Starting phenix.real_space_refine on Wed Sep 17 02:56:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgs_52166/09_2025/9hgs_52166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgs_52166/09_2025/9hgs_52166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hgs_52166/09_2025/9hgs_52166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgs_52166/09_2025/9hgs_52166.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hgs_52166/09_2025/9hgs_52166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgs_52166/09_2025/9hgs_52166.map" } resolution = 3.0 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= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 329 2.51 5 N 93 2.21 5 O 104 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: 526 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 526 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Time building chain proxies: 0.19, per 1000 atoms: 0.36 Number of scatterers: 526 At special positions: 0 Unit cell: (71.76, 66.24, 19.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 104 8.00 N 93 7.00 C 329 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: 0.02 Conformation dependent library (CDL) restraints added in 14.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 130 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... No hydrogen bonds 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: 0.00 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 - 1.29: 93 1.29 - 1.35: 83 1.35 - 1.42: 16 1.42 - 1.48: 64 1.48 - 1.54: 271 Bond restraints: 527 Sorted by residual: bond pdb=" N VAL C 40 " pdb=" CA VAL C 40 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.15e-02 7.56e+03 9.73e+00 bond pdb=" N VAL C 15 " pdb=" CA VAL C 15 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.73e+00 bond pdb=" N VAL C 49 " pdb=" CA VAL C 49 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.56e+00 bond pdb=" N VAL C 37 " pdb=" CA VAL C 37 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.26e-02 6.30e+03 8.03e+00 bond pdb=" N VAL C 48 " pdb=" CA VAL C 48 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.02e+00 ... (remaining 522 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 533 0.95 - 1.90: 121 1.90 - 2.85: 47 2.85 - 3.80: 5 3.80 - 4.75: 3 Bond angle restraints: 709 Sorted by residual: angle pdb=" N LYS C 45 " pdb=" CA LYS C 45 " pdb=" C LYS C 45 " ideal model delta sigma weight residual 113.88 109.13 4.75 1.23e+00 6.61e-01 1.49e+01 angle pdb=" CA THR C 44 " pdb=" CB THR C 44 " pdb=" OG1 THR C 44 " ideal model delta sigma weight residual 109.60 104.85 4.75 1.50e+00 4.44e-01 1.00e+01 angle pdb=" CA THR C 92 " pdb=" C THR C 92 " pdb=" O THR C 92 " ideal model delta sigma weight residual 121.47 118.08 3.39 1.15e+00 7.56e-01 8.68e+00 angle pdb=" CA LYS C 60 " pdb=" C LYS C 60 " pdb=" O LYS C 60 " ideal model delta sigma weight residual 122.03 118.40 3.63 1.25e+00 6.40e-01 8.44e+00 angle pdb=" CA THR C 92 " pdb=" CB THR C 92 " pdb=" OG1 THR C 92 " ideal model delta sigma weight residual 109.60 105.32 4.28 1.50e+00 4.44e-01 8.13e+00 ... (remaining 704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 272 14.97 - 29.94: 26 29.94 - 44.90: 5 44.90 - 59.87: 6 59.87 - 74.84: 5 Dihedral angle restraints: 314 sinusoidal: 110 harmonic: 204 Sorted by residual: dihedral pdb=" CA ASN C 65 " pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " pdb=" OD1 ASN C 65 " ideal model delta sinusoidal sigma weight residual -90.00 -153.83 63.83 2 2.00e+01 2.50e-03 9.67e+00 dihedral pdb=" N LEU C 100 " pdb=" CA LEU C 100 " pdb=" CB LEU C 100 " pdb=" CG LEU C 100 " ideal model delta sinusoidal sigma weight residual -180.00 -130.24 -49.76 3 1.50e+01 4.44e-03 8.82e+00 dihedral pdb=" CA GLN C 62 " pdb=" CB GLN C 62 " pdb=" CG GLN C 62 " pdb=" CD GLN C 62 " ideal model delta sinusoidal sigma weight residual 180.00 131.09 48.91 3 1.50e+01 4.44e-03 8.70e+00 ... (remaining 311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 45 0.041 - 0.082: 17 0.082 - 0.124: 16 0.124 - 0.165: 10 0.165 - 0.206: 4 Chirality restraints: 92 Sorted by residual: chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL C 40 " pdb=" CA VAL C 40 " pdb=" CG1 VAL C 40 " pdb=" CG2 VAL C 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CA VAL C 16 " pdb=" N VAL C 16 " pdb=" C VAL C 16 " pdb=" CB VAL C 16 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 89 not shown) Planarity restraints: 88 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 57 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.54e+00 pdb=" C GLU C 57 " 0.021 2.00e-02 2.50e+03 pdb=" O GLU C 57 " -0.008 2.00e-02 2.50e+03 pdb=" N LYS C 58 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 14 " 0.096 9.50e-02 1.11e+02 4.30e-02 1.14e+00 pdb=" NE ARG C 14 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG C 14 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 14 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 14 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 89 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.01e+00 pdb=" C ALA C 89 " 0.017 2.00e-02 2.50e+03 pdb=" O ALA C 89 " -0.007 2.00e-02 2.50e+03 pdb=" N ALA C 90 " -0.006 2.00e-02 2.50e+03 ... (remaining 85 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 169 2.85 - 3.36: 349 3.36 - 3.88: 675 3.88 - 4.39: 571 4.39 - 4.90: 908 Nonbonded interactions: 2672 Sorted by model distance: nonbonded pdb=" O GLY C 84 " pdb=" OG SER C 87 " model vdw 2.341 3.040 nonbonded pdb=" NE2 GLN C 79 " pdb=" O ALA C 89 " model vdw 2.551 3.120 nonbonded pdb=" O VAL C 82 " pdb=" CG1 VAL C 82 " model vdw 2.615 3.460 nonbonded pdb=" C THR C 92 " pdb=" OG1 THR C 92 " model vdw 2.647 2.616 nonbonded pdb=" N SER C 87 " pdb=" OG SER C 87 " model vdw 2.658 2.496 ... (remaining 2667 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: 3.110 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: 1.910 Find NCS groups from input model: 0.000 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:5.