Starting phenix.real_space_refine on Mon Feb 10 19:27:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgr_52165/02_2025/9hgr_52165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgr_52165/02_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_52165/02_2025/9hgr_52165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgr_52165/02_2025/9hgr_52165.map" model { file = "/net/cci-nas-00/data/ceres_data/9hgr_52165/02_2025/9hgr_52165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgr_52165/02_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-5592/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: 0.99, per 1000 atoms: 1.03 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: 0.23 Conformation dependent library (CDL) restraints added in 132.6 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: 0.40 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: 0.29 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: 2.910 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: 0.020 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.450 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: 0.000 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.540 ------------------------------------------------------------------------------- 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 : 0.098 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.8325 time to fit residues: 16.9727 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 : 0.103 ------------------------------------------------------------------------------- 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 : 0.098 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 26 average time/residue: 0.5905 time to fit residues: 15.6932 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 : 0.110 ------------------------------------------------------------------------------- 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 = 31)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.201007 restraints weight = 849.657| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 1.82 r_work: 0.4350 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4260 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 : 0.099 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 24 average time/residue: 0.6303 time to fit residues: 15.4622 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 : 0.105 ------------------------------------------------------------------------------- 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: 0.5980 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.4547 r_free = 0.4547 target = 0.209578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.195954 restraints weight = 852.264| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 1.80 r_work: 0.4268 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4178 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 962 Z= 0.195 Angle : 0.476 3.385 1298 Z= 0.267 Chirality : 0.050 0.115 170 Planarity : 0.002 0.010 162 Dihedral : 4.663 11.136 140 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 8.51 % Allowed : 19.15 % Favored : 72.34 % 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: -3.65 (0.59), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.45), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.015 0.005 PHE A 94 TYR 0.007 0.002 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 32 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.108 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 28 average time/residue: 0.8355 time to fit residues: 23.7661 Evaluate side-chains 30 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.0570 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- 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 = 0.4564 r_free = 0.4564 target = 0.211769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.198272 restraints weight = 863.843| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 1.86 r_work: 0.4320 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.4228 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 962 Z= 0.093 Angle : 0.378 2.808 1298 Z= 0.212 Chirality : 0.048 0.115 170 Planarity : 0.002 0.009 162 Dihedral : 3.761 8.659 140 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 6.38 % Allowed : 23.40 % 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 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.013 0.004 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 27 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.105 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.7018 time to fit residues: 17.8951 Evaluate side-chains 25 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.105 ------------------------------------------------------------------------------- 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: 0.5980 chunk 4 optimal weight: 0.0000 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.0020 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.3592 ------------------------------------------------------------------------------- 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 = 0.4605 r_free = 0.4605 target = 0.215768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.202599 restraints weight = 832.095| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 1.83 r_work: 0.4365 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.4280 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1286 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= 0.061 Angle : 0.330 2.731 1298 Z= 0.187 Chirality : 0.048 0.117 170 Planarity : 0.001 0.007 162 Dihedral : 3.022 7.519 140 Min Nonbonded Distance : 2.647 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: -3.51 (0.61), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.47), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.012 0.003 PHE A 94 TYR 0.001 0.000 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 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: 2 residues processed: 24 average time/residue: 0.6272 time to fit residues: 15.4027 Evaluate side-chains 22 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain B residue 15 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.4529 r_free = 0.4529 target = 0.207206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.193182 restraints weight = 828.853| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 1.88 r_work: 0.4277 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4188 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 962 Z= 0.306 Angle : 0.567 3.504 1298 Z= 0.321 Chirality : 0.054 0.121 170 Planarity : 0.003 0.012 162 Dihedral : 5.377 13.950 140 Min Nonbonded Distance : 2.634 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: -3.77 (0.57), 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 0.005 0.003 HIS A 50 PHE 0.020 0.007 PHE A 94 TYR 0.011 0.003 TYR B 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 30 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.193 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.8596 time to fit residues: 24.4842 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 : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4564 r_free = 0.4564 target = 0.210583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.196863 restraints weight = 855.439| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 1.86 r_work: 0.4314 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.4219 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1864 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= 0.189 Angle : 0.473 3.283 1298 Z= 0.265 Chirality : 0.050 0.115 170 Planarity : 0.002 0.011 162 Dihedral : 4.765 11.037 140 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % 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: -3.84 (0.58), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (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 B 94 TYR 0.007 0.002 TYR B 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 : 0.103 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 28 average time/residue: 0.8335 time to fit residues: 23.7094 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 : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 54 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: 7.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 3 optimal weight: 0.0970 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.0000 chunk 10 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4582 r_free = 0.4582 target = 0.213106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.199695 restraints weight = 844.652| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 1.84 r_work: 0.4342 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.4250 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 962 Z= 0.101 Angle : 0.385 2.870 1298 Z= 0.217 Chirality : 0.049 0.116 170 Planarity : 0.002 0.010 162 Dihedral : 3.997 9.116 140 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 6.38 % Allowed : 23.40 % 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: -3.73 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.016 0.004 PHE A 94 TYR 0.003 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 31 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.081 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 29 average time/residue: 0.7808 time to fit residues: 23.0138 Evaluate side-chains 31 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.104 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.4557 r_free = 0.4557 target = 0.210375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.196638 restraints weight = 835.050| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 1.83 r_work: 0.4291 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4202 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 962 Z= 0.206 Angle : 0.480 3.084 1298 Z= 0.271 Chirality : 0.050 0.118 170 Planarity : 0.002 0.012 162 Dihedral : 4.875 12.227 140 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 6.38 % Allowed : 23.40 % 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: -3.78 (0.57), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.44), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 50 PHE 0.019 0.005 PHE B 94 TYR 0.007 0.002 TYR A 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 32 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.129 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 30 average time/residue: 0.8210 time to fit residues: 25.0634 Evaluate side-chains 32 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.106 ------------------------------------------------------------------------------- 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 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: 0.0030 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 0.0050 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.1608 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.213582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.200075 restraints weight = 851.895| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 1.86 r_work: 0.4348 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.4255 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1843 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= 0.104 Angle : 0.393 2.846 1298 Z= 0.221 Chirality : 0.048 0.118 170 Planarity : 0.002 0.010 162 Dihedral : 4.086 9.321 140 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 6.38 % Allowed : 23.40 % 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: -3.68 (0.60), residues: 134 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.46), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.016 0.005 PHE A 94 TYR 0.003 0.001 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1433.72 seconds wall clock time: 26 minutes 10.76 seconds (1570.76 seconds total)