Starting phenix.real_space_refine on Wed Jul 1 22:50:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws5_37798/07_2026/8ws5_37798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws5_37798/07_2026/8ws5_37798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ws5_37798/07_2026/8ws5_37798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws5_37798/07_2026/8ws5_37798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ws5_37798/07_2026/8ws5_37798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws5_37798/07_2026/8ws5_37798.map" } resolution = 3.29 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= 0.014 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 74 5.49 5 S 3 5.16 5 C 2133 2.51 5 N 684 2.21 5 O 876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3770 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2226 Classifications: {'peptide': 282} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 254} Chain breaks: 3 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: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 562 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 843 Classifications: {'RNA': 40} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 16, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 33} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 1.16, per 1000 atoms: 0.31 Number of scatterers: 3770 At special positions: 0 Unit cell: (69.3, 107.58, 93.06, 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 74 15.00 O 876 8.00 N 684 7.00 C 2133 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: 0.40 Conformation dependent library (CDL) restraints added in 83.6 milliseconds 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 2 sheets defined 39.7% alpha, 5.7% beta 17 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 94 through 100 removed outlier: 4.093A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 116 removed outlier: 5.223A pdb=" N PHE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 169 removed outlier: 4.539A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 283 through 292 removed outlier: 4.217A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64 removed outlier: 3.745A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 83 hydrogen bonds defined for protein. 219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 0.37 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 577 1.33 - 1.45: 1376 1.45 - 1.57: 1905 1.57 - 1.69: 145 1.69 - 1.80: 4 Bond restraints: 4007 Sorted by residual: bond pdb=" C ASP A 338 " pdb=" N PRO A 339 " ideal model delta sigma weight residual 1.330 1.371 -0.041 1.22e-02 6.72e+03 1.13e+01 bond pdb=" C1' DT C -18 " pdb=" N1 DT C -18 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" CA ASP A 338 " pdb=" C ASP A 338 " ideal model delta sigma weight residual 1.525 1.562 -0.036 1.12e-02 7.97e+03 1.05e+01 bond pdb=" C3' DG C -12 " pdb=" C2' DG C -12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC D 0 " pdb=" C2' DC D 0 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.30e+00 ... (remaining 4002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 5495 1.98 - 3.96: 231 3.96 - 5.94: 30 5.94 - 7.91: 2 7.91 - 9.89: 2 Bond angle restraints: 5760 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 106.00 103.11 2.89 6.00e-01 2.78e+00 2.33e+01 angle pdb=" C4' DA C -6 " pdb=" O4' DA C -6 " pdb=" C1' DA C -6 " ideal model delta sigma weight residual 110.10 105.55 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" N3 DT C -7 " pdb=" C4 DT C -7 " pdb=" O4 DT C -7 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" N3 DT D -1 " pdb=" C4 DT D -1 " pdb=" O4 DT D -1 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT C 3 " pdb=" C4 DT C 3 " pdb=" O4 DT C 3 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 5755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 2145 34.83 - 69.66: 236 69.66 - 104.49: 17 104.49 - 139.32: 0 139.32 - 174.14: 2 Dihedral angle restraints: 2400 sinusoidal: 1596 harmonic: 804 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 54.15 145.85 1 1.50e+01 4.44e-03 7.80e+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 57.86 174.14 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" CA VAL A 279 " pdb=" C VAL A 279 " pdb=" N LEU A 280 " pdb=" CA LEU A 280 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 2397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 484 0.051 - 0.101: 125 0.101 - 0.152: 44 0.152 - 0.203: 10 0.203 - 0.253: 4 