Starting phenix.real_space_refine on Fri Aug 22 14:02:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws5_37798/08_2025/8ws5_37798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws5_37798/08_2025/8ws5_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_2025/8ws5_37798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws5_37798/08_2025/8ws5_37798.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws5_37798/08_2025/8ws5_37798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws5_37798/08_2025/8ws5_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-2.0-5787/lib/python3.9/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: 1.20, per 1000 atoms: 0.32 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: 0.52 Conformation dependent library (CDL) restraints added in 128.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.55 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: 0.59 Time building geometry restraints manager: 0.56 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=" 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=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.12e-02 7.97e+03 6.74e+00 bond pdb=" C ILE A 294 " pdb=" N PRO A 295 " ideal model delta sigma weight residual 1.333 1.364 -0.031 1.20e-02 6.94e+03 6.62e+00 bond pdb=" O3' DC C -11 " pdb=" P DA C -10 " ideal model delta sigma weight residual 1.607 1.638 -0.031 1.50e-02 4.44e+03 4.31e+00 ... (remaining 4002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 5522 1.98 - 3.96: 204 3.96 - 5.94: 30 5.94 - 7.91: 2 7.91 - 9.89: 2 Bond angle restraints: 5760 Sorted by residual: angle pdb=" C ILE A 296 " pdb=" N ILE A 297 " pdb=" CA ILE A 297 " ideal model delta sigma weight residual 123.10 117.81 5.29 1.36e+00 5.41e-01 1.51e+01 angle pdb=" C ILE A 132 " pdb=" CA ILE A 132 " pdb=" CB ILE A 132 " ideal model delta sigma weight residual 112.04 107.14 4.90 1.31e+00 5.83e-01 1.40e+01 angle pdb=" N ARG A 272 " pdb=" CA ARG A 272 " pdb=" C ARG A 272 " ideal model delta sigma weight residual 108.23 114.50 -6.27 1.72e+00 3.38e-01 1.33e+01 angle pdb=" C ILE A 294 " pdb=" N PRO A 295 " pdb=" CA PRO A 295 " ideal model delta sigma weight residual 120.25 115.49 4.76 1.35e+00 5.49e-01 1.24e+01 angle pdb=" NE ARG A 165 " pdb=" CZ ARG A 165 " pdb=" NH1 ARG A 165 " ideal model delta sigma weight residual 121.50 118.16 3.34 1.00e+00 1.00e+00 1.12e+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: 513 0.051 - 0.101: 104 0.101 - 0.152: 36 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: 5.640 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 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 : 0.005 0.041 4007 Z= 0.277 Angle : 0.848 9.893 5760 Z= 0.502 Chirality : 0.053 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 aren 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 covalent geometry : bond 0.00487 ( 4007) covalent geometry : angle 0.84820 ( 5760) hydrogen bonds : bond 0.17456 ( 126) hydrogen bonds : angle 7.61178 ( 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 : 0.086 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.0690 time to fit residues: 2.6877 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 : 0.093 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4460 r_free = 0.4460 target = 0.198163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165694 restraints weight = 5998.240| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 1.56 r_work: 0.3978 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4007 Z= 0.232 Angle : 0.682 5.649 5760 Z= 0.366 Chirality : 0.041 0.213 667 Planarity : 0.006 0.039 472 Dihedral : 25.233 178.574 1324 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % Rotamer: Outliers : 1.71 % Allowed : 9.83 % 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 aren not related in a simple way. whole: -1.69 (0.52), residues: 274 helix: -0.86 (0.51), residues: 105 sheet: -0.56 (0.98), residues: 28 loop : -1.39 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 260 TYR 0.020 0.002 TYR A 317 PHE 0.007 0.002 PHE A 219 TRP 0.021 0.002 TRP A 249 HIS 0.002 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 4007) covalent geometry : angle 0.68241 ( 5760) hydrogen bonds : bond 0.06275 ( 126) hydrogen bonds : angle 4.77265 ( 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 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 323 LYS cc_start: 0.7815 (tppt) cc_final: 0.7337 (tppt) outliers start: 4 outliers final: 2 residues processed: 32 average time/residue: 0.0893 time to fit residues: 3.3606 Evaluate side-chains 30 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS 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: 0.8980 chunk 33 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.0070 chunk 19 optimal weight: 0.2980 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 15 optimal weight: 0.0980 overall best weight: 0.