Starting phenix.real_space_refine on Thu Nov 14 01:40:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7p_36045/11_2024/8j7p_36045.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7p_36045/11_2024/8j7p_36045.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7p_36045/11_2024/8j7p_36045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7p_36045/11_2024/8j7p_36045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7p_36045/11_2024/8j7p_36045.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7p_36045/11_2024/8j7p_36045.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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2082 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 3.19, per 1000 atoms: 0.98 Number of scatterers: 3258 At special positions: 0 Unit cell: (99.6, 98.77, 36.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 636 8.00 N 519 7.00 C 2082 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 398.1 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 16 sheets defined 0.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 125 through 126 removed outlier: 6.014A pdb=" N TYR B 125 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR A 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 129 through 130 removed outlier: 6.702A pdb=" N LYS B 129 " --> pdb=" O SER A 130 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS A 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 133 through 137 removed outlier: 6.487A pdb=" N SER B 134 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL A 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ASP B 136 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL C 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP A 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 144 removed outlier: 6.555A pdb=" N ILE B 142 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE A 142 " --> pdb=" O TYR C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 154 through 157 Processing sheet with id=AA7, first strand: chain 'B' and resid 163 through 164 Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175 removed outlier: 8.065A pdb=" N LYS B 173 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N LYS A 173 " --> pdb=" O THR C 174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AB2, first strand: chain 'B' and resid 190 through 191 Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.214A pdb=" N VAL B 202 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 202 " --> pdb=" O ILE C 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 210 through 211 Processing sheet with id=AB5, first strand: chain 'B' and resid 222 through 230 removed outlier: 6.971A pdb=" N ASN A 223 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE B 224 " --> pdb=" O ASN A 223 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 225 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU B 226 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET A 227 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET B 228 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLN A 229 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN C 223 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE A 224 " --> pdb=" O ASN C 223 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL C 225 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 226 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N MET C 227 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET A 228 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN C 229 " --> pdb=" O MET A 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 242 through 244 removed outlier: 6.419A pdb=" N GLN B 242 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN A 242 " --> pdb=" O ILE C 243 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 251 through 252 removed outlier: 6.434A pdb=" N VAL B 251 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 22 hydrogen bonds defined for protein. 