Starting phenix.real_space_refine on Tue Aug 4 13:45:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws6_37799/08_2026/8ws6_37799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws6_37799/08_2026/8ws6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ws6_37799/08_2026/8ws6_37799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws6_37799/08_2026/8ws6_37799.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws6_37799/08_2026/8ws6_37799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws6_37799/08_2026/8ws6_37799.cif" } 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-2.2rc3-6140/lib/python3.11/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: 1.09, per 1000 atoms: 0.31 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: 0.50 Conformation dependent library (CDL) restraints added in 92.9 milliseconds 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: 0.32 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: 0.34 Time building geometry restraints manager: 0.53 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=" C3' DA C -6 " pdb=" C2' DA C -6 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.32e+00 bond pdb=" C3' DA C 2 " pdb=" C2' DA C 2 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.60e+00 bond pdb=" C3' DG C -5 " pdb=" C2' DG C -5 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.37e+00 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=" C3' DA C -10 " pdb=" C2' DA C -10 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 4.82e+00 ... (remaining 3757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 4951 1.44 - 2.88: 365 2.88 - 4.32: 37 4.32 - 5.77: 5 5.77 - 7.21: 2 Bond angle restraints: 5360 Sorted by residual: angle pdb=" O4' DG C -3 " pdb=" C4' DG C -3 " pdb=" C3' DG C -3 " ideal model delta sigma weight residual 106.00 103.50 2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sigma weight residual 117.70 122.68 -4.98 1.20e+00 6.94e-01 1.72e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT D -2 " pdb=" C4 DT D -2 " pdb=" O4 DT D -2 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 ... (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: 352 0.029 - 0.058: 138 0.058 - 0.087: 59 0.087 - 0.117: 29 0.117 - 0.146: 32 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=" C2' U B 6 " pdb=" C3' U B 6 " pdb=" O2' U B 6 " pdb=" C1' U B 6 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 4.99e-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 4.94e-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: 3.740 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.140 Find NCS groups from input model: 0.010 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:0.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 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 : 0.004 0.031 3762 Z= 0.330 Angle : 0.776 7.208 5360 Z= 0.590 Chirality : 0.050 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 are 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/Z covalent geometry : bond 0.00400 / 0.33 ( 3762) covalent geometry : angle 0.77567 / 0.59 ( 5360) hydrogen bonds : bond 0.26783 / 19.11 ( 106) hydrogen bonds : angle 10.01247 / 7.52 ( 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 : 0.061 Fit side-chains revert: symmetry clash REVERT: A 104 THR cc_start: 0.7057 (p) cc_final: 0.6843 (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: 0.0785 time to fit residues: 4.0696 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 : 0.058 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.151992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.129159 restraints weight = 5192.323| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.45 r_work: 0.3459 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3762 Z= 0.254 Angle : 0.742 7.162 5360 Z= 0.407 Chirality : 0.052 0.320 610 Planarity : 0.009 0.054 484 Dihedral : 24.261 175.168 1121 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.21 % Allowed : 10.53 % Favored : 88.26 % 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 are not related in a simple way. whole: -1.20 (0.47), residues: 296 helix: -1.24 (0.49), residues: 97 sheet: 0.01 (1.07), residues: 31 loop : -0.58 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 106 TYR 0.019 0.003 TYR A 140 PHE 0.014 0.003 PHE A 335 TRP 0.020 0.003 TRP A 264 HIS 0.006 0.002 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.25 ( 3762) covalent geometry : angle 0.74214 / 0.41 ( 5360) hydrogen bonds : bond 0.06906 / 4.72 ( 106) hydrogen bonds : angle 5.12190 / 3.71 ( 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 46 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.107 Fit side-chains REVERT: A 134 ARG cc_start: 0.7853 (tmm-80) cc_final: 0.7553 (ttp-110) REVERT: A 261 ILE cc_start: 0.7804 (tt) cc_final: 0.7528 (pt) outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.1035 time to fit residues: 5.3185 Evaluate side-chains 47 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 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: 2.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.0020 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.0050 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130565 restraints weight = 5148.241| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.37 r_work: 0.3486 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1758 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= 0.170 Angle : 0.612 6.011 5360 Z= 0.348 Chirality : 0.044 0.139 610 Planarity : 0.007 0.047 484 Dihedral : 24.381 174.519 1121 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.81 % Allowed : 13.77 % Favored : 85.43 % 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 are not related in a simple way. whole: -0.98 (0.49), residues: 296 helix: -1.22 (0.49), residues: 103 sheet: 0.36 (1.15), residues: 29 loop : -0.33 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.012 0.002 TYR A 265 PHE 0.013 0.002 PHE A 335 TRP 0.023 0.002 TRP A 264 