Starting phenix.real_space_refine on Tue Feb 3 13:14:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hgb_52133/02_2026/9hgb_52133.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hgb_52133/02_2026/9hgb_52133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hgb_52133/02_2026/9hgb_52133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hgb_52133/02_2026/9hgb_52133.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hgb_52133/02_2026/9hgb_52133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hgb_52133/02_2026/9hgb_52133.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians C 924 2.51 5 N 216 2.21 5 O 240 1.98 5 H 1596 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2976 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "B" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "E" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "G" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "H" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "I" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "J" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "K" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Chain: "L" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 248 Classifications: {'peptide': 16} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 15} Time building chain proxies: 0.73, per 1000 atoms: 0.25 Number of scatterers: 2976 At special positions: 0 Unit cell: (113.05, 45.05, 29.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 240 8.00 N 216 7.00 C 924 6.00 H 1596 1.00 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: 0.26 Conformation dependent library (CDL) restraints added in 67.8 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 312 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 10 removed outlier: 6.379A pdb=" N ILE E 6 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL I 9 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS E 8 " --> pdb=" O VAL I 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 6 through 10 Processing sheet with id=AA3, first strand: chain 'C' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'D' and resid 6 through 10 removed outlier: 6.345A pdb=" N ILE H 6 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL L 9 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS H 8 " --> pdb=" O VAL L 9 " (cutoff:3.500A) 24 hydrogen bonds defined for protein. 72 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: 0.53 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.50 - 0.71: 7 0.71 - 0.93: 5 0.93 - 1.14: 1584 1.14 - 1.36: 408 1.36 - 1.57: 972 Warning: very small bond lengths. Bond restraints: 2976 Sorted by residual: bond pdb=" CD1 LEU E 16 " pdb="HD11 LEU E 16 " ideal model delta sigma weight residual 0.970 0.496 0.474 2.00e-02 2.50e+03 5.62e+02 bond pdb=" CD1 LEU E 16 " pdb="HD12 LEU E 16 " ideal model delta sigma weight residual 0.970 0.513 0.457 2.00e-02 2.50e+03 5.23e+02 bond pdb=" CD1 LEU E 16 " pdb="HD13 LEU E 16 " ideal model delta sigma weight residual 0.970 0.569 0.401 2.00e-02 2.50e+03 4.02e+02 bond pdb=" CD1 LEU I 16 " pdb="HD13 LEU I 16 " ideal model delta sigma weight residual 0.970 0.655 0.315 2.00e-02 2.50e+03 2.49e+02 bond pdb=" CD1 LEU I 16 " pdb="HD12 LEU I 16 " ideal model delta sigma weight residual 0.970 0.661 0.309 2.00e-02 2.50e+03 2.38e+02 ... (remaining 2971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.65: 5404 7.65 - 15.31: 17 15.31 - 22.96: 24 22.96 - 30.62: 13 30.62 - 38.27: 26 Bond angle restraints: 5484 Sorted by residual: angle pdb="HD12 LEU E 16 " pdb=" CD1 LEU E 16 " pdb="HD13 LEU E 16 " ideal model delta sigma weight residual 110.00 71.73 38.27 3.00e+00 1.11e-01 1.63e+02 angle pdb="HD11 LEU E 16 " pdb=" CD1 LEU E 16 " pdb="HD13 LEU E 16 " ideal model delta sigma weight residual 110.00 73.75 36.25 3.00e+00 1.11e-01 1.46e+02 angle pdb=" CB LEU B 16 " pdb=" CG LEU B 16 " pdb=" HG LEU B 16 " ideal model delta sigma weight residual 109.00 73.21 35.79 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CB LEU G 16 " pdb=" CG LEU G 16 " pdb=" HG LEU G 16 " ideal model delta sigma weight residual 109.00 73.22 35.78 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CD1 LEU F 16 " pdb=" CG LEU F 16 " pdb=" HG LEU F 16 " ideal model delta sigma weight residual 108.00 73.58 34.42 3.00e+00 1.11e-01 1.32e+02 ... (remaining 5479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 1140 16.95 - 33.90: 57 33.90 - 50.85: 44 50.85 - 67.81: 51 67.81 - 84.76: 4 Dihedral angle restraints: 1296 sinusoidal: 744 harmonic: 552 Sorted by residual: dihedral pdb=" C LEU F 16 " pdb=" N LEU F 16 " pdb=" CA LEU F 16 " pdb=" CB LEU F 16 " ideal model delta harmonic sigma weight residual -122.60 -134.39 11.79 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" C LEU D 16 " pdb=" N LEU D 16 " pdb=" CA LEU D 16 " pdb=" CB LEU D 16 " ideal model delta harmonic sigma weight residual -122.60 -133.99 11.39 0 2.50e+00 1.60e-01 2.08e+01 dihedral pdb=" C LEU J 16 " pdb=" N LEU J 16 " pdb=" CA LEU J 16 " pdb=" CB LEU J 16 " ideal model delta harmonic sigma weight residual -122.60 -133.62 11.02 0 2.50e+00 1.60e-01 1.94e+01 ... (remaining 1293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 221 0.216 - 0.433: 8 0.433 - 0.649: 1 0.649 - 0.865: 3 0.865 - 1.081: 7 Chirality restraints: 240 Sorted by residual: chirality pdb=" CG LEU A 16 " pdb=" CB LEU A 16 " pdb=" CD1 LEU A 16 " pdb=" CD2 LEU A 16 " both_signs ideal model delta sigma weight residual False -2.59 -1.51 -1.08 2.00e-01 2.50e+01 2.92e+01 chirality pdb=" CG LEU K 16 " pdb=" CB LEU K 16 " pdb=" CD1 LEU K 16 " pdb=" CD2 LEU K 16 " both_signs ideal model delta sigma weight residual False -2.59 -1.56 -1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" CG LEU J 16 " pdb=" CB LEU J 16 " pdb=" CD1 LEU J 16 " pdb=" CD2 LEU J 16 " both_signs ideal model delta sigma weight residual False -2.59 -1.62 -0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 237 not shown) Planarity restraints: 396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 3 " 0.043 2.00e-02 2.50e+03 2.61e-02 2.04e+01 pdb=" CG PHE L 3 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE L 3 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE L 3 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE L 3 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE L 3 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE L 3 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE L 3 " -0.029 2.00e-02 2.50e+03 pdb=" HD2 PHE L 3 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE L 3 " 0.049 2.00e-02 2.50e+03 pdb=" HE2 PHE L 3 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE L 3 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 3 " -0.034 2.00e-02 2.50e+03 1.99e-02 1.19e+01 pdb=" CG PHE F 3 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE F 3 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE F 3 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE F 3 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 3 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE F 3 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE F 3 " 0.015 2.00e-02 2.50e+03 pdb=" HD2 PHE F 3 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 PHE F 3 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 PHE F 3 " -0.016 2.00e-02 2.50e+03 pdb=" HZ PHE F 3 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 3 " -0.030 2.00e-02 2.50e+03 1.94e-02 1.13e+01 pdb=" CG PHE J 3 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE J 3 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE J 3 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE J 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE J 3 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE J 3 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE J 3 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE J 3 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE J 3 " -0.038 2.00e-02 2.50e+03 pdb=" HE2 PHE J 3 " -0.007 2.00e-02 2.50e+03 pdb=" HZ PHE J 3 " -0.008 2.00e-02 2.50e+03 ... (remaining 393 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.78: 27 1.78 - 2.46: 1374 2.46 - 3.14: 8798 3.14 - 3.82: 9438 3.82 - 4.50: 14856 Nonbonded interactions: 34493 Sorted by model distance: nonbonded pdb="HD12 LEU B 16 " pdb="HD21 LEU J 16 " model vdw 1.103 2.440 nonbonded pdb="HG21 ILE D 13 " pdb="HD11 LEU D 16 " model vdw 1.467 2.440 nonbonded pdb="HD13 LEU B 16 " pdb="HD21 LEU J 16 " model vdw 1.497 2.440 nonbonded pdb=" CD1 LEU B 16 " pdb="HD21 LEU J 16 " model vdw 1.553 2.920 nonbonded pdb=" HB3 LEU B 16 " pdb=" HG LEU B 16 " model vdw 1.593 1.952 ... (remaining 34488 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.870 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.450 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 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 : 0.012 0.092 1380 Z= 0.639 Angle : 2.460 26.250 1836 Z= 1.139 Chirality : 0.215 1.081 240 Planarity : 0.008 0.028 216 Dihedral : 14.140 84.756 492 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.81 % Favored : 76.19 % Rotamer: Outliers : 0.69 % Allowed : 6.25 % Favored : 93.06 % Cbeta Deviations : 1.92 % 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 