Starting phenix.real_space_refine on Wed Mar 5 14:17:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgs_52166/03_2025/9hgs_52166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgs_52166/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9hgs_52166/03_2025/9hgs_52166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgs_52166/03_2025/9hgs_52166.map" model { file = "/net/cci-nas-00/data/ceres_data/9hgs_52166/03_2025/9hgs_52166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgs_52166/03_2025/9hgs_52166.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 0.92, per 1000 atoms: 1.75 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: 0.11 Conformation dependent library (CDL) restraints added in 68.7 milliseconds 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: 0.35 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: 0.15 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: 3.140 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: 0.010 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.370 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:15.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS C 50 PHE 0.004 0.001 PHE C 94 TYR 0.002 0.001 TYR C 39 ARG 0.001 0.001 ARG C 14 *********************** 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 : 0.062 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 8 average time/residue: 0.9107 time to fit residues: 7.4185 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 : 0.055 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 1.2653 ------------------------------------------------------------------------------- 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 = 0.4523 r_free = 0.4523 target = 0.192963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.169874 restraints weight = 475.694| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.49 r_work: 0.4174 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4062 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 527 Z= 0.120 Angle : 0.459 2.180 709 Z= 0.264 Chirality : 0.050 0.129 92 Planarity : 0.002 0.007 88 Dihedral : 4.056 12.394 75 Min Nonbonded Distance : 2.673 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.70), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.54), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.007 0.002 PHE C 94 TYR 0.003 0.001 TYR C 39 ARG 0.000 0.000 ARG C 14 *********************** 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 11 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.047 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 10 average time/residue: 0.7107 time to fit residues: 7.2429 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 : 0.118 ------------------------------------------------------------------------------- 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: 0.0770 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.2140 ------------------------------------------------------------------------------- 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 = 0.4521 r_free = 0.4521 target = 0.190618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.167074 restraints weight = 489.869| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.63 r_work: 0.4254 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4141 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 527 Z= 0.051 Angle : 0.337 1.753 709 Z= 0.196 Chirality : 0.049 0.119 92 Planarity : 0.001 0.006 88 Dihedral : 3.165 11.363 75 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.66 % Allowed : 18.87 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.76), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.58), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.001 0.000 PHE C 94 TYR 0.001 0.000 TYR C 39 ARG 0.000 0.000 ARG C 14 *********************** 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 : 0.060 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 11 average time/residue: 0.5874 time to fit residues: 6.6098 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 : 0.058 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 2.3320 ------------------------------------------------------------------------------- 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 = 0.4319 r_free = 0.4319 target = 0.164603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.144020 restraints weight = 556.846| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.82 r_work: 0.4037 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 527 Z= 0.207 Angle : 0.505 3.066 709 Z= 0.287 Chirality : 0.051 0.115 92 Planarity : 0.002 0.006 88 Dihedral : 4.816 14.150 75 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.68 % Favored : 87.32 % Rotamer: Outliers : 3.77 % Allowed : 24.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.68), 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 HIS 0.003 0.002 HIS C 50 PHE 0.013 0.004 PHE C 94 TYR 0.004 0.002 TYR C 39 ARG 0.001 0.000 ARG C 14 *********************** 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 : 0.058 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.6967 time to fit residues: 7.1121 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 : 0.061 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 1.3983 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.187083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.165174 restraints weight = 501.643| |-----------------------------------------------------------------------------| r_work (start): 0.4084 rms_B_bonded: 2.54 r_work: 0.3976 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3873 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 527 Z= 0.126 Angle : 0.418 1.832 709 Z= 0.240 Chirality : 0.049 0.121 92 Planarity : 0.002 0.006 88 Dihedral : 4.401 13.928 75 Min Nonbonded Distance : 2.675 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.67), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.51), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.009 0.003 PHE C 94 TYR 0.003 0.001 TYR C 39 ARG 0.000 0.000 ARG C 14 *********************** 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 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.054 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.6722 time to fit residues: 6.8599 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 : 0.061 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9987 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.183138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.162029 restraints weight = 488.542| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.44 r_work: 0.4131 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 527 Z= 0.175 Angle : 0.477 2.148 709 Z= 0.272 Chirality : 0.050 0.120 92 