Starting phenix.real_space_refine on Wed Sep 17 02:57:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uiu_26553/09_2025/7uiu_26553.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uiu_26553/09_2025/7uiu_26553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uiu_26553/09_2025/7uiu_26553.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uiu_26553/09_2025/7uiu_26553.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uiu_26553/09_2025/7uiu_26553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uiu_26553/09_2025/7uiu_26553.map" } resolution = 2.8 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= -0.007 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 382 2.51 5 N 106 2.21 5 O 116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 607 Number of models: 1 Model: "" Number of chains: 1 Chain: "x" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 607 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 81} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 0.22, per 1000 atoms: 0.36 Number of scatterers: 607 At special positions: 0 Unit cell: (36.55, 62.05, 59.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 116 8.00 N 106 7.00 C 382 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: 0.03 Conformation dependent library (CDL) restraints added in 34.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 158 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 2 sheets defined 44.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.01 Creating SS restraints... Processing helix chain 'x' and resid 269 through 276 Processing helix chain 'x' and resid 279 through 290 removed outlier: 3.512A pdb=" N MET x 290 " --> pdb=" O PHE x 286 " (cutoff:3.500A) Processing helix chain 'x' and resid 302 through 312 Processing helix chain 'x' and resid 322 through 328 removed outlier: 3.623A pdb=" N GLU x 326 " --> pdb=" O ASN x 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 260 through 261 Processing sheet with id=AA2, first strand: chain 'x' and resid 266 through 268 23 hydrogen bonds defined for protein. 69 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.04 Time building geometry restraints manager: 0.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 210 1.34 - 1.45: 51 1.45 - 1.57: 347 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 614 Sorted by residual: bond pdb=" CB VAL x 269 " pdb=" CG1 VAL x 269 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.16e+00 bond pdb=" CB GLN x 302 " pdb=" CG GLN x 302 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CG GLN x 302 " pdb=" CD GLN x 302 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.23e-01 bond pdb=" CB VAL x 283 " pdb=" CG1 VAL x 283 " ideal model delta sigma weight residual 1.521 1.504 0.017 3.30e-02 9.18e+02 2.68e-01 bond pdb=" CA HIS x 248 " pdb=" C HIS x 248 " ideal model delta sigma weight residual 1.525 1.514 0.011 2.10e-02 2.27e+03 2.52e-01 ... (remaining 609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 741 0.86 - 1.72: 71 1.72 - 2.58: 18 2.58 - 3.44: 2 3.44 - 4.30: 2 Bond angle restraints: 834 Sorted by residual: angle pdb=" N GLU x 265 " pdb=" CA GLU x 265 " pdb=" C GLU x 265 " ideal model delta sigma weight residual 113.41 110.70 2.71 1.22e+00 6.72e-01 4.92e+00 angle pdb=" N GLN x 302 " pdb=" CA GLN x 302 " pdb=" C GLN x 302 " ideal model delta sigma weight residual 111.07 112.78 -1.71 1.07e+00 8.73e-01 2.54e+00 angle pdb=" N GLY x 291 " pdb=" CA GLY x 291 " pdb=" C GLY x 291 " ideal model delta sigma weight residual 113.18 116.91 -3.73 2.37e+00 1.78e-01 2.47e+00 angle pdb=" C LYS x 315 " pdb=" CA LYS x 315 " pdb=" CB LYS x 315 " ideal model delta sigma weight residual 109.75 112.24 -2.49 1.65e+00 3.67e-01 2.27e+00 angle pdb=" C ASP x 301 " pdb=" N GLN x 302 " pdb=" CA GLN x 302 " ideal model delta sigma weight residual 120.44 122.35 -1.91 1.30e+00 5.92e-01 2.16e+00 ... (remaining 829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.39: 338 15.39 - 30.79: 27 30.79 - 46.18: 5 46.18 - 61.58: 2 61.58 - 76.97: 1 Dihedral angle restraints: 373 sinusoidal: 131 harmonic: 242 Sorted by residual: dihedral pdb=" CA GLY x 291 " pdb=" C GLY x 291 " pdb=" N SER x 292 " pdb=" CA SER x 292 " ideal model delta harmonic sigma weight residual -180.00 -166.66 -13.34 0 5.00e+00 4.00e-02 7.12e+00 dihedral pdb=" CA MET x 290 " pdb=" C MET