Starting phenix.real_space_refine on Fri Oct 10 11:09:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws6_37799/10_2025/8ws6_37799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws6_37799/10_2025/8ws6_37799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ws6_37799/10_2025/8ws6_37799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws6_37799/10_2025/8ws6_37799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ws6_37799/10_2025/8ws6_37799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws6_37799/10_2025/8ws6_37799.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.015 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: 5 Type Number sf(0) Gaussians P 58 5.49 5 S 3 5.16 5 C 2058 2.51 5 N 645 2.21 5 O 794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3558 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2348 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 268} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 401 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 650 Classifications: {'RNA': 31} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 11, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 24} Chain: "D" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 159 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Time building chain proxies: 1.21, per 1000 atoms: 0.34 Number of scatterers: 3558 At special positions: 0 Unit cell: (65.34, 88.44, 91.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 P 58 15.00 O 794 8.00 N 645 7.00 C 2058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.38 Conformation dependent library (CDL) restraints added in 101.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 542 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 1 sheets defined 35.6% alpha, 8.7% beta 13 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.635A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 3.894A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 132 through 149 removed outlier: 4.143A pdb=" N PHE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 removed outlier: 3.750A pdb=" N SER A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.817A pdb=" N LYS A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 287 through 292' Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.891A pdb=" N ALA A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.538A pdb=" N LEU A 341 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 204 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 844 1.33 - 1.45: 1012 1.45 - 1.57: 1789 1.57 - 1.69: 113 1.69 - 1.81: 4 Bond restraints: 3762 Sorted by residual: bond pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 1.524 1.552 -0.028 1.26e-02 6.30e+03 5.04e+00 bond pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.01e-02 9.80e+03 1.86e+00 bond pdb=" N PRO A 324 " pdb=" CA PRO A 324 " ideal model delta sigma weight residual 1.472 1.454 0.018 1.32e-02 5.74e+03 1.78e+00 bond pdb=" C LEU A 217 " pdb=" N PRO A 218 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.76e+00 bond pdb=" C GLU A 152 " pdb=" O GLU A 152 " ideal model delta sigma weight residual 1.237 1.222 0.015 1.17e-02 7.31e+03 1.63e+00 ... (remaining 3757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 5097 1.44 - 2.88: 221 2.88 - 4.32: 35 4.32 - 5.77: 5 5.77 - 7.21: 2 Bond angle restraints: 5360 Sorted by residual: angle pdb=" N ARG A 150 " pdb=" CA ARG A 150 " pdb=" C ARG A 150 " ideal model delta sigma weight residual 113.55 108.80 4.75 1.26e+00 6.30e-01 1.42e+01 angle pdb=" N GLY A 244 " pdb=" CA GLY A 244 " pdb=" C GLY A 244 " ideal model delta sigma weight residual 114.95 110.19 4.76 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C GLU A 176 " pdb=" N PRO A 177 " pdb=" CA PRO A 177 " ideal model delta sigma weight residual 119.84 115.76 4.08 1.25e+00 6.40e-01 1.07e+01 angle pdb=" N LYS A 157 " pdb=" CA LYS A 157 " pdb=" C LYS A 157 " ideal model delta sigma weight residual 111.36 107.95 3.41 1.09e+00 8.42e-01 9.76e+00 angle pdb=" C GLN A 242 " pdb=" N PRO A 243 " pdb=" CA PRO A 243 " ideal model delta sigma weight residual 119.84 123.65 -3.81 1.25e+00 6.40e-01 9.28e+00 ... (remaining 5355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.53: 2059 34.53 - 69.07: 180 69.07 - 103.60: 16 103.60 - 138.13: 0 138.13 - 172.67: 2 Dihedral angle restraints: 2257 sinusoidal: 1408 harmonic: 849 Sorted by residual: dihedral pdb=" O4' U B 10 " pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sinusoidal sigma weight residual 200.00 58.29 141.71 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 59.33 172.67 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA GLU A 148 " pdb=" C GLU A 148 " pdb=" N THR A 149 " pdb=" CA THR A 149 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 2254 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 420 0.029 - 0.058: 125 0.058 - 0.087: 37 0.087 - 0.117: 22 0.117 - 0.146: 6 Chirality restraints: 610 Sorted by residual: chirality pdb=" CA ILE A 347 " pdb=" N ILE A 347 " pdb=" C ILE A 347 " pdb=" CB ILE A 347 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" C1' U B 10 " pdb=" O4' U B 10 " pdb=" C2' U B 10 " pdb=" N1 U B 10 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CB ILE A 261 " pdb=" CA ILE A 261 " pdb=" CG1 ILE A 261 " pdb=" CG2 ILE A 261 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 607 not shown) Planarity restraints: 484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 338 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO A 339 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 339 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 339 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 191 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO A 192 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 238 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO A 239 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 239 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 239 " 0.028 5.00e-02 4.00e+02 ... (remaining 481 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 387 2.74 - 3.28: 3109 3.28 - 3.82: 6018 3.82 - 4.36: 7409 4.36 - 4.90: 11478 Nonbonded interactions: 28401 Sorted by model distance: nonbonded pdb=" O ASP A 110 " pdb=" OD1 ASP A 110 " model vdw 2.204 3.040 nonbonded pdb=" O TRP A 112 " pdb=" OG1 THR A 116 " model vdw 2.243 3.040 nonbonded pdb=" NH1 ARG A 314 " pdb=" O4 U B -17 " model vdw 2.250 3.120 nonbonded pdb=" ND2 ASN A 138 " pdb=" OP1 DG C -2 " model vdw 2.312 3.120 nonbonded pdb=" NH1 ARG A 260 " pdb=" O6 G B -16 " model vdw 2.353 3.120 ... (remaining 28396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 3.910 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.870 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 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 : 0.003 0.031 3762 Z= 0.179 Angle : 0.665 7.208 5360 Z= 0.410 Chirality : 0.036 0.146 610 Planarity : 0.007 0.073 484 Dihedral : 21.116 172.666 1715 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.46), residues: 296 helix: -1.76 (0.47), residues: 95 sheet: -0.73 (1.04), residues: 29 loop : -0.72 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.006 0.001 TYR A 265 PHE 0.010 0.001 PHE A 219 TRP 0.013 0.002 TRP A 304 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 3762) covalent geometry : angle 0.66540 ( 5360) hydrogen bonds : bond 0.26783 ( 106) hydrogen bonds : angle 10.01247 ( 260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 104 THR cc_start: 0.7057 (p) cc_final: 0.6844 (p) REVERT: A 331 LEU cc_start: 0.7261 (tp) cc_final: 0.6999 (tt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0973 time to fit residues: 5.0169 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.151045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.128567 restraints weight = 5212.563| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.40 r_work: 0.3456 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3762 Z= 0.275 Angle : 0.703 5.324 5360 Z= 0.378 Chirality : 0.046 0.159 610 Planarity : 0.008 0.055 484 Dihedral : 24.294 173.090 1121 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.21 % Allowed : 10.93 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.48), residues: 296 helix: -1.53 (0.47), residues: 103 sheet: -0.20 (1.05), residues: 31 loop : -0.51 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 139 TYR 0.017 0.003 TYR A 140 PHE 0.015 0.003 PHE A 335 TRP 0.018 0.002 TRP A 112 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 3762) covalent geometry : angle 0.70273 ( 5360) hydrogen bonds : bond 0.05869 ( 106) hydrogen bonds : angle 4.97069 ( 260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.104 Fit side-chains REVERT: A 134 ARG cc_start: 0.7814 (tmm-80) cc_final: 0.7603 (ttp-110) REVERT: A 261 ILE cc_start: 0.7805 (tt) cc_final: 0.7563 (pt) outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.0990 time to fit residues: 5.0598 Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 255 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 6 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.153874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131397 restraints weight = 5164.240| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.38 r_work: 0.3501 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3762 Z= 0.147 Angle : 0.584 6.303 5360 Z= 0.317 Chirality : 0.039 0.138 610 Planarity : 0.007 0.048 484 Dihedral : 24.265 173.910 1121 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.62 % Allowed : 13.77 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.49), residues: 296 helix: -1.17 (0.48), residues: 109 sheet: 0.31 (1.12), residues: 29 loop : -0.34 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 139 TYR 0.010 0.002 TYR A 265 PHE 0.008 0.002 PHE A 335 TRP 0.020 0.002 TRP A 264 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3762) covalent geometry : angle 0.58433 ( 5360) hydrogen bonds : bond 0.04337 ( 106) hydrogen bonds : angle 4.34138 ( 260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.077 Fit side-chains REVERT: A 134 ARG cc_start: 0.7819 (tmm-80) cc_final: 0.7605 (ttp-110) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.0954 time to fit residues: 4.6515 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 19 