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 3762) covalent geometry : angle 0.61153 / 0.35 ( 5360) hydrogen bonds : bond 0.05595 / 3.78 ( 106) hydrogen bonds : angle 4.59471 / 3.33 ( 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 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.087 Fit side-chains REVERT: A 134 ARG cc_start: 0.7833 (tmm-80) cc_final: 0.7623 (ttp-110) REVERT: A 331 LEU cc_start: 0.7472 (tp) cc_final: 0.7156 (tt) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.1074 time to fit residues: 5.2575 Evaluate side-chains 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 3 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.152975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130615 restraints weight = 5109.125| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.35 r_work: 0.3485 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3762 Z= 0.163 Angle : 0.598 6.218 5360 Z= 0.338 Chirality : 0.043 0.170 610 Planarity : 0.007 0.042 484 Dihedral : 24.380 174.882 1121 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.83 % Allowed : 15.79 % 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 are not related in a simple way. whole: -0.75 (0.49), residues: 296 helix: -1.08 (0.49), residues: 103 sheet: 0.47 (1.16), residues: 29 loop : -0.14 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.010 0.002 TYR A 265 PHE 0.009 0.002 PHE A 350 TRP 0.017 0.002 TRP A 264 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 3762) covalent geometry : angle 0.59764 / 0.34 ( 5360) hydrogen bonds : bond 0.04914 / 3.20 ( 106) hydrogen bonds : angle 4.36928 / 3.16 ( 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 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7850 (tmm-80) cc_final: 0.7620 (ttp-110) REVERT: A 279 VAL cc_start: 0.6667 (OUTLIER) cc_final: 0.6367 (p) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 0.1185 time to fit residues: 5.6793 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 : 0.110 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 4 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124267 restraints weight = 5176.360| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.51 r_work: 0.3444 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3762 Z= 0.207 Angle : 0.637 6.356 5360 Z= 0.355 Chirality : 0.047 0.192 610 Planarity : 0.007 0.046 484 Dihedral : 24.414 174.356 1121 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.43 % Allowed : 17.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.49), residues: 296 helix: -1.12 (0.49), residues: 103 sheet: -0.14 (1.08), residues: 30 loop : -0.09 (0.50), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 260 TYR 0.013 0.002 TYR A 265 PHE 0.012 0.003 PHE A 350 TRP 0.026 0.003 TRP A 264 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 ( 3762) covalent geometry : angle 0.63749 / 0.36 ( 5360) hydrogen bonds : bond 0.05362 / 3.71 ( 106) hydrogen bonds : angle 4.40429 / 3.17 ( 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 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7965 (tmm-80) cc_final: 0.7721 (ttp-110) REVERT: A 279 VAL cc_start: 0.6665 (OUTLIER) cc_final: 0.6429 (p) REVERT: A 331 LEU cc_start: 0.7529 (tp) cc_final: 0.7184 (tt) outliers start: 6 outliers final: 4 residues processed: 41 average time/residue: 0.1173 time to fit residues: 5.6068 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 : 0.106 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 0.4980 chunk 28 optimal weight: 0.0570 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 0.0020 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.3980 chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 overall best weight: 0.2306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.153484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.131310 restraints weight = 5229.073| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.36 r_work: 0.3502 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3762 Z= 0.128 Angle : 0.554 6.668 5360 Z= 0.317 Chirality : 0.042 0.141 610 Planarity : 0.006 0.039 484 Dihedral : 24.344 174.132 1121 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.43 % Allowed : 17.00 % 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 are not related in a simple way. whole: -0.24 (0.50), residues: 296 helix: -0.52 (0.53), residues: 97 sheet: 0.27 (1.09), residues: 29 loop : 0.12 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 260 TYR 0.008 0.001 TYR A 265 PHE 0.009 0.002 PHE A 352 TRP 0.028 0.002 TRP A 264 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 ( 3762) covalent geometry : angle 0.55391 / 0.32 ( 5360) hydrogen bonds : bond 0.04337 / 2.82 ( 106) hydrogen bonds : angle 4.16232 / 3.02 ( 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 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7903 (tmm-80) cc_final: 0.7582 (ttp-110) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 0.1087 time to fit residues: 5.0499 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 : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 104 THR 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: 0.0870 chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.126726 restraints weight = 5220.194| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.52 r_work: 0.3472 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3762 Z= 0.150 Angle : 0.568 6.548 5360 Z= 0.320 Chirality : 0.042 0.144 610 Planarity : 0.006 0.041 484 Dihedral : 24.311 174.566 1121 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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 are not related in a simple way. whole: -0.20 (0.50), residues: 296 helix: -0.49 (0.52), residues: 97 sheet: 0.39 (1.08), residues: 29 loop : 0.13 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.010 0.002 TYR A 265 PHE 0.009 0.002 PHE A 350 TRP 0.025 0.002 TRP A 264 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 3762) covalent geometry : angle 0.56761 / 0.32 ( 5360) hydrogen bonds : bond 0.04517 / 3.13 ( 106) hydrogen bonds : angle 4.15088 / 2.99 ( 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 40 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7966 (tmm-80) cc_final: 0.7627 (ttp-110) REVERT: A 331 LEU cc_start: 0.7505 (tp) cc_final: 0.7106 (tt) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.0903 time to fit residues: 3.9454 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 : 0.070 ------------------------------------------------------------------------------- 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 326 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.0000 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 0.0870 overall best weight: 0.