66 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: 0.78 Time building geometry restraints manager: 0.93 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: 478 1.45 - 1.57: 1772 1.57 - 1.68: 0 1.68 - 1.80: 36 Bond restraints: 3312 Sorted by residual: bond pdb=" CA ILE A 187 " pdb=" CB ILE A 187 " ideal model delta sigma weight residual 1.540 1.519 0.021 1.36e-02 5.41e+03 2.47e+00 bond pdb=" CA ILE B 187 " pdb=" CB ILE B 187 " ideal model delta sigma weight residual 1.540 1.520 0.020 1.36e-02 5.41e+03 2.25e+00 bond pdb=" CA ILE C 187 " pdb=" CB ILE C 187 " ideal model delta sigma weight residual 1.540 1.520 0.020 1.36e-02 5.41e+03 2.25e+00 bond pdb=" C MET A 192 " pdb=" N LYS A 193 " ideal model delta sigma weight residual 1.334 1.313 0.021 1.58e-02 4.01e+03 1.81e+00 bond pdb=" C MET C 192 " pdb=" N LYS C 193 " ideal model delta sigma weight residual 1.334 1.313 0.021 1.58e-02 4.01e+03 1.78e+00 ... (remaining 3307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 4052 1.20 - 2.40: 372 2.40 - 3.60: 52 3.60 - 4.79: 21 4.79 - 5.99: 6 Bond angle restraints: 4503 Sorted by residual: angle pdb=" C LEU C 144 " pdb=" N ASN C 145 " pdb=" CA ASN C 145 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.96e+00 angle pdb=" C LEU A 144 " pdb=" N ASN A 145 " pdb=" CA ASN A 145 " ideal model delta sigma weight residual 121.54 127.25 -5.71 1.91e+00 2.74e-01 8.93e+00 angle pdb=" C LEU B 144 " pdb=" N ASN B 145 " pdb=" CA ASN B 145 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.89e+00 angle pdb=" C GLN A 245 " pdb=" N GLU A 246 " pdb=" CA GLU A 246 " ideal model delta sigma weight residual 122.36 117.75 4.61 1.60e+00 3.91e-01 8.31e+00 angle pdb=" C GLN C 245 " pdb=" N GLU C 246 " pdb=" CA GLU C 246 " ideal model delta sigma weight residual 122.36 117.76 4.60 1.60e+00 3.91e-01 8.27e+00 ... (remaining 4498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.06: 1750 14.06 - 28.11: 191 28.11 - 42.17: 36 42.17 - 56.22: 9 56.22 - 70.28: 3 Dihedral angle restraints: 1989 sinusoidal: 771 harmonic: 1218 Sorted by residual: 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 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+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 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 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 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 1986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 252 0.035 - 0.070: 176 0.070 - 0.105: 75 0.105 - 0.140: 37 0.140 - 0.175: 3 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 2.34 0.18 2.00e-01 2.50e+01 7.68e-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 7.50e-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 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 540 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 143 " 0.016 2.00e-02 2.50e+03 9.85e-03 1.94e+00 pdb=" CG TYR C 143 " -0.023 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 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 143 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 143 " 0.016 2.00e-02 2.50e+03 9.76e-03 1.90e+00 pdb=" CG TYR B 143 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 143 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 143 " 0.000 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 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.015 2.00e-02 2.50e+03 9.74e-03 1.90e+00 pdb=" CG TYR A 143 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " 0.003 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 " 0.003 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 26 2.60 - 3.18: 2874 3.18 - 3.75: 4489 3.75 - 4.33: 6662 4.33 - 4.90: 12205 Nonbonded interactions: 26256 Sorted by model distance: nonbonded pdb=" SG CYS A 214 " pdb=" SG CYS A 253 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS C 214 " pdb=" SG CYS C 253 " model vdw 2.025 3.760 nonbonded pdb=" CE1 TYR A 143 " pdb=" CD1 ILE A 146 " model vdw 2.402 3.760 nonbonded pdb=" CE1 TYR C 143 " pdb=" CD1 ILE C 146 " model vdw 2.403 3.760 nonbonded pdb=" OG1 THR A 233 " pdb=" N THR A 234 " model vdw 2.404 3.120 ... (remaining 26251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 0.042 3312 Z= 0.590 Angle : 0.807 5.994 4503 Z= 0.458 Chirality : 0.056 0.175 543 Planarity : 0.003 0.011 558 Dihedral : 12.537 70.278 1206 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.04 % Favored : 84.96 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.75 (0.29), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.37 (0.22), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 239 PHE 0.010 0.003 PHE C 237 TYR 0.023 0.003 TYR C 143 ARG 0.002 0.000 ARG A 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 78 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.315 Fit side-chains REVERT: B 146 ILE cc_start: 0.8983 (pt) cc_final: 0.8697 (pt) REVERT: B 161 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8075 (mm-30) REVERT: B 207 MET cc_start: 0.7786 (mtm) cc_final: 