_start: 0.8174 (p0) cc_final: 0.7691 (p0) REVERT: C 146 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7710 (pt) REVERT: C 178 LYS cc_start: 0.8155 (mttt) cc_final: 0.7629 (tptt) outliers start: 20 outliers final: 15 residues processed: 55 average time/residue: 0.1307 time to fit residues: 9.2009 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 : 0.363 ------------------------------------------------------------------------------- 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 141 THR 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 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: 6.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 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 = 0.4622 r_free = 0.4622 target = 0.262530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4832 r_free = 0.4832 target = 0.215480 restraints weight = 4033.308| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 0.85 r_work: 0.4840 rms_B_bonded: 0.40 restraints_weight: 0.5000 r_work: 0.4816 rms_B_bonded: 0.67 restraints_weight: 0.2500 r_work: 0.4676 rms_B_bonded: 2.46 restraints_weight: 0.1250 r_work (final): 0.4676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3312 Z= 0.413 Angle : 0.686 6.665 4503 Z= 0.381 Chirality : 0.056 0.191 543 Planarity : 0.003 0.012 558 Dihedral : 6.505 19.211 447 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.79 % Favored : 82.21 % Rotamer: Outliers : 5.03 % Allowed : 14.81 % 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: -5.29 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 239 PHE 0.014 0.003 PHE C 213 TYR 0.026 0.002 TYR A 143 ARG 0.002 0.000 ARG B 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 57 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 38 time to evaluate : 0.364 Fit side-chains REVERT: B 141 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8679 (t) REVERT: B 145 ASN cc_start: 0.8346 (p0) cc_final: 0.7757 (p0) REVERT: B 178 LYS cc_start: 0.8419 (mttt) cc_final: 0.7943 (tptt) REVERT: A 141 THR cc_start: 0.8846 (t) cc_final: 0.8580 (t) REVERT: A 145 ASN cc_start: 0.8171 (p0) cc_final: 0.7886 (p0) REVERT: A 178 LYS cc_start: 0.8093 (mttt) cc_final: 0.7691 (tptt) REVERT: C 145 ASN cc_start: 0.8274 (p0) cc_final: 0.7805 (p0) REVERT: C 178 LYS cc_start: 0.8169 (mttt) cc_final: 0.7641 (tptt) outliers start: 19 outliers final: 17 residues processed: 56 average time/residue: 0.1201 time to fit residues: 8.5255 Evaluate side-chains 54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4669 r_free = 0.4669 target = 0.269636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.4889 r_free = 0.4889 target = 0.222704 restraints weight = 4050.621| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 0.86 r_work: 0.4896 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.4871 rms_B_bonded: 0.68 restraints_weight: 0.2500 r_work: 0.4728 rms_B_bonded: 2.55 restraints_weight: 0.1250 r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3312 Z= 0.265 Angle : 0.602 6.656 4503 Z= 0.334 Chirality : 0.054 0.177 543 Planarity : 0.002 0.010 558 Dihedral : 6.165 16.798 447 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 5.29 % Allowed : 15.34 % 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: -5.17 (0.32), 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 0.002 HIS A 239 PHE 0.015 0.002 PHE C 213 TYR 0.019 0.002 TYR A 143 ARG 0.002 0.001 ARG B 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 56 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.395 Fit side-chains REVERT: B 141 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8699 (t) REVERT: B 145 ASN cc_start: 0.8300 (p0) cc_final: 0.7829 (p0) REVERT: B 146 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8241 (pt) REVERT: B 178 LYS cc_start: 0.8370 (mttt) cc_final: 0.7949 (tptt) REVERT: A 141 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8555 (t) REVERT: A 178 LYS cc_start: 0.8028 (mttt) cc_final: 0.7637 (tptt) REVERT: C 145 ASN cc_start: 0.8223 (p0) cc_final: 0.7724 (p0) REVERT: C 146 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7724 (pt) REVERT: C 178 LYS cc_start: 0.8131 (mttt) cc_final: 0.7613 (tptt) outliers start: 20 outliers final: 16 residues processed: 54 average time/residue: 0.1324 time to fit residues: 9.1454 Evaluate side-chains 56 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 141 THR 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: 0.8980 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.4651 r_free = 0.4651 target = 0.266965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.219520 restraints weight = 3982.344| |-----------------------------------------------------------------------------| r_work (start): 0.4599 rms_B_bonded: 0.87 r_work: 0.4872 rms_B_bonded: 0.40 restraints_weight: 0.5000 r_work: 0.4852 rms_B_bonded: 0.68 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: 0.8013 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3312 Z= 0.320 Angle : 0.631 6.775 4503 Z= 0.351 Chirality : 0.054 0.184 543 Planarity : 0.002 0.011 558 Dihedral : 6.233 17.943 447 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.29 % Favored : 84.71 % Rotamer: Outliers : 5.29 % Allowed : 15.61 % 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: -5.20 (0.32), 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 0.006 0.003 HIS A 239 PHE 0.015 0.002 PHE C 213 TYR 0.022 0.002 TYR A 143 ARG 0.002 0.001 ARG B 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 59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.356 Fit side-chains REVERT: B 141 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8653 (t) REVERT: B 145 ASN cc_start: 0.8310 (p0) cc_final: 0.8054 (p0) REVERT: B 146 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8240 (pt) REVERT: B 178 LYS cc_start: 0.8403 (mttt) cc_final: 0.7942 (tptt) REVERT: A 141 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8561 (t) REVERT: A 178 LYS cc_start: 0.8058 (mttt) cc_final: 0.7634 (tptt) REVERT: C 145 ASN cc_start: 0.8211 (p0) cc_final: 0.7704 (p0) REVERT: C 146 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7751 (pt) REVERT: C 178 LYS cc_start: 0.8141 (mttt) cc_final: 0.7566 (tptt) outliers start: 20 outliers final: 16 residues processed: 57 average time/residue: 0.1299 time to fit residues: 9.4805 Evaluate side-chains 56 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 36 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 141 THR 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 4 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.4704 r_free = 0.4704 target = 0.275490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.4934 r_free = 0.4934 target = 0.228783 restraints weight = 4047.442| |-----------------------------------------------------------------------------| r_work (start): 0.4657 rms_B_bonded: 0.88 r_work: 0.4938 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.4918 rms_B_bonded: 0.66 restraints_weight: 0.2500 r_work: 0.4761 rms_B_bonded: 2.59 restraints_weight: 0.1250 r_work (final): 0.4761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3312 Z= 0.194 Angle : 0.576 7.635 4503 Z= 0.319 Chirality : 0.053 0.164 543 Planarity : 0.002 0.011 558 Dihedral : 5.862 15.995 447 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 4.76 % Allowed : 16.40 % Favored : 78.84 % 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 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 239 PHE 0.014 0.002 PHE C 213 TYR 0.017 0.001 TYR A 143 ARG 0.002 0.001 ARG B 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2134.87 seconds wall clock time: 38 minutes 38.39 seconds (2318.39 seconds total)