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4487 r_free = 0.4487 target = 0.200539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.168077 restraints weight = 5924.254| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.57 r_work: 0.4015 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.1537 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= 0.142 Angle : 0.601 5.512 5760 Z= 0.326 Chirality : 0.038 0.202 667 Planarity : 0.007 0.058 472 Dihedral : 25.111 179.235 1321 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.57 % Favored : 93.07 % Rotamer: Outliers : 0.85 % Allowed : 11.11 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.53), residues: 274 helix: -0.64 (0.50), residues: 105 sheet: -0.67 (0.91), residues: 33 loop : -1.10 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 134 TYR 0.007 0.001 TYR A 245 PHE 0.006 0.001 PHE A 219 TRP 0.015 0.002 TRP A 249 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4007) covalent geometry : angle 0.60119 ( 5760) hydrogen bonds : bond 0.04629 ( 126) hydrogen bonds : angle 4.25097 ( 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 32 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.104 Fit side-chains REVERT: A 74 GLU cc_start: 0.6126 (tm-30) cc_final: 0.5656 (tm-30) REVERT: A 323 LYS cc_start: 0.7803 (tppt) cc_final: 0.7287 (tppt) outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.1031 time to fit residues: 3.9037 Evaluate side-chains 31 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 13 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.0030 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4457 r_free = 0.4457 target = 0.198135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165090 restraints weight = 5895.137| |-----------------------------------------------------------------------------| r_work (start): 0.4083 rms_B_bonded: 1.54 r_work: 0.3975 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3829 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4007 Z= 0.190 Angle : 0.631 5.669 5760 Z= 0.338 Chirality : 0.039 0.201 667 Planarity : 0.007 0.076 472 Dihedral : 25.066 179.194 1321 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % Rotamer: Outliers : 1.28 % Allowed : 15.38 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.53), residues: 274 helix: -0.81 (0.50), residues: 105 sheet: -0.58 (0.90), residues: 33 loop : -1.21 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 134 TYR 0.012 0.002 TYR A 317 PHE 0.007 0.002 PHE A 137 TRP 0.013 0.002 TRP A 264 HIS 0.014 0.002 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 4007) covalent geometry : angle 0.63076 ( 5760) hydrogen bonds : bond 0.04863 ( 126) hydrogen bonds : angle 4.40572 ( 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 39 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.107 Fit side-chains REVERT: A 74 GLU cc_start: 0.6367 (tm-30) cc_final: 0.5888 (tm-30) REVERT: A 323 LYS cc_start: 0.7843 (tppt) cc_final: 0.7531 (mmmt) outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.1310 time to fit residues: 5.7221 Evaluate side-chains 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 340 VAL 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: 0.5980 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 15 optimal weight: 0.0370 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.198141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.165339 restraints weight = 5857.837| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.52 r_work: 0.3973 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.2239 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= 0.172 Angle : 0.620 5.522 5760 Z= 0.333 Chirality : 0.038 0.210 667 Planarity : 0.006 0.036 472 Dihedral : 25.009 179.471 1321 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.66 % Favored : 91.97 % Rotamer: Outliers : 2.56 % Allowed : 14.96 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.52), residues: 274 helix: -0.81 (0.49), residues: 111 sheet: -0.43 (0.90), residues: 33 loop : -1.38 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 134 TYR 0.014 0.002 TYR A 265 PHE 0.005 0.001 PHE A 137 TRP 0.013 0.002 TRP A 264 HIS 0.002 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4007) covalent geometry : angle 0.61975 ( 5760) hydrogen bonds : bond 0.04050 ( 126) hydrogen bonds : angle 4.31524 ( 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: 6 poor density : 34 time to evaluate : 0.099 Fit side-chains REVERT: A 74 GLU cc_start: 0.6452 (tm-30) cc_final: 0.5930 (tm-30) REVERT: A 323 LYS cc_start: 0.7811 (tppt) cc_final: 0.7397 (mmmt) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.1070 time to fit residues: 4.6389 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 : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 0.0370 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.0470 chunk 6 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 overall best weight: 0.1756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.200552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.167876 restraints weight = 5887.383| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 1.50 r_work: 0.4009 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3876 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4007 Z= 0.128 Angle : 0.570 5.598 5760 Z= 0.311 Chirality : 0.036 0.204 667 Planarity : 0.006 0.034 472 Dihedral : 24.826 179.096 1321 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.43 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 aren not related in a simple way. whole: -0.84 (0.55), residues: 274 helix: -0.00 (0.54), residues: 99 sheet: -0.27 (0.92), residues: 33 loop : -0.98 (0.60), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 134 TYR 0.004 0.001 TYR A 245 PHE 0.004 0.001 PHE A 137 TRP 0.012 0.002 TRP A 112 HIS 0.001 0.000 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4007) covalent geometry : angle 0.57023 ( 5760) hydrogen bonds : bond 0.03209 ( 126) hydrogen bonds : angle 4.00474 ( 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 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.074 Fit side-chains REVERT: A 70 ARG cc_start: 0.6786 (ptt180) cc_final: 0.6542 (ptt180) REVERT: A 74 GLU cc_start: 0.6345 (tm-30) cc_final: 0.5774 (tm-30) REVERT: A 323 LYS cc_start: 0.7828 (tppt) cc_final: 0.7426 (mmmt) outliers start: 5 outliers final: 4 residues processed: 31 average time/residue: 0.0985 time to fit residues: 3.6135 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 : 0.078 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 0.5980 chunk 13 optimal weight: 0.0670 chunk 5 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.199382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.166586 restraints weight = 5927.368| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 1.52 r_work: 0.3987 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4007 Z= 0.149 Angle : 0.584 5.533 5760 Z= 0.316 Chirality : 0.037 0.200 667 Planarity : 0.006 0.034 472 Dihedral : 24.781 179.866 1321 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % Rotamer: Outliers : 1.71 % Allowed : 17.52 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.54), residues: 274 helix: -0.22 (0.52), residues: 105 sheet: 0.38 (1.06), residues: 27 loop : -1.10 (0.59), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.008 0.001 TYR A 140 PHE 0.007 0.001 PHE A 137 TRP 0.010 0.002 TRP A 249 HIS 0.003 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4007) covalent geometry : angle 0.58449 ( 5760) hydrogen bonds : bond 0.03519 ( 126) hydrogen bonds : angle 4.08805 ( 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 34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 74 GLU cc_start: 0.6436 (tm-30) cc_final: 0.5886 (tm-30) REVERT: A 292 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7063 (mt-10) REVERT: A 323 LYS cc_start: 0.7851 (tppt) cc_final: 0.7385 (mmmt) outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.0889 time to fit residues: 3.2435 Evaluate side-chains 34 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.197753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.164849 restraints weight = 5936.367| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.57 r_work: 0.3965 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.2771 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= 0.184 Angle : 0.618 5.531 5760 Z= 0.333 Chirality : 0.038 0.225 667 Planarity : 0.006 0.037 472 Dihedral : 24.902 178.457 1321 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.03 % Favored : 91.61 % 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 aren not related in a simple way. whole: -1.24 (0.53), residues: 274 helix: -0.48 (0.50), residues: 105 sheet: 0.12 (1.03), residues: 27 loop : -1.24 (0.58), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 134 TYR 0.011 0.002 TYR A 317 PHE 0.007 0.002 PHE A 137 TRP 0.009 0.002 TRP A 264 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 4007) covalent geometry : angle 0.61799 ( 5760) hydrogen bonds : bond 0.03967 ( 126) hydrogen bonds : angle 4.32788 ( 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: 4 poor density : 33 time to evaluate : 0.103 Fit side-chains REVERT: A 323 LYS cc_start: 0.7906 (tppt) cc_final: 0.7510 (mmmt) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.1038 time to fit residues: 4.0804 