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 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 : 0.010 0.036 527 Z= 0.689 Angle : 0.989 4.754 709 Z= 0.693 Chirality : 0.078 0.206 92 Planarity : 0.005 0.043 88 Dihedral : 18.247 74.839 184 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 1.89 % Allowed : 26.42 % Favored : 71.70 % 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: -4.52 (0.69), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.52), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG C 14 TYR 0.002 0.001 TYR C 39 PHE 0.004 0.001 PHE C 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00950 ( 527) covalent geometry : angle 0.98890 ( 709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 8 time to evaluate : 0.012 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 8 average time/residue: 0.2518 time to fit residues: 2.0442 Evaluate side-chains 8 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 overall best weight: 1.0650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.183857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.160743 restraints weight = 503.442| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 2.62 r_work: 0.4181 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4067 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 527 Z= 0.105 Angle : 0.431 2.226 709 Z= 0.249 Chirality : 0.049 0.124 92 Planarity : 0.002 0.007 88 Dihedral : 3.817 11.465 75 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.66 % Allowed : 20.75 % Favored : 73.58 % 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: -4.38 (0.71), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.54), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 14 TYR 0.003 0.001 TYR C 39 PHE 0.006 0.002 PHE C 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 527) covalent geometry : angle 0.43113 ( 709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.012 Fit side-chains REVERT: C 16 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8122 (m) outliers start: 3 outliers final: 1 residues processed: 9 average time/residue: 0.2471 time to fit residues: 2.2539 Evaluate side-chains 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8513 ------------------------------------------------------------------------------- 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 = 0.4487 r_free = 0.4487 target = 0.185824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.162557 restraints weight = 496.794| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.57 r_work: 0.4216 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4107 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 527 Z= 0.081 Angle : 0.373 1.603 709 Z= 0.214 Chirality : 0.049 0.119 92 Planarity : 0.001 0.006 88 Dihedral : 3.622 12.057 75 Min Nonbonded Distance : 2.689 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 5.66 % Allowed : 16.98 % Favored : 77.36 % 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: -4.25 (0.74), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.56), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 14 TYR 0.001 0.001 TYR C 39 PHE 0.004 0.001 PHE C 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00174 ( 527) covalent geometry : angle 0.37275 ( 709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.016 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 11 average time/residue: 0.2685 time to fit residues: 2.9906 Evaluate side-chains 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.184699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.161501 restraints weight = 482.857| |-----------------------------------------------------------------------------| r_work (start): 0.4304 rms_B_bonded: 2.59 r_work: 0.4202 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 527 Z= 0.083 Angle : 0.363 1.603 709 Z= 0.208 Chirality : 0.049 0.120 92 Planarity : 0.001 0.006 88 Dihedral : 3.764 12.115 75 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.77 % Allowed : 28.30 % Favored : 67.92 % 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: -4.32 (0.73), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.56), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 14 TYR 0.002 0.001 TYR C 39 PHE 0.006 0.002 PHE C 94 HIS 0.001 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00181 ( 527) covalent geometry : angle 0.36300 ( 709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.012 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.1953 time to fit residues: 1.9844 Evaluate side-chains 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.0987 ------------------------------------------------------------------------------- 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 = 0.4454 r_free = 0.4454 target = 0.181979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.161243 restraints weight = 501.024| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.63 r_work: 0.4140 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4030 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 527 Z= 0.185 Angle : 0.484 2.401 709 Z= 0.275 Chirality : 0.051 0.117 92 Planarity : 0.002 0.005 88 Dihedral : 4.753 14.237 75 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.77 % Allowed : 28.30 % Favored : 67.92 % 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: -4.54 (0.67), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.51), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 14 TYR 0.003 0.002 TYR C 39 PHE 0.011 0.004 PHE C 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 527) covalent geometry : angle 0.48430 ( 709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.016 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 11 average time/residue: 0.2099 time to fit residues: 2.3426 Evaluate side-chains 11 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.0653 ------------------------------------------------------------------------------- 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 = 0.183868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.162063 restraints weight = 515.184| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 2.52 r_work: 0.4142 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 527 Z= 0.177 Angle : 0.474 2.111 709 Z= 0.269 Chirality : 0.050 0.120 92 Planarity : 0.002 0.005 88 Dihedral : 4.820 15.873 75 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.77 % Allowed : 30.19 % Favored : 66.04 % 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: -4.57 (0.67), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.51), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 14 TYR 0.004 0.002 TYR C 39 PHE 0.012 0.004 PHE C 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 527) covalent geometry : angle 0.47432 ( 709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.011 