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 27 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.153948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131726 restraints weight = 5122.405| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.35 r_work: 0.3490 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3762 Z= 0.146 Angle : 0.573 6.443 5360 Z= 0.309 Chirality : 0.039 0.140 610 Planarity : 0.006 0.044 484 Dihedral : 24.210 173.911 1121 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.43 % Allowed : 14.17 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.49), residues: 296 helix: -0.87 (0.50), residues: 103 sheet: 0.42 (1.12), residues: 29 loop : 0.01 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 345 TYR 0.008 0.001 TYR A 265 PHE 0.010 0.002 PHE A 335 TRP 0.020 0.002 TRP A 264 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 3762) covalent geometry : angle 0.57285 ( 5360) hydrogen bonds : bond 0.03899 ( 106) hydrogen bonds : angle 4.09319 ( 260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7883 (tmm-80) cc_final: 0.7572 (ttp-110) REVERT: A 331 LEU cc_start: 0.7521 (tp) cc_final: 0.7183 (tt) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.1216 time to fit residues: 5.9764 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.150717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127583 restraints weight = 5169.525| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.53 r_work: 0.3480 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3762 Z= 0.152 Angle : 0.564 6.808 5360 Z= 0.302 Chirality : 0.039 0.132 610 Planarity : 0.006 0.039 484 Dihedral : 24.088 173.677 1121 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.24 % Allowed : 14.17 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.49), residues: 296 helix: -0.36 (0.52), residues: 97 sheet: 0.06 (1.04), residues: 30 loop : 0.15 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.008 0.001 TYR A 265 PHE 0.009 0.002 PHE A 350 TRP 0.025 0.002 TRP A 264 HIS 0.001 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3762) covalent geometry : angle 0.56363 ( 5360) hydrogen bonds : bond 0.03976 ( 106) hydrogen bonds : angle 4.06310 ( 260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7981 (tmm-80) cc_final: 0.7636 (ttp-110) REVERT: A 279 VAL cc_start: 0.6688 (OUTLIER) cc_final: 0.6412 (p) outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.1241 time to fit residues: 6.1114 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 27 optimal weight: 0.4980 chunk 19 optimal weight: 0.0470 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.0470 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 0.3980 overall best weight: 0.1576 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.152310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129249 restraints weight = 5197.356| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.52 r_work: 0.3516 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3762 Z= 0.115 Angle : 0.534 6.736 5360 Z= 0.285 Chirality : 0.037 0.133 610 Planarity : 0.006 0.038 484 Dihedral : 24.004 173.608 1121 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.21 % Allowed : 15.38 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.50), residues: 296 helix: 0.01 (0.53), residues: 97 sheet: 0.22 (1.03), residues: 30 loop : 0.24 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.005 0.001 TYR A 201 PHE 0.007 0.001 PHE A 350 TRP 0.027 0.002 TRP A 264 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3762) covalent geometry : angle 0.53389 ( 5360) hydrogen bonds : bond 0.03421 ( 106) hydrogen bonds : angle 3.87695 ( 260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.079 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7966 (tmm-80) cc_final: 0.7608 (ttp-110) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.1291 time to fit residues: 5.6904 Evaluate side-chains 38 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 166 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 chunk 31 optimal weight: 0.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.151918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.128922 restraints weight = 5226.323| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.49 r_work: 0.3492 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3762 Z= 0.126 Angle : 0.531 6.645 5360 Z= 0.283 Chirality : 0.037 0.132 610 Planarity : 0.005 0.037 484 Dihedral : 23.989 173.058 1121 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.02 % Allowed : 16.60 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.50), residues: 296 helix: 0.13 (0.54), residues: 97 sheet: 0.37 (1.04), residues: 30 loop : 0.32 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 345 TYR 0.008 0.001 TYR A 265 PHE 0.008 0.001 PHE A 350 TRP 0.024 0.002 TRP A 264 HIS 0.001 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 3762) covalent geometry : angle 0.53139 ( 5360) hydrogen bonds : bond 0.03566 ( 106) hydrogen bonds : angle 3.86875 ( 260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7994 (tmm-80) cc_final: 0.7630 (ttp-110) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.1265 time to fit residues: 5.4212 