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0370 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 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 = 0.4454 r_free = 0.4454 target = 0.197975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165546 restraints weight = 5878.840| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.51 r_work: 0.3968 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4007 Z= 0.192 Angle : 0.627 5.478 5760 Z= 0.337 Chirality : 0.039 0.230 667 Planarity : 0.006 0.036 472 Dihedral : 24.914 178.403 1321 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.03 % Favored : 91.61 % Rotamer: Outliers : 1.71 % Allowed : 19.66 % 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 aren not related in a simple way. whole: -1.56 (0.52), residues: 274 helix: -0.77 (0.48), residues: 111 sheet: -0.53 (0.90), residues: 33 loop : -1.32 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.012 0.002 TYR A 317 PHE 0.006 0.002 PHE A 137 TRP 0.012 0.002 TRP A 249 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 4007) covalent geometry : angle 0.62735 ( 5760) hydrogen bonds : bond 0.03977 ( 126) hydrogen bonds : angle 4.26495 ( 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 36 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.107 Fit side-chains REVERT: A 74 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6154 (tm-30) REVERT: A 323 LYS cc_start: 0.7914 (tppt) cc_final: 0.7488 (mmmt) outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.0911 time to fit residues: 3.4673 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 : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.0470 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 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 = 0.4447 r_free = 0.4447 target = 0.197230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.164698 restraints weight = 5969.174| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.51 r_work: 0.3961 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4007 Z= 0.209 Angle : 0.641 5.744 5760 Z= 0.345 Chirality : 0.040 0.233 667 Planarity : 0.006 0.040 472 Dihedral : 24.949 177.740 1321 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.39 % Favored : 91.24 % 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 aren not related in a simple way. whole: -1.71 (0.52), residues: 274 helix: -0.82 (0.48), residues: 111 sheet: -0.67 (0.91), residues: 33 loop : -1.46 (0.60), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 314 TYR 0.014 0.002 TYR A 317 PHE 0.007 0.002 PHE A 350 TRP 0.012 0.002 TRP A 249 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 4007) covalent geometry : angle 0.64121 ( 5760) hydrogen bonds : bond 0.04301 ( 126) hydrogen bonds : angle 4.43299 ( 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 35 residues out of total 236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.125 Fit side-chains REVERT: A 323 LYS cc_start: 0.7962 (tppt) cc_final: 0.7494 (mmmt) outliers start: 6 outliers final: 6 residues processed: 30 average time/residue: 0.1114 time to fit residues: 3.9539 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 : 0.131 ------------------------------------------------------------------------------- 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 262 ARG 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: 0.9990 chunk 17 optimal weight: 0.4980 chunk 19 optimal weight: 0.0870 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 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 = 0.4468 r_free = 0.4468 target = 0.199043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.166801 restraints weight = 5960.096| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.52 r_work: 0.3988 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.3156 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= 0.148 Angle : 0.594 5.461 5760 Z= 0.322 Chirality : 0.037 0.209 667 Planarity : 0.006 0.036 472 Dihedral : 24.852 178.721 1321 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.66 % Favored : 91.97 % Rotamer: Outliers : 1.28 % Allowed : 20.09 % 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 aren not related in a simple way. whole: -1.40 (0.53), residues: 274 helix: -0.53 (0.49), residues: 111 sheet: -0.54 (0.93), residues: 33 loop : -1.32 (0.61), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 134 TYR 0.006 0.001 TYR A 245 PHE 0.006 0.001 PHE A 350 TRP 0.014 0.002 TRP A 249 HIS 0.001 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4007) covalent geometry : angle 0.59410 ( 5760) hydrogen bonds : bond 0.03308 ( 126) hydrogen bonds : angle 4.15586 ( 301) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.33 seconds wall clock time: 24 minutes 25.59 seconds (1465.59 seconds total)