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.151048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.128088 restraints weight = 5235.122| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.52 r_work: 0.3495 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3762 Z= 0.120 Angle : 0.542 7.282 5360 Z= 0.310 Chirality : 0.041 0.139 610 Planarity : 0.006 0.039 484 Dihedral : 24.290 174.098 1121 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.43 % Allowed : 17.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.50), residues: 296 helix: -0.32 (0.52), residues: 97 sheet: 0.51 (1.08), residues: 29 loop : 0.21 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.009 0.001 TYR A 265 PHE 0.009 0.001 PHE A 335 TRP 0.034 0.002 TRP A 264 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.12 ( 3762) covalent geometry : angle 0.54229 / 0.31 ( 5360) hydrogen bonds : bond 0.04121 / 2.79 ( 106) hydrogen bonds : angle 4.04209 / 2.91 ( 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 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.7948 (tmm-80) cc_final: 0.7661 (ttp-110) outliers start: 6 outliers final: 6 residues processed: 41 average time/residue: 0.1148 time to fit residues: 5.4613 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.098 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125724 restraints weight = 5129.432| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.50 r_work: 0.3465 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3762 Z= 0.169 Angle : 0.582 6.891 5360 Z= 0.326 Chirality : 0.044 0.165 610 Planarity : 0.006 0.040 484 Dihedral : 24.292 174.466 1121 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.43 % Allowed : 17.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.50), residues: 296 helix: -0.39 (0.52), residues: 97 sheet: 0.36 (1.06), residues: 29 loop : 0.14 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 260 TYR 0.010 0.002 TYR A 265 PHE 0.009 0.002 PHE A 335 TRP 0.030 0.002 TRP A 264 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 ( 3762) covalent geometry : angle 0.58230 / 0.33 ( 5360) hydrogen bonds : bond 0.04700 / 3.31 ( 106) hydrogen bonds : angle 4.14069 / 3.00 ( 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 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8004 (tmm-80) cc_final: 0.7720 (ttp-110) REVERT: A 331 LEU cc_start: 0.7495 (tp) cc_final: 0.7121 (tt) outliers start: 6 outliers final: 6 residues processed: 42 average time/residue: 0.1110 time to fit residues: 5.3857 Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.148197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124663 restraints weight = 5247.907| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.55 r_work: 0.3448 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3762 Z= 0.189 Angle : 0.609 6.846 5360 Z= 0.340 Chirality : 0.045 0.182 610 Planarity : 0.006 0.040 484 Dihedral : 24.461 176.455 1121 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.43 % Allowed : 18.62 % Favored : 78.95 % 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 are not related in a simple way. whole: -0.31 (0.50), residues: 296 helix: -0.47 (0.52), residues: 97 sheet: -0.05 (1.03), residues: 30 loop : 0.07 (0.50), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 106 TYR 0.009 0.002 TYR A 87 PHE 0.011 0.002 PHE A 335 TRP 0.048 0.003 TRP A 264 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 ( 3762) covalent geometry : angle 0.60898 / 0.34 ( 5360) hydrogen bonds : bond 0.04948 / 3.51 ( 106) hydrogen bonds : angle 4.14759 / 3.00 ( 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 45 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: A 134 ARG cc_start: 0.8036 (tmm-80) cc_final: 0.7680 (ttp-110) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.1074 time to fit residues: 5.3649 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 : 0.121 ------------------------------------------------------------------------------- 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 222 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.0270 chunk 8 optimal weight: 0.6980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.149113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.125826 restraints weight = 5137.477| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 1.52 r_work: 0.3467 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3762 Z= 0.137 Angle : 0.573 7.140 5360 Z= 0.323 Chirality : 0.042 0.150 610 Planarity : 0.006 0.041 484 Dihedral : 24.448 178.679 1121 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.02 % Allowed : 18.62 % Favored : 79.35 % 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 are not related in a simple way. whole: -0.13 (0.50), residues: 296 helix: -0.30 (0.52), residues: 97 sheet: 0.05 (1.03), residues: 30 loop : 0.17 (0.51), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 96 TYR 0.006 0.001 TYR A 87 PHE 0.011 0.002 PHE A 137 TRP 0.043 0.003 TRP A 264 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 3762) covalent geometry : angle 0.57272 / 0.32 ( 5360) hydrogen bonds : bond 0.04525 / 3.15 ( 106) hydrogen bonds : angle 4.09789 / 2.97 ( 260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1246.05 seconds wall clock time: 21 minutes 59.22 seconds (1319.22 seconds total)