x 290 " pdb=" N GLY x 291 " pdb=" CA GLY x 291 " ideal model delta harmonic sigma weight residual 180.00 166.97 13.03 0 5.00e+00 4.00e-02 6.80e+00 dihedral pdb=" CA LEU x 328 " pdb=" C LEU x 328 " pdb=" N ALA x 329 " pdb=" CA ALA x 329 " ideal model delta harmonic sigma weight residual 180.00 167.45 12.55 0 5.00e+00 4.00e-02 6.30e+00 ... (remaining 370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 44 0.021 - 0.043: 29 0.043 - 0.064: 13 0.064 - 0.085: 8 0.085 - 0.106: 9 Chirality restraints: 103 Sorted by residual: chirality pdb=" CA VAL x 278 " pdb=" N VAL x 278 " pdb=" C VAL x 278 " pdb=" CB VAL x 278 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.80e-01 chirality pdb=" CA ILE x 263 " pdb=" N ILE x 263 " pdb=" C ILE x 263 " pdb=" CB ILE x 263 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.10 2.00e-01 2.50e+01 2.50e-01 chirality pdb=" CA VAL x 299 " pdb=" N VAL x 299 " pdb=" C VAL x 299 " pdb=" CB VAL x 299 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.50e-01 ... (remaining 100 not shown) Planarity restraints: 110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY x 264 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.06e+00 pdb=" C GLY x 264 " -0.018 2.00e-02 2.50e+03 pdb=" O GLY x 264 " 0.007 2.00e-02 2.50e+03 pdb=" N GLU x 265 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN x 252 " 0.011 5.00e-02 4.00e+02 1.65e-02 4.37e-01 pdb=" N PRO x 253 " -0.029 5.00e-02 4.00e+02 pdb=" CA PRO x 253 " 0.008 5.00e-02 4.00e+02 pdb=" CD PRO x 253 " 0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN x 252 " 0.003 2.00e-02 2.50e+03 6.55e-03 4.28e-01 pdb=" C ASN x 252 " -0.011 2.00e-02 2.50e+03 pdb=" O ASN x 252 " 0.004 2.00e-02 2.50e+03 pdb=" N PRO x 253 " 0.004 2.00e-02 2.50e+03 ... (remaining 107 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 209 2.86 - 3.37: 598 3.37 - 3.88: 906 3.88 - 4.39: 938 4.39 - 4.90: 1570 Nonbonded interactions: 4221 Sorted by model distance: nonbonded pdb=" OG1 THR x 268 " pdb=" OE2 GLU x 271 " model vdw 2.356 3.040 nonbonded pdb=" N GLU x 326 " pdb=" OE1 GLU x 326 " model vdw 2.466 3.120 nonbonded pdb=" N GLU x 321 " pdb=" OE1 GLU x 321 " model vdw 2.486 3.120 nonbonded pdb=" O ASN x 252 " pdb=" OD1 ASN x 252 " model vdw 2.495 3.040 nonbonded pdb=" O ASN x 322 " pdb=" OE1 GLU x 326 " model vdw 2.569 3.040 ... (remaining 4216 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 6.920 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 1.890 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 614 Z= 0.196 Angle : 0.622 4.300 834 Z= 0.364 Chirality : 0.044 0.106 103 Planarity : 0.003 0.017 110 Dihedral : 13.600 76.970 215 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.09 (0.81), residues: 83 helix: -1.03 (0.71), residues: 41 sheet: -1.98 (1.80), residues: 10 loop : -1.42 (0.93), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG x 259 PHE 0.008 0.002 PHE x 250 HIS 0.002 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 614) covalent geometry : angle 0.62220 ( 834) hydrogen bonds : bond 0.14514 ( 23) hydrogen bonds : angle 5.63313 ( 69) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.014 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.3819 time to fit residues: 9.9905 Evaluate side-chains 23 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1735 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.078810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068241 restraints weight = 1848.779| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.53 r_work: 0.3061 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 614 Z= 0.145 Angle : 0.664 5.648 834 Z= 0.351 Chirality : 0.043 0.101 103 Planarity : 0.003 0.012 110 Dihedral : 4.934 13.350 85 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % 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: -1.67 (0.84), residues: 83 helix: -0.55 (0.77), residues: 42 sheet: -2.36 (1.57), residues: 10 loop : -1.21 (0.95), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG x 259 PHE 0.010 0.002 PHE x 288 HIS 0.001 0.000 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 614) covalent geometry : angle 0.66371 ( 834) hydrogen bonds : bond 0.02802 ( 23) hydrogen bonds : angle 4.54725 ( 69) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.031 Fit side-chains REVERT: x 315 LYS cc_start: 0.8745 (pttm) cc_final: 