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.1318 time to fit residues: 1.3493 Evaluate side-chains 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 chunk 6 optimal weight: 0.2980 overall best weight: 0.2310 ------------------------------------------------------------------------------- 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 = 0.4602 r_free = 0.4602 target = 0.199455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.176660 restraints weight = 513.295| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 2.45 r_work: 0.4275 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 527 Z= 0.053 Angle : 0.342 2.099 709 Z= 0.198 Chirality : 0.049 0.125 92 Planarity : 0.001 0.006 88 Dihedral : 3.540 13.195 75 Min Nonbonded Distance : 2.682 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.77 % Allowed : 30.19 % Favored : 66.04 % 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: -4.32 (0.70), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.54), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 14 TYR 0.003 0.001 TYR C 39 PHE 0.003 0.001 PHE C 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00107 ( 527) covalent geometry : angle 0.34232 ( 709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.024 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 9 average time/residue: 0.2726 time to fit residues: 2.5098 Evaluate side-chains 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.2320 ------------------------------------------------------------------------------- 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 = 0.4468 r_free = 0.4468 target = 0.184045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.162334 restraints weight = 521.472| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.50 r_work: 0.4130 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4023 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 527 Z= 0.204 Angle : 0.479 2.239 709 Z= 0.270 Chirality : 0.051 0.116 92 Planarity : 0.002 0.006 88 Dihedral : 4.801 15.063 75 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 3.77 % Allowed : 32.08 % Favored : 64.15 % 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: -4.54 (0.67), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.51), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 14 TYR 0.004 0.002 TYR C 39 PHE 0.013 0.004 PHE C 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 527) covalent geometry : angle 0.47859 ( 709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.022 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 9 average time/residue: 0.2474 time to fit residues: 2.2838 Evaluate side-chains 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 0.0060 chunk 3 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.3637 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.190387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.167894 restraints weight = 477.963| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 2.42 r_work: 0.4266 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4157 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 527 Z= 0.058 Angle : 0.365 2.837 709 Z= 0.209 Chirality : 0.049 0.123 92 Planarity : 0.001 0.007 88 Dihedral : 3.791 14.052 75 Min Nonbonded Distance : 2.680 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 5.66 % Allowed : 28.30 % Favored : 66.04 % 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: -4.25 (0.71), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.54), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 14 TYR 0.004 0.001 TYR C 39 PHE 0.004 0.001 PHE C 94 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00119 ( 527) covalent geometry : angle 0.36497 ( 709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.022 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 10 average time/residue: 0.2213 time to fit residues: 2.2710 Evaluate side-chains 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 overall best weight: 1.7320 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.189168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.166574 restraints weight = 501.120| |-----------------------------------------------------------------------------| r_work (start): 0.4269 rms_B_bonded: 2.41 r_work: 0.4170 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.4068 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 527 Z= 0.159 Angle : 0.432 1.892 709 Z= 0.245 Chirality : 0.050 0.120 92 Planarity : 0.002 0.006 88 Dihedral : 4.488 14.798 75 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 3.77 % Allowed : 30.19 % Favored : 66.04 % 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: -4.42 (0.69), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.53), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 14 TYR 0.003 0.002 TYR C 39 PHE 0.011 0.003 PHE C 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 527) covalent geometry : angle 0.43160 ( 709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 142 Ramachandran restraints generated. 71 Oldfield, 0 Emsley, 71 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.013 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 9 average time/residue: 0.2416 time to fit residues: 2.2211 Evaluate side-chains 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 48 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.6243 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.188636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.165385 restraints weight = 493.820| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.44 r_work: 0.4232 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4126 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 527 Z= 0.068 Angle : 0.368 2.521 709 Z= 0.211 Chirality : 0.049 0.121 92 Planarity : 0.001 0.007 88 Dihedral : 3.930 14.431 75 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.77 % Allowed : 30.19 % Favored : 66.04 % 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: -4.24 (0.72), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.55), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 14 TYR 0.004 0.001 TYR C 39 PHE 0.006 0.002 PHE C 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00148 ( 527) covalent geometry : angle 0.36826 ( 709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 396.32 seconds wall clock time: 7 minutes 43.88 seconds (463.88 seconds total)