Starting phenix.real_space_refine on Fri Aug 22 12:37:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tif_41286/08_2025/8tif_41286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tif_41286/08_2025/8tif_41286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tif_41286/08_2025/8tif_41286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tif_41286/08_2025/8tif_41286.map" model { file = "/net/cci-nas-00/data/ceres_data/8tif_41286/08_2025/8tif_41286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tif_41286/08_2025/8tif_41286.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 sd= 0.029 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 559 2.51 5 N 146 2.21 5 O 184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 889 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 889 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Time building chain proxies: 0.28, per 1000 atoms: 0.31 Number of scatterers: 889 At special positions: 0 Unit cell: (47.52, 47.52, 99.36, 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 184 8.00 N 146 7.00 C 559 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: 0.05 Conformation dependent library (CDL) restraints added in 151.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 226 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 3 sheets defined 29.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 13 through 46 removed outlier: 3.552A pdb=" N VAL A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 removed outlier: 3.617A pdb=" N VAL A 119 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 59 removed outlier: 7.004A pdb=" N THR A 126 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA A 81 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN A 128 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 81 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 45 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.08 Time building geometry restraints manager: 0.07 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: 146 1.29 - 1.35: 144 1.35 - 1.42: 45 1.42 - 1.48: 154 1.48 - 1.54: 404 Bond restraints: 893 Sorted by residual: bond pdb=" CB ILE A 29 " pdb=" CG2 ILE A 29 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.20e-01 bond pdb=" CB GLN A 116 " pdb=" CG GLN A 116 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.16e-01 bond pdb=" CG1 ILE A 96 " pdb=" CD1 ILE A 96 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.16e-01 bond pdb=" CB THR A 45 " pdb=" CG2 THR A 45 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.10e-01 bond pdb=" CG LEU A 129 " pdb=" CD1 LEU A 129 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.05e-01 ... (remaining 888 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 1159 0.97 - 1.94: 46 1.94 - 2.91: 11 2.91 - 3.88: 4 3.88 - 4.84: 3 Bond angle restraints: 1223 Sorted by residual: angle pdb=" CB GLN A 128 " pdb=" CG GLN A 128 " pdb=" CD GLN A 128 " ideal model delta sigma weight residual 112.60 116.85 -4.25 1.70e+00 3.46e-01 6.26e+00 angle pdb=" CA GLN A 116 " pdb=" CB GLN A 116 " pdb=" CG GLN A 116 " ideal model delta sigma weight residual 114.10 118.94 -4.84 2.00e+00 2.50e-01 5.87e+00 angle pdb=" CA GLN A 128 " pdb=" CB GLN A 128 " pdb=" CG GLN A 128 " ideal model delta sigma weight residual 114.10 117.88 -3.78 2.00e+00 2.50e-01 3.56e+00 angle pdb=" CD1 LEU A 20 " pdb=" CG LEU A 20 " pdb=" CD2 LEU A 20 " ideal model delta sigma weight residual 110.80 106.76 4.04 2.20e+00 2.07e-01 3.38e+00 angle pdb=" C ALA A 19 " pdb=" N LEU A 20 " pdb=" CA LEU A 20 " ideal model delta sigma weight residual 120.29 118.21 2.08 1.42e+00 4.96e-01 2.15e+00 ... (remaining 1218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 428 15.75 - 31.51: 63 31.51 - 47.26: 15 47.26 - 63.02: 4 63.02 - 78.77: 2 Dihedral angle restraints: 512 sinusoidal: 155 harmonic: 357 Sorted by residual: dihedral pdb=" CA LYS A 70 " pdb=" CB LYS A 70 " pdb=" CG LYS A 70 " pdb=" CD LYS A 70 " ideal model delta sinusoidal sigma weight residual -60.00 -111.52 51.52 3 1.50e+01 4.44e-03 9.02e+00 dihedral pdb=" N LEU A 31 " pdb=" CA LEU A 31 " pdb=" CB LEU A 31 " pdb=" CG LEU A 31 " ideal model delta sinusoidal sigma weight residual -60.00 -107.85 47.85 3 1.50e+01 4.44e-03 8.55e+00 dihedral pdb=" N ASN A 117 " pdb=" CA ASN A 117 " pdb=" CB ASN A 117 " pdb=" CG ASN A 117 " ideal model delta sinusoidal sigma weight residual 180.00 -133.83 -46.17 3 1.50e+01 4.44e-03 8.29e+00 ... (remaining 509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 111 0.033 - 0.067: 41 0.067 - 0.100: 17 0.100 - 0.134: 5 0.134 - 0.167: 1 Chirality restraints: 175 Sorted by residual: chirality pdb=" CA ILE A 96 " pdb=" N ILE A 96 " pdb=" C ILE A 96 " pdb=" CB ILE A 96 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.96e-01 chirality pdb=" CA ILE A 140 " pdb=" N ILE A 140 " pdb=" C ILE A 140 " pdb=" CB ILE A 140 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE A 83 " pdb=" N ILE A 83 " pdb=" C ILE A 83 " pdb=" CB ILE A 83 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 172 not shown) Planarity restraints: 150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " 0.011 2.00e-02 2.50e+03 1.04e-02 2.16e+00 pdb=" CG TYR A 103 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 41 " -0.012 2.00e-02 2.50e+03 9.80e-03 1.68e+00 pdb=" CG PHE A 41 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 41 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 41 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 41 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 41 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 41 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 90 " -0.005 2.00e-02 2.50e+03 1.07e-02 1.15e+00 pdb=" C VAL A 90 " 