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA ILE A 294 " pdb=" N ILE A 294 " pdb=" C ILE A 294 " pdb=" CB ILE A 294 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL A 298 " pdb=" N VAL A 298 " pdb=" C VAL A 298 " pdb=" CB VAL A 298 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C3' G B 9 " pdb=" C4' G B 9 " pdb=" O3' G B 9 " pdb=" C2' G B 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 664 not shown) Planarity restraints: 472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 128 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C GLY A 128 " -0.037 2.00e-02 2.50e+03 pdb=" O GLY A 128 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 129 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 67 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ALA A 67 " -0.032 2.00e-02 2.50e+03 pdb=" O ALA A 67 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 68 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 228 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 229 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.023 5.00e-02 4.00e+02 ... (remaining 469 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 571 2.76 - 3.29: 3287 3.29 - 3.83: 6803 3.83 - 4.36: 7858 4.36 - 4.90: 11899 Nonbonded interactions: 30418 Sorted by model distance: nonbonded pdb=" NH1 ARG A 267 " pdb=" OP1 C B -15 " model vdw 2.219 3.120 nonbonded pdb=" NH2 ARG A 260 " pdb=" OP2 U B -17 " model vdw 2.260 3.120 nonbonded pdb=" OE1 GLN A 127 " pdb=" N6 DA C 1 " model vdw 2.277 3.120 nonbonded pdb=" NH1 ARG A 314 " pdb=" O4 U B -17 " model vdw 2.292 3.120 nonbonded pdb=" OE1 GLN A 202 " pdb=" N6 DA C 2 " model vdw 2.320 3.120 ... (remaining 30413 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.810 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:0.780 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: 0.6090 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 : 0.006 0.046 4007 Z= 0.428 Angle : 0.886 9.893 5760 Z= 0.645 Chirality : 0.056 0.253 667 Planarity : 0.006 0.041 472 Dihedral : 22.815 174.143 1884 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 1.71 % Allowed : 3.85 % Favored : 94.44 % 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: -1.93 (0.52), residues: 274 helix: -1.08 (0.49), residues: 100 sheet: -0.79 (0.99), residues: 28 loop : -1.50 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 165 TYR 0.008 0.002 TYR A 201 PHE 0.012 0.002 PHE A 352 TRP 0.014 0.002 TRP A 249 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.43 ( 4007) covalent geometry : angle 0.88636 / 0.64 ( 5760) hydrogen bonds : bond 0.17456 / 12.54 ( 126) hydrogen bonds : angle 7.61178 / 5.52 ( 301) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.100 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.0841 time to fit residues: 3.2881 Evaluate side-chains 27 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 13 optimal weight: 0.0980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.199844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.167836 restraints weight = 6029.964| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 1.51 r_work: 0.4009 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3865 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4007 Z= 0.190 Angle : 0.649 5.523 5760 Z= 0.382 Chirality : 0.045 0.261 667 Planarity : 0.007 0.044 472 Dihedral : 25.063 178.723 1324 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.03 % Favored : 91.61 % Rotamer: Outliers : 0.85 % Allowed : 10.68 % Favored : 88.46 % 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: -1.66 (0.51), residues: 274 helix: -0.91 (0.49), residues: 105 sheet: -0.47 (0.99), residues: 28 loop : -1.33 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 260 TYR 0.011 0.002 TYR A 317 PHE 0.008 0.002 PHE A 352 TRP 0.018 0.002 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.19 ( 4007) covalent geometry : angle 0.64922 / 0.38 ( 5760) hydrogen bonds : bond 0.07112 / 4.99 ( 126) hydrogen bonds : angle 4.85959 / 3.43 ( 301) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.071 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.1134 time to fit residues: 3.7287 Evaluate side-chains 26 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 26 optimal weight: 0.0470 chunk 33 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.200784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.167883 restraints weight = 5949.589| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 1.57 r_work: 0.4011 