Starting phenix.real_space_refine on Wed Mar 5 14:17:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgr_52165/03_2025/9hgr_52165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgr_52165/03_2025/9hgr_52165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hgr_52165/03_2025/9hgr_52165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgr_52165/03_2025/9hgr_52165.map" model { file = "/net/cci-nas-00/data/ceres_data/9hgr_52165/03_2025/9hgr_52165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgr_52165/03_2025/9hgr_52165.cif" } resolution = 2.7 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= 0.004 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 598 2.51 5 N 168 2.21 5 O 194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 960 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 480 Classifications: {'peptide': 71} Link IDs: {'TRANS': 70} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 0.94, per 1000 atoms: 0.98 Number of scatterers: 960 At special positions: 0 Unit cell: (109.48, 92.92, 22.08, 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 194 8.00 N 168 7.00 C 598 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: 0.21 Conformation dependent library (CDL) restraints added in 128.6 milliseconds 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 236 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: 0.36 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: 0.26 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: 170 1.29 - 1.35: 151 1.35 - 1.42: 33 1.42 - 1.48: 158 1.48 - 1.54: 450 Bond restraints: 962 Sorted by residual: bond pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.27e-02 6.20e+03 4.46e+00 bond pdb=" N ALA B 56 " pdb=" CA ALA B 56 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.27e-02 6.20e+03 4.45e+00 bond pdb=" N GLU B 57 " pdb=" CA GLU B 57 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.28e-02 6.10e+03 4.38e+00 bond pdb=" N GLU A 57 " pdb=" CA GLU A 57 " ideal model delta sigma weight residual 1.458 1.484 -0.026 1.28e-02 6.10e+03 4.25e+00 bond pdb=" CA ALA A 56 " pdb=" CB ALA A 56 " ideal model delta sigma weight residual 1.534 1.509 0.025 1.76e-02 3.23e+03 1.99e+00 ... (remaining 957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 1250 0.96 - 1.93: 36 1.93 - 2.89: 8 2.89 - 3.86: 2 3.86 - 4.82: 2 Bond angle restraints: 1298 Sorted by residual: angle pdb=" N GLU B 57 " pdb=" CA GLU B 57 " pdb=" C GLU B 57 " ideal model delta sigma weight residual 113.12 108.30 4.82 1.25e+00 6.40e-01 1.49e+01 angle pdb=" N GLU A 57 " pdb=" CA GLU A 57 " pdb=" C GLU A 57 " ideal model delta sigma weight residual 113.12 108.35 4.77 1.25e+00 6.40e-01 1.46e+01 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.33 118.99 2.34 1.08e+00 8.57e-01 4.71e+00 angle pdb=" CA ALA B 56 " pdb=" C ALA B 56 " pdb=" O ALA B 56 " ideal model delta sigma weight residual 121.33 119.00 2.33 1.08e+00 8.57e-01 4.66e+00 angle pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta sigma weight residual 121.70 124.82 -3.12 1.80e+00 3.09e-01 3.00e+00 ... (remaining 1293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.46: 502 13.46 - 26.93: 32 26.93 - 40.39: 10 40.39 - 53.85: 4 53.85 - 67.32: 8 Dihedral angle restraints: 556 sinusoidal: 180 harmonic: 376 Sorted by residual: dihedral pdb=" CA GLU B 61 " pdb=" CB GLU B 61 " pdb=" CG GLU B 61 " pdb=" CD GLU B 61 " ideal model delta sinusoidal sigma weight residual 60.00 115.57 -55.57 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA GLU A 61 " pdb=" CB GLU A 61 " pdb=" CG GLU A 61 " pdb=" CD GLU A 61 " ideal model delta sinusoidal sigma weight residual 60.00 115.56 -55.56 3 1.50e+01 4.44e-03 9.35e+00 dihedral pdb=" CA LYS B 80 " pdb=" CB LYS B 80 " pdb=" CG LYS B 80 " pdb=" CD LYS B 80 " ideal model delta sinusoidal sigma weight residual 180.00 130.22 49.78 3 1.50e+01 4.44e-03 8.82e+00 ... (remaining 553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 76 0.024 - 0.048: 48 0.048 - 0.072: 12 0.072 - 0.096: 14 0.096 - 0.120: 20 Chirality restraints: 170 Sorted by residual: chirality pdb=" CA GLU B 57 " pdb=" N GLU B 57 " pdb=" C GLU B 57 " pdb=" CB GLU B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.40e-01 ... (remaining 167 not shown) Planarity restraints: 162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 70 " 0.004 2.00e-02 2.50e+03 7.66e-03 5.86e-01 pdb=" C VAL A 70 " -0.013 2.00e-02 2.50e+03 pdb=" O VAL A 70 " 0.005 2.00e-02 2.50e+03 pdb=" N VAL A 71 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " 0.004 2.00e-02 2.50e+03 7.61e-03 5.79e-01 pdb=" C VAL B 70 " -0.013 2.00e-02 2.50e+03 pdb=" O VAL B 70 " 0.005 2.00e-02 2.50e+03 pdb=" N VAL B 71 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 39 " -0.004 2.00e-02 2.50e+03 3.45e-03 2.38e-01 pdb=" CG TYR B 39 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR B 39 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 39 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 39 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 39 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 39 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 39 " -0.000 2.00e-02 2.50e+03 ... (remaining 159 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 518 3.03 - 3.50: 748 3.50 - 3.97: 1074 3.97 - 4.43: 897 4.43 - 4.90: 1573 Nonbonded interactions: 4810 Sorted by model distance: nonbonded pdb=" O THR A 22 " pdb=" OG1 THR A 22 " model vdw 2.569 3.040 nonbonded pdb=" O THR B 22 " pdb=" OG1 THR B 22 " model vdw 2.569 3.040 nonbonded pdb=" C THR A 44 " pdb=" OG1 THR A 44 " model vdw 2.657 2.616 nonbonded pdb=" C THR B 44 " pdb=" OG1 THR B 44 " model vdw 2.658 2.616 nonbonded pdb=" C THR B 92 " pdb=" OG1 THR B 92 " model vdw 2.658 2.616 ... (remaining 4805 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.300 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.280 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 : 0.003 0.027 962 Z= 0.198 Angle : 0.471 4.823 1298 Z= 0.305 Chirality : 0.051 0.120 170 Planarity : 0.001 0.008 162 Dihedral : 14.287 67.318 320 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 23.40 % Favored : 76.60 % 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: -3.44 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.008 0.002 PHE B 94 TYR 0.009 0.002 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.104 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.7526 time to fit residues: 15.3573 Evaluate side-chains 18 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 5 optimal weight: 0.0770 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 0.0870 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 0.0070 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- 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 = 0.4613 r_free = 0.4613 target = 0.216439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.203374 restraints weight = 868.094| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 1.82 r_work: 0.4377 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4290 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.010 962 Z= 0.063 Angle : 0.341 3.022 1298 Z= 0.194 Chirality : 0.048 0.115 170 Planarity : 0.001 0.007 162 Dihedral : 2.840 6.590 140 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 8.51 % Allowed : 17.02 % Favored : 74.47 % 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: -3.43 (0.61), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.008 0.002 PHE B 94 TYR 0.001 0.000 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.094 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 26 average time/residue: 0.5824 time to fit residues: 15.5215 Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 chunk 5 optimal weight: 0.0870 chunk 8 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.6962 ------------------------------------------------------------------------------- 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 = 0.4601 r_free = 0.4601 target = 0.214480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.201100 restraints weight = 849.657| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 1.79 r_work: 0.4352 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4261 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 962 Z= 0.075 Angle : 0.351 3.071 1298 Z= 0.199 Chirality : 0.048 0.115 170 Planarity : 0.001 0.007 162 Dihedral : 3.126 7.187 140 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 8.51 % Allowed : 14.89 % Favored : 76.60 % 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: -3.39 (0.61), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.47), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.009 0.002 PHE A 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.101 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 24 average time/residue: 0.6149 time to fit residues: 15.0955 Evaluate side-chains 22 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 63 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.0070 overall best weight: 1.2202 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.211713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.197864 restraints weight = 861.354| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 1.92 r_work: 0.4315 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.4223 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 962 Z= 0.109 Angle : 0.392 2.817 1298 Z= 0.219 Chirality : 0.048 0.113 170 Planarity : 0.002 0.008 162 Dihedral : 3.715 9.380 140 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 8.51 % Allowed : 17.02 % Favored : 74.47 % 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: -3.56 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.011 0.003 PHE A 94 TYR 0.004 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.105 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 26 average time/residue: 0.7416 time to fit residues: 19.6252 Evaluate side-chains 26 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.0370 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.0862 ------------------------------------------------------------------------------- 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 = 0.4568 r_free = 0.4568 target = 0.212417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.199126 restraints weight = 869.634| |-----------------------------------------------------------------------------| r_work (start): 0.4401 rms_B_bonded: 1.85 r_work: 0.4323 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4235 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 962 Z= 0.098 Angle : 0.376 2.937 1298 Z= 0.211 Chirality : 0.048 0.115 170 Planarity : 0.002 0.008 162 Dihedral : 3.652 8.583 140 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 4.26 % Allowed : 25.53 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.53 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.011 0.003 PHE A 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.104 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.6513 time to fit residues: 15.9840 Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.9782 ------------------------------------------------------------------------------- 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 = 0.4563 r_free = 0.4563 target = 0.211423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.197939 restraints weight = 821.796| |-----------------------------------------------------------------------------| r_work (start): 0.4393 rms_B_bonded: 1.83 r_work: 0.4313 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4223 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 962 Z= 0.158 Angle : 0.437 3.129 1298 Z= 0.244 Chirality : 0.049 0.114 170 Planarity : 0.002 0.009 162 Dihedral : 4.335 10.198 140 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 4.26 % Allowed : 25.53 