0.5920 (mtm) REVERT: B 235 THR cc_start: 0.8687 (m) cc_final: 0.8169 (p) REVERT: A 146 ILE cc_start: 0.9005 (pt) cc_final: 0.8700 (pt) REVERT: A 161 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 207 MET cc_start: 0.7985 (mtm) cc_final: 0.7196 (mmm) REVERT: A 215 THR cc_start: 0.8543 (t) cc_final: 0.8298 (t) REVERT: A 235 THR cc_start: 0.8525 (m) cc_final: 0.8126 (p) REVERT: C 140 ARG cc_start: 0.8625 (mtt180) cc_final: 0.8414 (mtt-85) REVERT: C 146 ILE cc_start: 0.8834 (pt) cc_final: 0.8610 (pt) REVERT: C 161 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7552 (mm-30) REVERT: C 220 LYS cc_start: 0.9160 (mttt) cc_final: 0.8785 (mttm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1763 time to fit residues: 16.1580 Evaluate side-chains 73 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 3.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 ASN B 222 HIS B 229 GLN A 155 ASN A 156 ASN A 223 ASN C 155 ASN C 156 ASN C 223 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3312 Z= 0.176 Angle : 0.601 6.358 4503 Z= 0.322 Chirality : 0.053 0.175 543 Planarity : 0.002 0.008 558 Dihedral : 6.320 20.121 447 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 1.32 % Allowed : 11.90 % Favored : 86.77 % 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: -5.41 (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 C 239 PHE 0.008 0.001 PHE B 237 TYR 0.012 0.001 TYR B 132 ARG 0.002 0.000 ARG B 140 *********************** 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 101 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.347 Fit side-chains REVERT: B 129 LYS cc_start: 0.8957 (ptpt) cc_final: 0.8655 (ptmt) REVERT: B 146 ILE cc_start: 0.8854 (pt) cc_final: 0.8584 (pt) REVERT: B 170 GLN cc_start: 0.9158 (mp10) cc_final: 0.8904 (mp10) REVERT: B 207 MET cc_start: 0.7755 (mtm) cc_final: 0.6142 (mtm) REVERT: B 210 MET cc_start: 0.8596 (mtt) cc_final: 0.8370 (mtm) REVERT: A 146 ILE cc_start: 0.8785 (pt) cc_final: 0.8538 (pt) REVERT: A 207 MET cc_start: 0.7880 (mtm) cc_final: 0.7199 (mmm) REVERT: A 210 MET cc_start: 0.8349 (mtm) cc_final: 0.8095 (mtt) REVERT: C 207 MET cc_start: 0.7776 (mtm) cc_final: 0.7529 (mtm) REVERT: C 210 MET cc_start: 0.8057 (mtt) cc_final: 0.7724 (mtp) REVERT: C 220 LYS cc_start: 0.9139 (mttt) cc_final: 0.8706 (mttm) outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.1546 time to fit residues: 17.9484 Evaluate side-chains 83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain C residue 128 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 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 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3312 Z= 0.471 Angle : 0.711 5.652 4503 Z= 0.393 Chirality : 0.055 0.179 543 Planarity : 0.003 0.012 558 Dihedral : 6.718 22.754 447 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 2.91 % Allowed : 14.02 % Favored : 83.07 % 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: -5.33 (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 0.005 0.003 HIS C 239 PHE 0.011 0.002 PHE B 237 TYR 0.023 0.003 TYR B 143 ARG 0.001 0.000 ARG C 247 *********************** 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 88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.326 Fit side-chains REVERT: B 146 ILE cc_start: 0.9000 (pt) cc_final: 0.8725 (pt) REVERT: B 161 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 210 MET cc_start: 0.8755 (mtt) cc_final: 0.8505 (mtt) REVERT: A 146 ILE cc_start: 0.8940 (pt) cc_final: 0.8639 (pt) REVERT: A 161 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8062 (mm-30) REVERT: A 207 MET cc_start: 0.7927 (mtm) cc_final: 0.7608 (mtm) REVERT: A 210 MET cc_start: 0.8437 (mtm) cc_final: 0.8052 (mtp) REVERT: C 161 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7457 (mm-30) REVERT: C 210 MET cc_start: 0.8217 (mtt) cc_final: 0.7953 (mtp) REVERT: C 220 LYS cc_start: 0.9155 (mttt) cc_final: 0.8723 (mttm) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.1553 time to fit residues: 15.7595 Evaluate side-chains 83 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 232 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3312 Z= 0.160 Angle : 0.563 5.832 4503 Z= 0.308 Chirality : 0.052 0.170 543 Planarity : 0.002 0.009 558 Dihedral : 6.061 20.721 447 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.38 % Allowed : 15.61 % Favored : 82.01 % 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: -5.08 (0.32), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.007 