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3869 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4007 Z= 0.159 Angle : 0.582 5.605 5760 Z= 0.350 Chirality : 0.041 0.234 667 Planarity : 0.006 0.040 472 Dihedral : 25.074 179.882 1321 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.93 % Favored : 92.70 % Rotamer: Outliers : 1.71 % Allowed : 10.68 % Favored : 87.61 % 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: -1.38 (0.53), residues: 274 helix: -0.65 (0.50), residues: 105 sheet: -0.65 (0.92), residues: 33 loop : -1.11 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 260 TYR 0.010 0.002 TYR A 317 PHE 0.007 0.001 PHE A 219 TRP 0.016 0.002 TRP A 249 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 ( 4007) covalent geometry : angle 0.58216 / 0.35 ( 5760) hydrogen bonds : bond 0.05513 / 3.77 ( 126) hydrogen bonds : angle 4.41178 / 3.12 ( 301) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.105 Fit side-chains REVERT: A 74 GLU cc_start: 0.6126 (tm-30) cc_final: 0.5704 (tm-30) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.0871 time to fit residues: 3.5632 Evaluate side-chains 34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.0040 chunk 31 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.0060 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.198897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.166103 restraints weight = 5941.118| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.51 r_work: 0.3987 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4007 Z= 0.197 Angle : 0.621 6.501 5760 Z= 0.366 Chirality : 0.042 0.212 667 Planarity : 0.006 0.038 472 Dihedral : 25.057 179.454 1321 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % Rotamer: Outliers : 1.71 % Allowed : 13.68 % 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 are not related in a simple way. whole: -1.46 (0.52), residues: 274 helix: -0.72 (0.50), residues: 105 sheet: -0.12 (1.02), residues: 27 loop : -1.29 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.015 0.002 TYR A 317 PHE 0.007 0.002 PHE A 334 TRP 0.014 0.002 TRP A 249 HIS 0.001 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 ( 4007) covalent geometry : angle 0.62123 / 0.37 ( 5760) hydrogen bonds : bond 0.05688 / 3.89 ( 126) hydrogen bonds : angle 4.57576 / 3.22 ( 301) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6329 (tm-30) cc_final: 0.5803 (tm-30) REVERT: A 323 LYS cc_start: 0.7633 (tppt) cc_final: 0.7288 (tppt) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.0918 time to fit residues: 3.8563 Evaluate side-chains 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 6 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 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 = 0.4445 r_free = 0.4445 target = 0.197508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.164517 restraints weight = 5840.557| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.52 r_work: 0.3958 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4007 Z= 0.193 Angle : 0.621 5.566 5760 Z= 0.364 Chirality : 0.042 0.226 667 Planarity : 0.006 0.040 472 Dihedral : 25.089 178.427 1321 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % Rotamer: Outliers : 1.71 % Allowed : 16.24 % Favored : 82.05 % 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: -1.43 (0.52), residues: 274 helix: -0.55 (0.52), residues: 99 sheet: 0.02 (1.00), residues: 27 loop : -1.41 (0.56), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.019 0.002 TYR A 317 PHE 0.007 0.002 PHE A 334 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 0.00377 / 0.19 ( 4007) covalent geometry : angle 0.62066 / 0.36 ( 5760) hydrogen bonds : bond 0.05184 / 3.53 ( 126) hydrogen bonds : angle 4.56846 / 3.22 ( 301) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6468 (tm-30) cc_final: 0.5909 (tm-30) REVERT: A 323 LYS cc_start: 0.7644 (tppt) cc_final: 0.7422 (mmmt) outliers start: 4 outliers final: 4 residues processed: 35 average time/residue: 0.1179 time to fit residues: 4.8057 Evaluate side-chains 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 340 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 15 optimal weight: 0.0050 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 0.0670 chunk 14 optimal weight: 0.7980 overall best weight: 0.4532 ------------------------------------------------------------------------------- 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 = 0.4452 r_free = 0.4452 target = 0.198130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.165017 