Planarity : 0.002 0.006 88 Dihedral : 4.898 15.818 75 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.08 % Favored : 85.92 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.65), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.50), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.011 0.003 PHE C 94 TYR 0.004 0.002 TYR C 39 ARG 0.000 0.000 ARG C 14 *********************** 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 11 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.060 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 11 average time/residue: 0.6307 time to fit residues: 7.0851 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 : 0.058 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.3317 ------------------------------------------------------------------------------- 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 = 0.4500 r_free = 0.4500 target = 0.187502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.166077 restraints weight = 506.092| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.42 r_work: 0.4174 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 527 Z= 0.118 Angle : 0.415 1.974 709 Z= 0.237 Chirality : 0.050 0.122 92 Planarity : 0.002 0.005 88 Dihedral : 4.491 15.405 75 Min Nonbonded Distance : 2.663 Molprobity Statistics. All-atom Clashscore : 1.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.67), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.51), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.009 0.003 PHE C 94 TYR 0.003 0.001 TYR C 39 ARG 0.000 0.000 ARG C 14 *********************** 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 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.053 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.6801 time to fit residues: 6.9361 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 : 0.057 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 0.0040 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.9003 ------------------------------------------------------------------------------- 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 = 0.4530 r_free = 0.4530 target = 0.189428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.167610 restraints weight = 481.442| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.50 r_work: 0.4199 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4087 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 527 Z= 0.086 Angle : 0.382 2.686 709 Z= 0.218 Chirality : 0.049 0.122 92 Planarity : 0.001 0.007 88 Dihedral : 4.099 14.603 75 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 1.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.69), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.53), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.006 0.002 PHE C 94 TYR 0.003 0.001 TYR C 39 ARG 0.000 0.000 ARG C 14 *********************** 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 10 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.054 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 10 average time/residue: 0.6608 time to fit residues: 6.7432 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 : 0.058 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.0030 overall best weight: 0.4663 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.194964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.173016 restraints weight = 496.356| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.46 r_work: 0.4258 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4151 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2783 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= 0.056 Angle : 0.343 1.887 709 Z= 0.197 Chirality : 0.049 0.121 92 Planarity : 0.001 0.006 88 Dihedral : 3.649 13.324 75 Min Nonbonded Distance : 2.673 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (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 HIS 0.001 0.000 HIS C 50 PHE 0.004 0.001 PHE C 94 TYR 0.003 0.001 TYR C 39 ARG 0.000 0.000 ARG C 14 *********************** 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 9 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.059 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 9 average time/residue: 0.4954 time to fit residues: 4.5958 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 : 0.057 ------------------------------------------------------------------------------- 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: 7.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.0470 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.9813 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.190706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.168306 restraints weight = 489.979| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 2.48 r_work: 0.4204 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.4098 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2853 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= 0.094 Angle : 0.368 1.947 709 Z= 0.210 Chirality : 0.049 0.120 92 Planarity : 0.001 0.006 88 Dihedral : 3.995 13.480 75 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 2.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.72), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.55), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.007 0.002 PHE C 94 TYR 0.003 0.001 TYR C 39 ARG 0.000 0.000 ARG C 14 ********************** 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 8 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.060 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 8 average time/residue: 0.5486 time to fit residues: 4.5262 Evaluate side-chains 8 residues out of total 53 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 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 = 0.4567 r_free = 0.4567 target = 0.195025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.172237 restraints weight = 473.882| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 2.40 r_work: 0.4223 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.4115 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2878 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= 0.085 Angle : 0.368 1.969 709 Z= 0.211 Chirality : 0.049 0.121 92 Planarity : 0.001 0.006 88 Dihedral : 3.980 14.019 75 Min Nonbonded Distance : 2.667 Molprobity Statistics. All-atom Clashscore : 1.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.72), residues: 71 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.55), residues: 71 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.007 0.002 PHE C 94 TYR 0.003 0.001 TYR C 39 ARG 0.000 0.000 ARG C 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 848.12 seconds wall clock time: 15 minutes 20.46 seconds (920.46 seconds total)