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.59 (0.59), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.45), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.014 0.004 PHE A 94 TYR 0.005 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.091 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.8103 time to fit residues: 23.0741 Evaluate side-chains 28 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 6 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8540 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.212609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.199359 restraints weight = 832.264| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 1.83 r_work: 0.4273 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4187 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.009 962 Z= 0.086 Angle : 0.368 2.822 1298 Z= 0.207 Chirality : 0.048 0.116 170 Planarity : 0.002 0.008 162 Dihedral : 3.603 8.388 140 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.26 % Allowed : 25.53 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.62 (0.59), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.45), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.013 0.004 PHE B 94 TYR 0.003 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.186 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.6429 time to fit residues: 15.8305 Evaluate side-chains 24 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 1 optimal weight: 0.0470 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- 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 = 0.4541 r_free = 0.4541 target = 0.208688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.194655 restraints weight = 858.332| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 1.93 r_work: 0.4280 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4188 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 962 Z= 0.304 Angle : 0.566 3.344 1298 Z= 0.322 Chirality : 0.053 0.122 170 Planarity : 0.003 0.012 162 Dihedral : 5.408 14.218 140 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 4.26 % Allowed : 25.53 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.79 (0.56), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.43), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.021 0.007 PHE A 94 TYR 0.010 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.105 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.7762 time to fit residues: 23.6682 Evaluate side-chains 28 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4570 r_free = 0.4570 target = 0.211666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.198054 restraints weight = 847.912| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 1.85 r_work: 0.4324 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4234 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 962 Z= 0.158 Angle : 0.448 3.079 1298 Z= 0.251 Chirality : 0.049 0.116 170 Planarity : 0.002 0.011 162 Dihedral : 4.520 10.317 140 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 5.32 % Allowed : 24.47 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.76 (0.58), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.44), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.016 0.005 PHE A 94 TYR 0.006 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.115 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 28 average time/residue: 0.8150 time to fit residues: 23.2053 Evaluate side-chains 29 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 3 optimal weight: 5.9990 chunk 9 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 0.0570 chunk 1 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.8902 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.210617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.197078 restraints weight = 832.350| |-----------------------------------------------------------------------------| r_work (start): 0.4406 rms_B_bonded: 1.85 r_work: 0.4327 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.4234 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 962 Z= 0.153 Angle : 0.436 3.039 1298 Z= 0.246 Chirality : 0.050 0.116 170 Planarity : 0.002 0.011 162 Dihedral : 4.494 10.863 140 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 5.32 % Allowed : 24.47 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.70 (0.59), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.45), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.002 HIS B 50 PHE 0.016 0.005 PHE A 94 TYR 0.006 0.001 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 268 Ramachandran restraints generated. 134 Oldfield, 0 Emsley, 134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.092 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 30 average time/residue: 0.7730 time to fit residues: 23.5724 Evaluate side-chains 29 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.0030 overall best weight: 2.3796 ------------------------------------------------------------------------------- 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 = 0.211471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.197729 restraints weight = 855.473| |-----------------------------------------------------------------------------| r_work (start): 0.4399 rms_B_bonded: 1.84 r_work: 0.4316 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 962 Z= 0.185 Angle : 0.469 3.070 1298 Z= 0.265 Chirality : 0.050 0.117 170 Planarity : 0.002 0.011 162 Dihedral : 4.720 11.384 140 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.32 % Allowed : 24.47 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.74 (0.58), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.44), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.017 0.005 PHE A 94 TYR 0.007 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1419.62 seconds wall clock time: 25 minutes 14.75 seconds (1514.75 seconds total)