restraints weight = 5834.015| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.52 r_work: 0.3974 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6642 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4007 Z= 0.164 Angle : 0.580 5.602 5760 Z= 0.345 Chirality : 0.040 0.214 667 Planarity : 0.006 0.040 472 Dihedral : 25.047 179.264 1321 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % Rotamer: Outliers : 2.14 % Allowed : 16.24 % Favored : 81.62 % 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 are not related in a simple way. whole: -1.46 (0.53), residues: 274 helix: -0.59 (0.51), residues: 105 sheet: 0.16 (1.02), residues: 27 loop : -1.47 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.009 0.002 TYR A 317 PHE 0.005 0.001 PHE A 350 TRP 0.014 0.002 TRP A 249 HIS 0.002 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 ( 4007) covalent geometry : angle 0.58012 / 0.34 ( 5760) hydrogen bonds : bond 0.04438 / 3.04 ( 126) hydrogen bonds : angle 4.37616 / 3.09 ( 301) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.102 Fit side-chains REVERT: A 70 ARG cc_start: 0.6884 (ptt180) cc_final: 0.6650 (ptt180) REVERT: A 74 GLU cc_start: 0.6469 (tm-30) cc_final: 0.5837 (tm-30) REVERT: A 323 LYS cc_start: 0.7685 (tppt) cc_final: 0.7427 (mmmt) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 0.0726 time to fit residues: 3.0403 Evaluate side-chains 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.198274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.165363 restraints weight = 5905.952| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.52 r_work: 0.3976 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4007 Z= 0.167 Angle : 0.579 5.536 5760 Z= 0.344 Chirality : 0.040 0.213 667 Planarity : 0.006 0.038 472 Dihedral : 25.005 179.160 1321 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.66 % Favored : 91.97 % Rotamer: Outliers : 1.28 % Allowed : 18.38 % Favored : 80.34 % 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: -1.43 (0.52), residues: 274 helix: -0.50 (0.51), residues: 105 sheet: 0.13 (1.02), residues: 27 loop : -1.50 (0.56), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.012 0.002 TYR A 317 PHE 0.005 0.002 PHE A 350 TRP 0.014 0.002 TRP A 249 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 ( 4007) covalent geometry : angle 0.57882 / 0.34 ( 5760) hydrogen bonds : bond 0.04377 / 2.99 ( 126) hydrogen bonds : angle 4.37238 / 3.09 ( 301) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.105 Fit side-chains REVERT: A 70 ARG cc_start: 0.6913 (ptt180) cc_final: 0.6670 (ptt180) REVERT: A 74 GLU cc_start: 0.6509 (tm-30) cc_final: 0.5825 (tm-30) REVERT: A 323 LYS cc_start: 0.7715 (tppt) cc_final: 0.7400 (mmmt) outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.0854 time to fit residues: 3.3014 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.198385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.165847 restraints weight = 5965.029| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.51 r_work: 0.3981 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4007 Z= 0.161 Angle : 0.572 5.663 5760 Z= 0.340 Chirality : 0.040 0.212 667 Planarity : 0.006 0.039 472 Dihedral : 25.003 179.105 1321 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.03 % Favored : 91.61 % Rotamer: Outliers : 2.14 % Allowed : 18.38 % Favored : 79.49 % 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: -1.40 (0.53), residues: 274 helix: -0.63 (0.50), residues: 111 sheet: 0.20 (1.04), residues: 27 loop : -1.37 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.010 0.002 TYR A 317 PHE 0.006 0.001 PHE A 350 TRP 0.013 0.002 TRP A 249 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 ( 4007) covalent geometry : angle 0.57192 / 0.34 ( 5760) hydrogen bonds : bond 0.04108 / 2.81 ( 126) hydrogen bonds : angle 4.32428 / 3.06 ( 301) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.6891 (ptt180) cc_final: 0.6656 (ptt180) REVERT: A 74 GLU cc_start: 0.6508 (tm-30) cc_final: 0.5825 (tm-30) REVERT: A 323 LYS cc_start: 0.7736 (tppt) cc_final: 0.7387 (mmmt) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.0853 time to fit residues: 3.4846 Evaluate side-chains 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 11 optimal weight: 0.0030 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.0670 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.3328 ------------------------------------------------------------------------------- 