Starting phenix.real_space_refine on Tue Aug 4 14:04:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws5_37798/08_2026/8ws5_37798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws5_37798/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ws5_37798/08_2026/8ws5_37798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws5_37798/08_2026/8ws5_37798.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws5_37798/08_2026/8ws5_37798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws5_37798/08_2026/8ws5_37798.cif" } 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-2.2rc3-6140/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: 1.01, per 1000 atoms: 0.27 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: 0.38 Conformation dependent library (CDL) restraints added in 63.8 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: 0.31 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: 0.35 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: 5425 1.98 - 3.96: 301 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=" O5' U B -9 " pdb=" C5' U B -9 " pdb=" C4' U B -9 " ideal model delta sigma weight residual 109.40 112.72 -3.32 8.00e-01 1.56e+00 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 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+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: 457 0.051 - 0.101: 131 0.101 - 0.152: 67 0.152 - 0.203: 8 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: 3.840 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.410 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.270 ------------------------------------------------------------------------------- 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= 0.438 Angle : 0.930 9.893 5760 Z= 0.692 Chirality : 0.060 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 0.00556 / 0.44 ( 4007) covalent geometry : angle 0.93031 / 0.69 ( 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 : 0.064 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.0674 time to fit residues: 2.6788 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 : 0.101 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4473 r_free = 0.4473 target = 0.199159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.167006 restraints weight = 6033.634| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.52 r_work: 0.4000 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4007 Z= 0.207 Angle : 0.676 5.577 5760 Z= 0.392 Chirality : 0.045 0.199 667 Planarity : 0.007 0.044 472 Dihedral : 25.055 178.048 1324 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % 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: -1.75 (0.51), residues: 274 helix: -0.97 (0.49), residues: 105 sheet: -0.54 (0.98), residues: 28 loop : -1.38 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 260 TYR 0.015 0.002 TYR A 317 PHE 0.008 0.002 PHE A 352 TRP 0.018 0.002 TRP A 249 HIS 0.004 0.001 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.21 ( 4007) covalent geometry : angle 0.67577 / 0.39 ( 5760) hydrogen bonds : bond 0.07468 / 5.22 ( 126) hydrogen bonds : angle 4.93007 / 3.47 ( 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 32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.089 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.0834 time to fit residues: 3.0463 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 : 0.102 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 17 optimal weight: 0.2980 chunk 15 optimal weight: 0.0670 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.199644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166925 restraints weight = 5912.341| |-----------------------------------------------------------------------------| r_work (start): 0.4109 rms_B_bonded: 1.58 r_work: 0.3993 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.1340 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= 0.173 Angle : 0.607 5.629 5760 Z= 0.361 Chirality : 0.042 0.204 667 Planarity : 0.006 0.040 472 Dihedral : 25.064 178.457 1321 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.30 % Favored : 92.34 % 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: -1.55 (0.52), residues: 274 helix: -0.85 (0.49), residues: 105 sheet: -0.22 (1.00), residues: 28 loop : -1.28 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 260 TYR 0.012 0.002 TYR A 317 PHE 0.006 0.002 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 0.00319 / 0.17 ( 4007) covalent geometry : angle 0.60725 / 0.36 ( 5760) hydrogen bonds : bond 0.06022 / 4.12 ( 126) hydrogen bonds : angle 4.56301 / 3.22 ( 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 : 0.099 Fit side-chains REVERT: A 74 GLU cc_start: 0.6219 (tm-30) cc_final: 0.5750 (tm-30) outliers start: 4 outliers final: 3 residues processed: 34 average time/residue: 0.0929 time to fit residues: 3.8025 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 : 0.099 ------------------------------------------------------------------------------- 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: 0.3980 chunk 13 optimal weight: 0.4980 chunk 31 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4464 r_free = 0.4464 target = 0.198583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.165702 restraints weight = 5922.158| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 1.57 r_work: 0.3975 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.1658 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= 0.203 Angle : 0.635 5.559 5760 Z= 0.372 Chirality : 0.042 0.212 667 Planarity : 0.006 0.040 472 Dihedral : 25.051 178.207 1321 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.12 % Favored : 90.51 % Rotamer: Outliers : 2.14 % Allowed : 13.68 % Favored : 84.19 % 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: -1.58 (0.52), residues: 274 helix: -0.79 (0.51), residues: 105 sheet: -0.22 (0.99), residues: 28 loop : -1.39 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 150 TYR 0.015 0.002 TYR A 317 PHE 0.006 0.002 PHE A 219 TRP 0.014 0.002 TRP A 112 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 ( 4007) covalent geometry : angle 0.63535 / 0.37 ( 5760) hydrogen bonds : bond 0.05873 / 4.01 ( 126) hydrogen bonds : angle 4.65486 / 3.27 ( 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: 5 poor density : 32 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6336 (tm-30) cc_final: 0.5749 (tm-30) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.0544 time to fit residues: 2.2479 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 : 0.054 ------------------------------------------------------------------------------- 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: 0.9980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4440 r_free = 0.4440 target = 0.196722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.163912 restraints weight = 5865.981| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 1.51 r_work: 0.3953 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4007 Z= 0.209 Angle : 0.654 5.927 5760 Z= 0.378 Chirality : 0.043 0.236 667 Planarity : 0.007 0.040 472 Dihedral : 25.110 177.221 1321 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.12 % Favored : 90.51 % 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: -1.88 (0.52), residues: 274 helix: -0.93 (0.50), residues: 105 sheet: -0.55 (0.89), residues: 33 loop : -1.64 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 150 TYR 0.021 0.002 TYR A 317 PHE 0.009 0.002 PHE A 334 TRP 0.018 0.002 TRP A 264 HIS 0.005 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 ( 4007) covalent geometry : angle 0.65390 / 0.38 ( 5760) hydrogen bonds : bond 0.05567 / 3.79 ( 126) hydrogen bonds : angle 4.78508 / 3.38 ( 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 40 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6502 (tm-30) cc_final: 0.5802 (tm-30) REVERT: A 323 LYS cc_start: 0.7792 (tppp) cc_final: 0.7456 (mmmt) outliers start: 5 outliers final: 5 residues processed: 36 average time/residue: 0.0562 time to fit residues: 2.4517 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 : 0.057 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 15 optimal weight: 0.0020 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.0050 chunk 6 optimal weight: 0.0980 chunk 14 optimal weight: 0.2980 overall best weight: 0.2602 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.199448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.166574 restraints weight = 5888.043| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 1.59 r_work: 0.3985 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3840 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4007 Z= 0.139 Angle : 0.568 5.513 5760 Z= 0.340 Chirality : 0.039 0.206 667 Planarity : 0.006 0.040 472 Dihedral : 24.958 178.468 1321 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.93 % Favored : 92.70 % 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: -1.46 (0.53), residues: 274 helix: -0.51 (0.51), residues: 105 sheet: -0.44 (0.89), residues: 33 loop : -1.43 (0.59), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.006 0.001 TYR A 245 PHE 0.005 0.001 PHE A 350 TRP 0.015 0.002 TRP A 112 HIS 0.001 0.001 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 ( 4007) covalent geometry : angle 0.56825 / 0.34 ( 5760) hydrogen bonds : bond 0.03914 / 2.68 ( 126) hydrogen bonds : angle 4.26890 / 3.03 ( 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 : 0.107 Fit side-chains REVERT: A 74 GLU cc_start: 0.6321 (tm-30) cc_final: 0.5996 (tm-30) REVERT: A 292 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7086 (mt-10) REVERT: A 323 LYS cc_start: 0.7815 (tppp) cc_final: 0.7516 (mmmt) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.1199 time to fit residues: 4.7686 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 : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 248 GLU 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: 3.9990 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.0030 chunk 19 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 = 0.4454 r_free = 0.4454 target = 0.198036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.165127 restraints weight = 5915.157| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.57 r_work: 0.3964 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4007 Z= 0.174 Angle : 0.590 5.618 5760 Z= 0.348 Chirality : 0.040 0.216 667 Planarity : 0.006 0.038 472 Dihedral : 24.924 178.658 1321 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.76 % Favored : 90.88 % Rotamer: Outliers : 2.56 % Allowed : 17.95 % 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: -1.45 (0.52), residues: 274 helix: -0.55 (0.51), residues: 105 sheet: 0.14 (1.02), residues: 27 loop : -1.49 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.012 0.002 TYR A 317 PHE 0.007 0.002 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 0.00332 / 0.17 ( 4007) covalent geometry : angle 0.59040 / 0.35 ( 5760) hydrogen bonds : bond 0.04504 / 3.07 ( 126) hydrogen bonds : angle 4.42755 / 3.13 ( 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 42 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.100 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6012 (tm-30) REVERT: A 323 LYS cc_start: 0.7876 (tppp) cc_final: 0.7506 (mmmt) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 0.1061 time to fit residues: 4.7403 Evaluate side-chains 41 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.070 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 351 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 20 optimal weight: 0.0170 chunk 28 optimal weight: 20.0000 chunk 22 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 overall best weight: 0.1414 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.200686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.168237 restraints weight = 6026.517| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.54 r_work: 0.4012 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4007 Z= 0.127 Angle : 0.549 5.550 5760 Z= 0.330 Chirality : 0.038 0.202 667 Planarity : 0.006 0.037 472 Dihedral : 24.863 179.048 1321 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.93 % Favored : 92.70 % Rotamer: Outliers : 2.99 % Allowed : 18.38 % Favored : 78.63 % 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: -1.00 (0.54), residues: 274 helix: -0.25 (0.52), residues: 105 sheet: 0.46 (1.06), residues: 27 loop : -1.18 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 260 TYR 0.010 0.001 TYR A 265 PHE 0.007 0.001 PHE A 334 TRP 0.014 0.002 TRP A 112 HIS 0.001 0.000 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.13 ( 4007) covalent geometry : angle 0.54888 / 0.33 ( 5760) hydrogen bonds : bond 0.03426 / 2.33 ( 126) hydrogen bonds : angle 4.08776 / 2.91 ( 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 37 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.098 Fit side-chains REVERT: A 74 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.6099 (tm-30) REVERT: A 323 LYS cc_start: 0.7821 (tppp) cc_final: 0.7462 (mmmt) outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.0960 time to fit residues: 3.6879 Evaluate side-chains 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLU 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 326 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 11 optimal weight: 0.0020 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.0370 chunk 22 optimal weight: 0.0770 chunk 13 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.2224 ------------------------------------------------------------------------------- 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 = 0.4487 r_free = 0.4487 target = 0.200598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.167938 restraints weight = 5938.062| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.58 r_work: 0.4008 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3870 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2650 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= 0.132 Angle : 0.543 5.657 5760 Z= 0.326 Chirality : 0.038 0.206 667 Planarity : 0.006 0.034 472 Dihedral : 24.792 179.922 1321 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.66 % Favored : 91.97 % Rotamer: Outliers : 2.56 % Allowed : 18.38 % 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: -0.69 (0.54), residues: 274 helix: 0.07 (0.54), residues: 99 sheet: 0.46 (1.07), residues: 27 loop : -0.97 (0.57), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 260 TYR 0.005 0.001 TYR A 140 PHE 0.005 0.001 PHE A 219 TRP 0.012 0.002 TRP A 249 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 ( 4007) covalent geometry : angle 0.54276 / 0.33 ( 5760) hydrogen bonds : bond 0.03444 / 2.34 ( 126) hydrogen bonds : angle 4.05627 / 2.89 ( 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 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.6063 (tm-30) REVERT: A 323 LYS cc_start: 0.7819 (tppp) cc_final: 0.7424 (mmmt) outliers start: 6 outliers final: 4 residues processed: 30 average time/residue: 0.0791 time to fit residues: 2.8711 Evaluate side-chains 34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 248 GLU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4464 r_free = 0.4464 target = 0.198748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165676 restraints weight = 5985.261| |-----------------------------------------------------------------------------| r_work (start): 0.4085 rms_B_bonded: 1.58 r_work: 0.3972 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4007 Z= 0.177 Angle : 0.594 5.437 5760 Z= 0.347 Chirality : 0.040 0.232 667 Planarity : 0.006 0.039 472 Dihedral : 24.860 178.522 1321 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.66 % Favored : 91.97 % Rotamer: Outliers : 2.56 % Allowed : 18.80 % Favored : 78.63 % 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: -1.23 (0.53), residues: 274 helix: -0.41 (0.51), residues: 105 sheet: 0.10 (1.03), residues: 27 loop : -1.28 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.010 0.002 TYR A 317 PHE 0.006 0.002 PHE A 350 TRP 0.012 0.002 TRP A 264 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 ( 4007) covalent geometry : angle 0.59385 / 0.35 ( 5760) hydrogen bonds : bond 0.04237 / 2.88 ( 126) hydrogen bonds : angle 4.30084 / 3.04 ( 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 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.063 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.6101 (tm-30) REVERT: A 323 LYS cc_start: 0.7887 (tppp) cc_final: 0.7406 (mmmt) outliers start: 6 outliers final: 5 residues processed: 32 average time/residue: 0.0734 time to fit residues: 2.7750 Evaluate side-chains 38 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS Chi-restraints excluded: chain A residue 74 GLU 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 326 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 22 optimal weight: 0.0870 chunk 17 optimal weight: 0.0170 chunk 19 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.4474 r_free = 0.4474 target = 0.199536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.166517 restraints weight = 5966.167| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.58 r_work: 0.3986 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4007 Z= 0.146 Angle : 0.562 5.619 5760 Z= 0.334 Chirality : 0.038 0.220 667 Planarity : 0.006 0.035 472 Dihedral : 24.851 178.330 1321 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.66 % Favored : 91.97 % Rotamer: Outliers : 2.14 % Allowed : 19.66 % Favored : 78.21 % 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: -0.31 (0.51), residues: 105 sheet: 0.12 (1.05), residues: 27 loop : -1.24 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 260 TYR 0.007 0.001 TYR A 317 PHE 0.005 0.001 PHE A 350 TRP 0.012 0.002 TRP A 249 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 ( 4007) covalent geometry : angle 0.56169 / 0.33 ( 5760) hydrogen bonds : bond 0.03647 / 2.47 ( 126) hydrogen bonds : angle 4.17177 / 2.96 ( 301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1239.02 seconds wall clock time: 21 minutes 48.95 seconds (1308.95 seconds total)