0.019 2.00e-02 2.50e+03 pdb=" O VAL A 90 " -0.007 2.00e-02 2.50e+03 pdb=" N SER A 91 " -0.006 2.00e-02 2.50e+03 ... (remaining 147 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 338 2.83 - 3.35: 817 3.35 - 3.87: 1399 3.87 - 4.38: 1319 4.38 - 4.90: 2520 Nonbonded interactions: 6393 Sorted by model distance: nonbonded pdb=" O LEU A 118 " pdb=" OG SER A 121 " model vdw 2.317 3.040 nonbonded pdb=" NE2 GLN A 52 " pdb=" O GLY A 54 " model vdw 2.333 3.120 nonbonded pdb=" OG1 THR A 76 " pdb=" OG SER A 130 " model vdw 2.413 3.040 nonbonded pdb=" O THR A 72 " pdb=" OG1 THR A 72 " model vdw 2.443 3.040 nonbonded pdb=" OG1 THR A 76 " pdb=" N GLN A 77 " model vdw 2.512 3.120 ... (remaining 6388 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.960 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.220 Find NCS groups from input model: 0.010 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 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 : 0.005 0.031 893 Z= 0.189 Angle : 0.547 4.844 1223 Z= 0.301 Chirality : 0.044 0.167 175 Planarity : 0.002 0.011 150 Dihedral : 17.043 78.773 286 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.02 % Allowed : 43.88 % Favored : 55.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.74), residues: 129 helix: 3.77 (0.73), residues: 34 sheet: -1.42 (0.89), residues: 37 loop : -1.10 (0.73), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.007 TYR A 103 PHE 0.022 0.002 PHE A 41 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 893) covalent geometry : angle 0.54718 ( 1223) hydrogen bonds : bond 0.19992 ( 45) hydrogen bonds : angle 7.21426 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.018 Fit side-chains REVERT: A 128 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7834 (tp40) outliers start: 1 outliers final: 1 residues processed: 5 average time/residue: 0.0205 time to fit residues: 0.1407 Evaluate side-chains 5 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.2931 r_free = 0.2931 target = 0.068921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.062234 restraints weight = 3090.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.063585 restraints weight = 1570.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.064499 restraints weight = 969.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.065094 restraints weight = 671.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.065540 restraints weight = 512.846| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 893 Z= 0.140 Angle : 0.482 4.922 1223 Z= 0.252 Chirality : 0.041 0.133 175 Planarity : 0.002 0.007 150 Dihedral : 5.083 40.455 134 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.04 % Allowed : 38.78 % Favored : 59.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.77), residues: 129 helix: 4.42 (0.68), residues: 34 sheet: -1.21 (0.85), residues: 44 loop : -1.03 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR A 103 PHE 0.006 0.001 PHE A 41 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 893) covalent geometry : angle 0.48223 ( 1223) hydrogen bonds : bond 0.03335 ( 45) hydrogen bonds : angle 4.96013 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.019 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 9 average time/residue: 0.0179 time to fit residues: 0.2095 Evaluate side-chains 7 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.2950 r_free = 0.2950 target = 0.070605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.064220 restraints weight = 2896.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.065517 restraints weight = 1511.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.066340 restraints weight = 936.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.066895 restraints weight = 656.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.067374 restraints weight = 496.914| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 893 Z= 0.126 Angle : 0.420 3.543 1223 Z= 0.224 Chirality : 0.041 0.135 175 Planarity : 0.001 0.006 150 Dihedral : 3.201 9.823 132 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.04 % Allowed : 35.71 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.77), residues: 129 helix: 4.42 (0.68), residues: 34 sheet: -1.12 (0.83), residues: 44 loop : -1.26 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR A 103 PHE 0.005 0.001 PHE A 41 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 893) covalent geometry : angle 0.41978 ( 1223) hydrogen bonds : bond 0.03208 ( 45) hydrogen bonds : angle 4.11386 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.018 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 10 average time/residue: 0.0169 time to fit residues: 0.2195 Evaluate side-chains 7 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 overall best weight: 3.0106 ------------------------------------------------------------------------------- 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 = 0.2879 r_free = 0.2879 target = 0.067132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.060259 restraints weight = 3039.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.061626 restraints weight = 1561.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.062546 restraints weight = 969.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.063202 restraints weight = 672.