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 = 0.4472 r_free = 0.4472 target = 0.199386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166629 restraints weight = 5879.094| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.56 r_work: 0.3988 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4007 Z= 0.145 Angle : 0.558 5.500 5760 Z= 0.333 Chirality : 0.039 0.217 667 Planarity : 0.006 0.040 472 Dihedral : 24.964 179.568 1321 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.93 % Favored : 92.70 % Rotamer: Outliers : 2.14 % Allowed : 18.80 % Favored : 79.06 % 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: -1.18 (0.53), residues: 274 helix: -0.29 (0.52), residues: 105 sheet: 0.23 (1.04), residues: 27 loop : -1.35 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.007 0.001 TYR A 317 PHE 0.005 0.001 PHE A 350 TRP 0.014 0.002 TRP A 249 HIS 0.001 0.000 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 4007) covalent geometry : angle 0.55807 / 0.33 ( 5760) hydrogen bonds : bond 0.03777 / 2.59 ( 126) hydrogen bonds : angle 4.20753 / 2.98 ( 301) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.065 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.6872 (ptt180) cc_final: 0.6641 (ptt180) REVERT: A 74 GLU cc_start: 0.6468 (tm-30) cc_final: 0.5773 (tm-30) REVERT: A 323 LYS cc_start: 0.7744 (tppt) cc_final: 0.7360 (mmmt) outliers start: 5 outliers final: 5 residues processed: 33 average time/residue: 0.0682 time to fit residues: 2.6894 Evaluate side-chains 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.197303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.164357 restraints weight = 5915.191| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.59 r_work: 0.3959 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4007 Z= 0.204 Angle : 0.614 5.902 5760 Z= 0.358 Chirality : 0.042 0.235 667 Planarity : 0.006 0.038 472 Dihedral : 25.066 178.185 1321 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % Rotamer: Outliers : 2.14 % Allowed : 18.38 % Favored : 79.49 % 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: -1.70 (0.52), residues: 274 helix: -0.80 (0.49), residues: 111 sheet: -0.63 (0.87), residues: 33 loop : -1.48 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 314 TYR 0.013 0.002 TYR A 317 PHE 0.008 0.002 PHE A 350 TRP 0.012 0.002 TRP A 264 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 ( 4007) covalent geometry : angle 0.61421 / 0.36 ( 5760) hydrogen bonds : bond 0.04765 / 3.27 ( 126) hydrogen bonds : angle 4.49865 / 3.17 ( 301) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 548 Ramachandran restraints generated. 274 Oldfield, 0 Emsley, 274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: A 323 LYS cc_start: 0.7800 (tppt) cc_final: 0.7328 (mmmt) outliers start: 5 outliers final: 5 residues processed: 36 average time/residue: 0.0878 time to fit residues: 3.7179 Evaluate side-chains 40 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 22 optimal weight: 0.0970 chunk 17 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.0020 chunk 16 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 0.0370 chunk 21 optimal weight: 0.5980 overall best weight: 0.2064 ------------------------------------------------------------------------------- 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 = 0.4478 r_free = 0.4478 target = 0.199928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.167335 restraints weight = 5939.321| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.58 r_work: 0.3994 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4007 Z= 0.133 Angle : 0.551 5.444 5760 Z= 0.330 Chirality : 0.038 0.215 667 Planarity : 0.006 0.042 472 Dihedral : 25.004 179.376 1321 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.93 % Favored : 92.70 % Rotamer: Outliers : 1.71 % Allowed : 18.80 % Favored : 79.49 % 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: -1.13 (0.53), residues: 274 helix: -0.21 (0.52), residues: 105 sheet: 0.10 (1.06), residues: 27 loop : -1.32 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 260 TYR 0.009 0.001 TYR A 265 PHE 0.005 0.001 PHE A 137 TRP 0.016 0.002 TRP A 249 HIS 0.001 0.000 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 ( 4007) covalent geometry : angle 0.55093 / 0.33 ( 5760) hydrogen bonds : bond 0.03430 / 2.33 ( 126) hydrogen bonds : angle 4.16858 / 2.96 ( 301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1320.49 seconds wall clock time: 23 minutes 14.94 seconds (1394.94 seconds total)