0.8522 (ptmm) REVERT: x 318 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8274 (pp) outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.3924 time to fit residues: 9.9268 Evaluate side-chains 25 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 1.1483 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.077757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.066953 restraints weight = 1781.377| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 3.31 r_work: 0.3046 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 614 Z= 0.147 Angle : 0.684 6.414 834 Z= 0.360 Chirality : 0.042 0.102 103 Planarity : 0.003 0.014 110 Dihedral : 4.891 12.654 85 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.00 % Allowed : 18.33 % Favored : 76.67 % 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: -1.87 (0.82), residues: 83 helix: -0.72 (0.79), residues: 41 sheet: -2.14 (1.52), residues: 10 loop : -1.43 (0.87), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG x 259 PHE 0.006 0.001 PHE x 288 HIS 0.002 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 614) covalent geometry : angle 0.68434 ( 834) hydrogen bonds : bond 0.03041 ( 23) hydrogen bonds : angle 4.45136 ( 69) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.015 Fit side-chains REVERT: x 315 LYS cc_start: 0.8743 (pttm) cc_final: 0.8522 (ptmm) REVERT: x 318 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8238 (pp) outliers start: 3 outliers final: 1 residues processed: 26 average time/residue: 0.3836 time to fit residues: 10.0400 Evaluate side-chains 27 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 296 ILE Chi-restraints excluded: chain x residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.1985 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.076644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.066324 restraints weight = 1781.981| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 3.39 r_work: 0.3022 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 614 Z= 0.150 Angle : 0.701 6.886 834 Z= 0.368 Chirality : 0.043 0.104 103 Planarity : 0.003 0.012 110 Dihedral : 4.991 12.888 85 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.00 % Allowed : 23.33 % Favored : 71.67 % 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: -1.92 (0.83), residues: 83 helix: -0.74 (0.80), residues: 41 sheet: -2.13 (1.53), residues: 10 loop : -1.49 (0.85), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG x 259 PHE 0.006 0.001 PHE x 288 HIS 0.002 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 614) covalent geometry : angle 0.70080 ( 834) hydrogen bonds : bond 0.02816 ( 23) hydrogen bonds : angle 4.49644 ( 69) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.024 Fit side-chains REVERT: x 251 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: x 318 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8250 (pp) outliers start: 3 outliers final: 0 residues processed: 25 average time/residue: 0.6413 time to fit residues: 16.1598 Evaluate side-chains 26 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 251 GLN Chi-restraints excluded: chain x residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.9485 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.077302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.066375 restraints weight = 1793.008| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.48 r_work: 0.3038 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 614 Z= 0.146 Angle : 0.755 7.350 834 Z= 0.396 Chirality : 0.042 0.107 103 Planarity : 0.003 0.013 110 Dihedral : 4.988 12.180 85 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 5.00 % Allowed : 25.00 % Favored : 70.00 % 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: -2.07 (0.82), residues: 83 helix: -0.85 (0.80), residues: 41 sheet: -1.98 (1.55), residues: 10 loop : -1.67 (0.84), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG x 259 PHE 0.005 0.001 PHE x 288 HIS 0.002 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 614) covalent geometry : angle 0.75539 ( 834) hydrogen bonds : bond 0.02850 ( 23) hydrogen bonds : angle 4.45070 ( 69) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.028 Fit side-chains REVERT: x 251 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: x 318 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8213 (pp) outliers start: 3 outliers final: 0 residues processed: 25 average time/residue: 0.6172 time to fit residues: 15.5622 Evaluate side-chains 25 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 251 GLN Chi-restraints excluded: chain x residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.0733 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 327 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.077115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.066246 restraints weight = 1825.127| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.53 r_work: 0.3031 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 614 Z= 0.149 Angle : 0.739 8.321 834 Z= 0.390 Chirality : 0.043 0.101 103 Planarity : 0.003 0.015 110 Dihedral : 4.973 12.090 85 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.33 % Allowed : 26.67 % Favored : 70.00 % 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: -2.16 (0.82), residues: 83 helix: -1.00 (0.79), residues: 41 sheet: -1.98 (1.50), residues: 10 loop : -1.61 (0.87), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG x 259 PHE 0.011 0.002 PHE x 288 HIS 0.003 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 614) covalent geometry : angle 0.73882 ( 834) hydrogen bonds : bond 0.02879 ( 23) hydrogen bonds : angle 4.48606 ( 69) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.027 Fit side-chains REVERT: x 251 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: x 318 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8149 (pp) outliers start: 2 outliers final: 0 residues processed: 24 average time/residue: 0.6076 time to fit residues: 14.7086 Evaluate side-chains 26 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 251 GLN Chi-restraints excluded: chain x residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** 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 = 0.3364 r_free = 0.3364 target = 0.077160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.066332 restraints weight = 1818.994| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.55 r_work: 0.3027 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 614 Z= 0.162 Angle : 0.823 10.263 834 Z= 0.425 Chirality : 0.042 0.101 103 Planarity : 0.004 0.020 110 Dihedral : 5.042 12.310 85 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.33 % Allowed : 31.67 % Favored : 65.00 % 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: -2.32 (0.82), residues: 83 helix: -1.16 (0.79), residues: 41 sheet: -1.86 (1.53), residues: 10 loop : -1.72 (0.86), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG x 259 PHE 0.002 0.001 PHE x 250 HIS 0.002 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 614) covalent geometry : angle 0.82334 ( 834) hydrogen bonds : bond 0.02980 ( 23) hydrogen bonds : angle 4.54927 ( 69) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.031 Fit side-chains REVERT: x 315 LYS cc_start: 0.8998 (ptmm) cc_final: 0.8480 (pptt) REVERT: x 318 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8156 (pp) outliers start: 2 outliers final: 0 residues processed: 24 average time/residue: 0.6033 time to fit residues: 14.6082 Evaluate side-chains 25 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** 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 = 0.3353 r_free = 0.3353 target = 0.076469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.065817 restraints weight = 1814.059| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.47 r_work: 0.3011 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 614 Z= 0.192 Angle : 0.817 9.494 834 Z= 0.427 Chirality : 0.044 0.100 103 Planarity : 0.003 0.015 110 Dihedral : 5.140 12.355 85 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.67 % Allowed : 36.67 % Favored : 61.67 % 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: -2.45 (0.81), residues: 83 helix: -1.24 (0.78), residues: 41 sheet: -1.94 (1.45), residues: 10 loop : -1.82 (0.88), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG x 259 PHE 0.003 0.001 PHE x 250 HIS 0.003 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 614) covalent geometry : angle 0.81664 ( 834) hydrogen bonds : bond 0.03288 ( 23) hydrogen bonds : angle 4.77413 ( 69) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.027 Fit side-chains REVERT: x 315 LYS cc_start: 0.9014 (ptmm) cc_final: 0.8491 (pptt) REVERT: x 318 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8231 (pp) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.6109 time to fit residues: 14.7647 Evaluate side-chains 24 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** 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 = 0.3379 r_free = 0.3379 target = 0.077638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.066853 restraints weight = 1705.965| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.38 r_work: 0.3042 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 614 Z= 0.156 Angle : 0.777 8.565 834 Z= 0.413 Chirality : 0.042 0.101 103 Planarity : 0.003 0.015 110 Dihedral : 4.733 11.494 85 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.67 % Allowed : 35.00 % Favored : 63.33 % 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: -2.27 (0.84), residues: 83 helix: -1.11 (0.80), residues: 41 sheet: -1.90 (1.54), residues: 10 loop : -1.68 (0.90), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG x 259 PHE 0.001 0.000 PHE x 250 HIS 0.003 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 614) covalent geometry : angle 0.77701 ( 834) hydrogen bonds : bond 0.02891 ( 23) hydrogen bonds : angle 4.54987 ( 69) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.027 Fit side-chains REVERT: x 315 LYS cc_start: 0.9031 (ptmm) cc_final: 0.8505 (pptt) REVERT: x 317 LYS cc_start: 0.8947 (tmmm) cc_final: 0.8725 (tppp) REVERT: x 318 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8168 (pp) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.6586 time to fit residues: 15.2545 Evaluate side-chains 23 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** 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 = 0.3367 r_free = 0.3367 target = 0.077050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.065840 restraints weight = 1877.839| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.65 r_work: 0.3012 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 614 Z= 0.180 Angle : 0.885 11.249 834 Z= 0.441 Chirality : 0.044 0.100 103 Planarity : 0.003 0.012 110 Dihedral : 4.902 12.268 85 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.67 % Allowed : 40.00 % Favored : 58.33 % 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: -2.29 (0.84), residues: 83 helix: -1.22 (0.78), residues: 42 sheet: -1.81 (1.52), residues: 10 loop : -1.58 (0.96), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG x 259 PHE 0.003 0.001 PHE x 250 HIS 0.003 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 614) covalent geometry : angle 0.88485 ( 834) hydrogen bonds : bond 0.03119 ( 23) hydrogen bonds : angle 4.66322 ( 69) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 166 Ramachandran restraints generated. 83 Oldfield, 0 Emsley, 83 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.028 Fit side-chains REVERT: x 318 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8139 (pp) outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.6458 time to fit residues: 14.9595 Evaluate side-chains 23 residues out of total 71 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 overall best weight: 2.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 298 GLN ** 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 = 0.3334 r_free = 0.3334 target = 0.075430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.064184 restraints weight = 1777.293| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.50 r_work: 0.2981 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 614 Z= 0.218 Angle : 0.839 12.008 834 Z= 0.434 Chirality : 0.045 0.101 103 Planarity : 0.004 0.021 110 Dihedral : 5.315 13.744 85 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.67 % Allowed : 38.33 % Favored : 60.00 % 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: -2.70 (0.83), residues: 83 helix: -1.59 (0.76), residues: 42 sheet: -2.13 (1.50), residues: 10 loop : -1.67 (0.97), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG x 259 PHE 0.003 0.001 PHE x 250 HIS 0.003 0.001 HIS x 314 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 614) covalent geometry : angle 0.83950 ( 834) hydrogen bonds : bond 0.03390 ( 23) hydrogen bonds : angle 4.89351 ( 69) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 679.19 seconds wall clock time: 12 minutes 33.85 seconds (753.85 seconds total)