0.001 PHE B 237 TYR 0.021 0.001 TYR C 236 ARG 0.001 0.000 ARG A 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 92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.365 Fit side-chains REVERT: B 146 ILE cc_start: 0.8959 (pt) cc_final: 0.8664 (pt) REVERT: B 210 MET cc_start: 0.8645 (mtt) cc_final: 0.8379 (mtp) REVERT: A 146 ILE cc_start: 0.8964 (pt) cc_final: 0.8651 (pt) REVERT: A 210 MET cc_start: 0.8364 (mtm) cc_final: 0.8061 (mtp) REVERT: C 210 MET cc_start: 0.8156 (mtt) cc_final: 0.7943 (mtp) REVERT: C 220 LYS cc_start: 0.9154 (mttt) cc_final: 0.8725 (mttm) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 0.1669 time to fit residues: 16.5637 Evaluate side-chains 80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 232 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3312 Z= 0.415 Angle : 0.687 6.206 4503 Z= 0.380 Chirality : 0.053 0.175 543 Planarity : 0.002 0.010 558 Dihedral : 6.438 21.488 447 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.53 % Favored : 88.47 % Rotamer: Outliers : 2.65 % Allowed : 17.20 % 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: -5.11 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 239 PHE 0.012 0.002 PHE B 237 TYR 0.022 0.002 TYR C 209 ARG 0.001 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.400 Fit side-chains REVERT: B 146 ILE cc_start: 0.9099 (pt) cc_final: 0.8810 (pt) REVERT: B 210 MET cc_start: 0.8692 (mtt) cc_final: 0.8342 (mtp) REVERT: A 146 ILE cc_start: 0.8945 (pt) cc_final: 0.8633 (pt) REVERT: A 210 MET cc_start: 0.8393 (mtm) cc_final: 0.8067 (mtp) REVERT: A 235 THR cc_start: 0.8386 (m) cc_final: 0.8143 (p) REVERT: C 210 MET cc_start: 0.8188 (mtt) cc_final: 0.7971 (mtp) REVERT: C 220 LYS cc_start: 0.9159 (mttt) cc_final: 0.8726 (mttm) outliers start: 10 outliers final: 9 residues processed: 74 average time/residue: 0.1671 time to fit residues: 14.9152 Evaluate side-chains 73 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 232 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3312 Z= 0.136 Angle : 0.560 5.919 4503 Z= 0.305 Chirality : 0.052 0.169 543 Planarity : 0.002 0.008 558 Dihedral : 5.796 20.097 447 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.91 % Allowed : 16.67 % 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: -4.94 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.006 0.001 PHE B 237 TYR 0.013 0.001 TYR C 209 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: B 129 LYS cc_start: 0.8921 (ptmt) cc_final: 0.8719 (pttt) REVERT: B 146 ILE cc_start: 0.9014 (pt) cc_final: 0.8710 (pt) REVERT: B 209 TYR cc_start: 0.7911 (m-80) cc_final: 0.7698 (m-80) REVERT: B 210 MET cc_start: 0.8601 (mtt) cc_final: 0.8384 (mtp) REVERT: A 146 ILE cc_start: 0.8902 (pt) cc_final: 0.8611 (pt) REVERT: A 210 MET cc_start: 0.8307 (mtm) cc_final: 0.7959 (mtp) REVERT: C 128 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8379 (t) REVERT: C 220 LYS cc_start: 0.9169 (mttt) cc_final: 0.8798 (mttm) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.1760 time to fit residues: 17.0148 Evaluate side-chains 80 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 232 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 3312 Z= 0.545 Angle : 0.759 6.658 4503 Z= 0.421 Chirality : 0.054 0.182 543 Planarity : 0.003 0.011 558 Dihedral : 6.611 22.408 447 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 3.44 % Allowed : 16.67 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.12 (0.30), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.90 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 239 PHE 0.014 0.002 PHE B 237 TYR 0.023 0.003 TYR C 209 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 88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: B 146 ILE cc_start: 0.9068 (pt) cc_final: 0.8792 (pt) REVERT: A 146 ILE cc_start: 0.8969 (pt) cc_final: 0.8654 (pt) REVERT: A 161 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8048 (mm-30) REVERT: A 207 MET cc_start: 0.7924 (mtm) cc_final: 0.7559 (mtm) REVERT: A 210 MET cc_start: 0.8373 (mtm) cc_final: 0.7984 (mtp) REVERT: C 161 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7422 (mm-30) REVERT: C 220 LYS cc_start: 0.9202 (mttt) cc_final: 0.8774 (mttm) outliers start: 13 outliers final: 10 residues processed: 83 average time/residue: 0.1774 time to fit residues: 17.4164 Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 232 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3312 Z= 0.211 Angle : 0.617 6.138 4503 Z= 0.338 Chirality : 0.052 0.169 543 Planarity : 0.002 0.010 558 Dihedral : 6.089 21.711 447 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.17 % Allowed : 16.67 % 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: -4.99 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.008 0.001 PHE B 237 TYR 0.017 0.002 TYR C 209 ARG 0.001 0.000 ARG A 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 129 LYS cc_start: 0.8914 (ptmt) cc_final: 0.8706 (pttt) REVERT: B 146 ILE cc_start: 0.9040 (pt) cc_final: 0.8756 (pt) REVERT: B 210 MET cc_start: 0.8621 (mtt) cc_final: 0.8320 (mtp) REVERT: A 146 ILE cc_start: 0.8935 (pt) cc_final: 0.8642 (pt) REVERT: A 207 MET cc_start: 0.7862 (mtm) cc_final: 0.7544 (mtm) REVERT: A 210 MET cc_start: 0.8303 (mtm) cc_final: 0.7988 (mtp) REVERT: C 220 LYS cc_start: 0.9169 (mttt) cc_final: 0.8812 (mttm) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 0.1877 time to fit residues: 17.7119 Evaluate side-chains 79 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 232 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 30 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2754 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= 0.326 Angle : 0.664 5.771 4503 Z= 0.365 Chirality : 0.052 0.175 543 Planarity : 0.002 0.010 558 Dihedral : 6.240 20.112 447 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 3.44 % Allowed : 17.99 % Favored : 78.57 % 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: -5.06 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 239 PHE 0.011 0.002 PHE A 237 TYR 0.021 0.002 TYR C 236 ARG 0.002 0.000 ARG A 247 *********************** 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 88 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: B 129 LYS cc_start: 0.8905 (ptmt) cc_final: 0.8574 (pttt) REVERT: B 146 ILE cc_start: 0.9066 (pt) cc_final: 0.8776 (pt) REVERT: B 210 MET cc_start: 0.8608 (mtt) cc_final: 0.8348 (mtp) REVERT: A 146 ILE cc_start: 0.8953 (pt) cc_final: 0.8650 (pt) REVERT: A 170 GLN cc_start: 0.9214 (mp10) cc_final: 0.8958 (mp10) REVERT: A 207 MET cc_start: 0.7870 (mtm) cc_final: 0.7463 (mtm) REVERT: A 210 MET cc_start: 0.8352 (mtm) cc_final: 0.8023 (mtp) REVERT: C 220 LYS cc_start: 0.9178 (mttt) cc_final: 0.8812 (mttm) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.1933 time to fit residues: 18.5808 Evaluate side-chains 86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3312 Z= 0.316 Angle : 0.659 6.000 4503 Z= 0.361 Chirality : 0.053 0.176 543 Planarity : 0.002 0.010 558 Dihedral : 6.226 21.058 447 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 3.17 % Allowed : 18.52 % 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: -5.06 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.23), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS B 239 PHE 0.010 0.002 PHE A 237 TYR 0.022 0.002 TYR C 236 ARG 0.002 0.000 ARG A 247 ********************** 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 84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 129 LYS cc_start: 0.8916 (ptmt) cc_final: 0.8584 (pttt) REVERT: B 146 ILE cc_start: 0.9058 (pt) cc_final: 0.8760 (pt) REVERT: B 210 MET cc_start: 0.8611 (mtt) cc_final: 0.8365 (mtp) REVERT: A 146 ILE cc_start: 0.8943 (pt) cc_final: 0.8635 (pt) REVERT: A 207 MET cc_start: 0.7882 (mtm) cc_final: 0.7545 (mtm) REVERT: A 210 MET cc_start: 0.8366 (mtm) cc_final: 0.8044 (mtp) REVERT: C 220 LYS cc_start: 0.9150 (mttt) cc_final: 0.8725 (mttm) outliers start: 12 outliers final: 12 residues processed: 79 average time/residue: 0.1938 time to fit residues: 18.0693 Evaluate side-chains 84 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 0.0270 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.151904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.131377 restraints weight = 3947.400| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.81 r_work: 0.3914 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3312 Z= 0.171 Angle : 0.608 6.503 4503 Z= 0.327 Chirality : 0.052 0.167 543 Planarity : 0.002 0.010 558 Dihedral : 5.858 21.004 447 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.38 % Allowed : 19.05 % Favored : 78.57 % 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: -4.93 (0.31), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS B 239 PHE 0.007 0.001 PHE B 237 TYR 0.024 0.001 TYR C 236 ARG 0.002 0.000 ARG A 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1272.19 seconds wall clock time: 23 minutes 46.64 seconds (1426.64 seconds total)