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.063550 restraints weight = 507.007| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 893 Z= 0.191 Angle : 0.475 3.481 1223 Z= 0.254 Chirality : 0.042 0.132 175 Planarity : 0.002 0.006 150 Dihedral : 3.423 11.348 132 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 7.14 % Allowed : 35.71 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.75), residues: 129 helix: 4.13 (0.68), residues: 34 sheet: -1.13 (0.81), residues: 44 loop : -1.37 (0.78), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR A 103 PHE 0.008 0.001 PHE A 41 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 893) covalent geometry : angle 0.47521 ( 1223) hydrogen bonds : bond 0.03625 ( 45) hydrogen bonds : angle 4.21857 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 6 time to evaluate : 0.033 Fit side-chains REVERT: A 44 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8084 (t80) outliers start: 7 outliers final: 5 residues processed: 13 average time/residue: 0.0282 time to fit residues: 0.4636 Evaluate side-chains 12 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 6 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.2952 r_free = 0.2952 target = 0.070931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.064236 restraints weight = 3055.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.065653 restraints weight = 1508.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.066605 restraints weight = 908.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.067237 restraints weight = 611.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.067514 restraints weight = 450.023| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 893 Z= 0.083 Angle : 0.369 4.054 1223 Z= 0.203 Chirality : 0.040 0.123 175 Planarity : 0.001 0.004 150 Dihedral : 2.954 9.641 132 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.06 % Allowed : 39.80 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.76), residues: 129 helix: 4.35 (0.73), residues: 34 sheet: -1.03 (0.81), residues: 44 loop : -1.28 (0.80), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR A 103 PHE 0.002 0.000 PHE A 41 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 893) covalent geometry : angle 0.36935 ( 1223) hydrogen bonds : bond 0.02874 ( 45) hydrogen bonds : angle 3.59828 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.029 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 9 average time/residue: 0.0304 time to fit residues: 0.3784 Evaluate side-chains 9 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 7 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.2867 r_free = 0.2867 target = 0.066746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.060212 restraints weight = 3087.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.061560 restraints weight = 1557.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.062450 restraints weight = 949.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.063082 restraints weight = 651.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.063499 restraints weight = 483.446| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 893 Z= 0.223 Angle : 0.486 3.905 1223 Z= 0.261 Chirality : 0.043 0.132 175 Planarity : 0.002 0.006 150 Dihedral : 3.475 11.632 132 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.10 % Allowed : 37.76 % Favored : 57.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.73), residues: 129 helix: 4.01 (0.70), residues: 34 sheet: -1.08 (0.79), residues: 44 loop : -1.32 (0.76), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.004 TYR A 103 PHE 0.010 0.001 PHE A 41 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 893) covalent geometry : angle 0.48608 ( 1223) hydrogen bonds : bond 0.03715 ( 45) hydrogen bonds : angle 4.19343 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.033 Fit side-chains REVERT: A 44 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8146 (t80) outliers start: 5 outliers final: 4 residues processed: 11 average time/residue: 0.0310 time to fit residues: 0.4654 Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.2940 r_free = 0.2940 target = 0.070033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.063220 restraints weight = 3133.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.064609 restraints weight = 1615.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.065573 restraints weight = 997.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.066192 restraints weight = 687.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.066587 restraints weight = 515.674| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 893 Z= 0.083 Angle : 0.367 4.575 1223 Z= 0.202 Chirality : 0.040 0.122 175 Planarity : 0.001 0.004 150 Dihedral : 2.912 9.775 132 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 5.10 % Allowed : 36.73 % Favored : 58.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.76), residues: 129 helix: 4.32 (0.74), residues: 34 sheet: -0.88 (0.80), residues: 44 loop : -1.17 (0.80), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 103 PHE 0.003 0.000 PHE A 44 Details of bonding type rmsd covalent geometry : bond 0.00184 ( 893) covalent geometry : angle 0.36706 ( 1223) hydrogen bonds : bond 0.02828 ( 45) hydrogen bonds : angle 3.50807 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.033 Fit side-chains REVERT: A 44 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8199 (t80) outliers start: 5 outliers final: 3 residues processed: 11 average time/residue: 0.0284 time to fit residues: 0.4020 Evaluate side-chains 10 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 6 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.2993 r_free = 0.2993 target = 0.072725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.065974 restraints weight = 2858.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.067394 restraints weight = 1457.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.068328 restraints weight = 893.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.068769 restraints weight = 611.