Evaluate side-chains 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 5 optimal weight: 0.0470 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.150589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127546 restraints weight = 5229.712| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.53 r_work: 0.3473 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3762 Z= 0.152 Angle : 0.555 6.760 5360 Z= 0.295 Chirality : 0.039 0.134 610 Planarity : 0.006 0.036 484 Dihedral : 24.050 172.615 1121 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.62 % Allowed : 17.00 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.50), residues: 296 helix: -0.00 (0.52), residues: 105 sheet: 0.19 (1.01), residues: 30 loop : 0.09 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 345 TYR 0.007 0.001 TYR A 265 PHE 0.009 0.001 PHE A 350 TRP 0.030 0.002 TRP A 264 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3762) covalent geometry : angle 0.55544 ( 5360) hydrogen bonds : bond 0.03900 ( 106) hydrogen bonds : angle 3.93107 ( 260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8018 (tmm-80) cc_final: 0.7639 (ttp-110) REVERT: A 279 VAL cc_start: 0.6744 (OUTLIER) cc_final: 0.6464 (p) REVERT: A 331 LEU cc_start: 0.7469 (tp) cc_final: 0.7128 (tt) outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.1152 time to fit residues: 5.2661 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 12 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 overall best weight: 0.4384 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.149797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126965 restraints weight = 5119.257| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.51 r_work: 0.3473 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3762 Z= 0.169 Angle : 0.572 6.725 5360 Z= 0.303 Chirality : 0.039 0.134 610 Planarity : 0.006 0.038 484 Dihedral : 24.094 172.324 1121 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.02 % Allowed : 17.00 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.49), residues: 296 helix: 0.01 (0.53), residues: 99 sheet: 0.05 (1.01), residues: 30 loop : 0.13 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 96 TYR 0.008 0.002 TYR A 265 PHE 0.009 0.002 PHE A 137 TRP 0.040 0.003 TRP A 264 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 3762) covalent geometry : angle 0.57163 ( 5360) hydrogen bonds : bond 0.04065 ( 106) hydrogen bonds : angle 3.98056 ( 260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8021 (tmm-80) cc_final: 0.7642 (ttp-110) REVERT: A 279 VAL cc_start: 0.6805 (OUTLIER) cc_final: 0.6526 (p) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.1211 time to fit residues: 5.6774 Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 0.0670 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.149768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126719 restraints weight = 5258.353| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.54 r_work: 0.3467 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3762 Z= 0.138 Angle : 0.559 6.990 5360 Z= 0.296 Chirality : 0.038 0.136 610 Planarity : 0.006 0.037 484 Dihedral : 24.098 172.118 1121 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.62 % Allowed : 17.41 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.49), residues: 296 helix: 0.04 (0.53), residues: 99 sheet: 0.02 (1.01), residues: 30 loop : 0.17 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.008 0.001 TYR A 265 PHE 0.010 0.002 PHE A 137 TRP 0.041 0.002 TRP A 264 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3762) covalent geometry : angle 0.55878 ( 5360) hydrogen bonds : bond 0.03906 ( 106) hydrogen bonds : angle 3.94371 ( 260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8040 (tmm-80) cc_final: 0.7658 (ttp-110) REVERT: A 279 VAL cc_start: 0.6799 (OUTLIER) cc_final: 0.6521 (p) outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.1007 time to fit residues: 4.8419 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 279 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.0060 chunk 28 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.150402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127536 restraints weight = 5148.992| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.51 r_work: 0.3478 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3762 Z= 0.147 Angle : 0.560 7.133 5360 Z= 0.297 Chirality : 0.038 0.133 610 Planarity : 0.006 0.037 484 Dihedral : 24.073 172.285 1121 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.83 % Allowed : 16.60 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.49), residues: 296 helix: 0.05 (0.53), residues: 99 sheet: -0.02 (1.00), residues: 30 loop : 0.18 (0.50), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 96 TYR 0.009 0.001 TYR A 265 PHE 0.012 0.002 PHE A 137 TRP 0.039 0.002 TRP A 264 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3762) covalent geometry : angle 0.55970 ( 5360) hydrogen bonds : bond 0.03841 ( 106) hydrogen bonds : angle 3.92449 ( 260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1279.60 seconds wall clock time: 22 minutes 39.03 seconds (1359.03 seconds total)