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.069334 restraints weight = 481.948| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 893 Z= 0.074 Angle : 0.385 5.055 1223 Z= 0.212 Chirality : 0.041 0.122 175 Planarity : 0.001 0.011 150 Dihedral : 2.647 9.076 132 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.04 % Allowed : 38.78 % Favored : 59.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.78), residues: 129 helix: 4.45 (0.76), residues: 34 sheet: -0.98 (0.89), residues: 38 loop : -0.81 (0.80), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 103 PHE 0.001 0.000 PHE A 44 Details of bonding type rmsd covalent geometry : bond 0.00163 ( 893) covalent geometry : angle 0.38528 ( 1223) hydrogen bonds : bond 0.02464 ( 45) hydrogen bonds : angle 3.19250 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.034 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 9 average time/residue: 0.0296 time to fit residues: 0.3484 Evaluate side-chains 8 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 7 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.2918 r_free = 0.2918 target = 0.068970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.061948 restraints weight = 3020.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.063366 restraints weight = 1581.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.064328 restraints weight = 987.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.064900 restraints weight = 687.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.065421 restraints weight = 532.676| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 893 Z= 0.161 Angle : 0.492 5.864 1223 Z= 0.254 Chirality : 0.042 0.130 175 Planarity : 0.001 0.010 150 Dihedral : 3.011 10.372 132 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 3.06 % Allowed : 36.73 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.76), residues: 129 helix: 4.27 (0.75), residues: 34 sheet: -0.72 (0.81), residues: 44 loop : -1.12 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR A 103 PHE 0.006 0.001 PHE A 41 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 893) covalent geometry : angle 0.49180 ( 1223) hydrogen bonds : bond 0.03225 ( 45) hydrogen bonds : angle 3.67019 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.031 Fit side-chains REVERT: A 44 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8183 (t80) outliers start: 3 outliers final: 2 residues processed: 9 average time/residue: 0.0303 time to fit residues: 0.3553 Evaluate side-chains 9 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 134 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.0670 chunk 11 optimal weight: 0.0170 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 = 0.2989 r_free = 0.2989 target = 0.072290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.065123 restraints weight = 3083.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.066569 restraints weight = 1643.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.067572 restraints weight = 1037.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.068138 restraints weight = 726.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.068677 restraints weight = 566.056| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 893 Z= 0.075 Angle : 0.434 5.883 1223 Z= 0.223 Chirality : 0.041 0.121 175 Planarity : 0.001 0.009 150 Dihedral : 2.669 9.086 132 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.06 % Allowed : 36.73 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.78), residues: 129 helix: 4.43 (0.77), residues: 34 sheet: -0.95 (0.89), residues: 38 loop : -0.80 (0.81), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 103 PHE 0.002 0.000 PHE A 44 Details of bonding type rmsd covalent geometry : bond 0.00161 ( 893) covalent geometry : angle 0.43446 ( 1223) hydrogen bonds : bond 0.02505 ( 45) hydrogen bonds : angle 3.18224 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.035 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 10 average time/residue: 0.0292 time to fit residues: 0.3796 Evaluate side-chains 9 residues out of total 98 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 8 optimal weight: 0.0770 chunk 3 optimal weight: 5.9990 chunk 10 optimal weight: 0.0670 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 0.9878 ------------------------------------------------------------------------------- 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 = 0.2970 r_free = 0.2970 target = 0.071521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.064526 restraints weight = 2918.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.065959 restraints weight = 1534.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.066900 restraints weight = 958.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.067582 restraints weight = 673.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.068035 restraints weight = 503.007| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 893 Z= 0.085 Angle : 0.431 5.919 1223 Z= 0.222 Chirality : 0.041 0.124 175 Planarity : 0.001 0.009 150 Dihedral : 2.627 9.416 132 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.04 % Allowed : 37.76 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.78), residues: 129 helix: 4.43 (0.76), residues: 34 sheet: -0.91 (0.89), residues: 38 loop : -0.73 (0.82), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 103 PHE 0.002 0.000 PHE A 41 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 893) covalent geometry : angle 0.43148 ( 1223) hydrogen bonds : bond 0.02618 ( 45) hydrogen bonds : angle 3.23478 ( 126) =============================================================================== Job complete usr+sys time: 426.76 seconds wall clock time: 8 minutes 30.69 seconds (510.69 seconds total)