are not related in a simple way. whole: -5.14 (0.55), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.009 PHE L 3 Details of bonding type rmsd covalent geometry : bond 0.01163 ( 1380) covalent geometry : angle 2.45968 ( 1836) hydrogen bonds : bond 0.04194 ( 24) hydrogen bonds : angle 7.28273 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.085 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 23 average time/residue: 0.0987 time to fit residues: 2.7095 Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.5285 r_free = 0.5285 target = 0.179452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.141447 restraints weight = 4890.822| |-----------------------------------------------------------------------------| r_work (start): 0.4928 rms_B_bonded: 3.94 r_work: 0.4737 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 1380 Z= 0.181 Angle : 1.250 12.098 1836 Z= 0.467 Chirality : 0.365 1.649 240 Planarity : 0.002 0.005 216 Dihedral : 15.050 83.059 192 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.88 % Favored : 85.12 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % 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 are not related in a simple way. whole: -4.95 (0.55), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE E 3 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 1380) covalent geometry : angle 1.24978 ( 1836) hydrogen bonds : bond 0.01571 ( 24) hydrogen bonds : angle 4.61702 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.079 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 23 average time/residue: 0.0852 time to fit residues: 2.3626 Evaluate side-chains 21 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.5232 r_free = 0.5232 target = 0.168918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4884 r_free = 0.4884 target = 0.132363 restraints weight = 4866.261| |-----------------------------------------------------------------------------| r_work (start): 0.4909 rms_B_bonded: 3.76 r_work: 0.4725 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 1380 Z= 0.154 Angle : 1.249 10.928 1836 Z= 0.449 Chirality : 0.373 1.706 240 Planarity : 0.001 0.004 216 Dihedral : 13.798 88.773 192 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.88 % Favored : 85.12 % Rotamer: Outliers : 1.39 % Allowed : 10.42 % Favored : 88.19 % 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 are not related in a simple way. whole: -4.85 (0.55), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.69 (0.42), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE K 3 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 1380) covalent geometry : angle 1.24946 ( 1836) hydrogen bonds : bond 0.01091 ( 24) hydrogen bonds : angle 3.96917 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.090 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 15 average time/residue: 0.1100 time to fit residues: 1.9808 Evaluate side-chains 15 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 4 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.5257 r_free = 0.5257 target = 0.174804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.136330 restraints weight = 5037.137| |-----------------------------------------------------------------------------| r_work (start): 0.4863 rms_B_bonded: 3.95 r_work: 0.4672 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1380 Z= 0.139 Angle : 1.243 11.784 1836 Z= 0.450 Chirality : 0.380 1.773 240 Planarity : 0.001 0.004 216 Dihedral : 11.903 70.980 192 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 1.39 % Allowed : 11.11 % Favored : 87.50 % 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 are not related in a simple way. whole: -4.70 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 3 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 1380) covalent geometry : angle 1.24295 ( 1836) hydrogen bonds : bond 0.00880 ( 24) hydrogen bonds : angle 3.38555 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.052 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 13 average time/residue: 0.0506 time to fit residues: 0.8396 Evaluate side-chains 14 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 16 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.5163 r_free = 0.5163 target = 0.159953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.123489 restraints weight = 5109.083| |-----------------------------------------------------------------------------| r_work (start): 0.4781 rms_B_bonded: 3.73 r_work: 0.4603 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1380 Z= 0.155 Angle : 1.244 11.102 1836 Z= 0.451 Chirality : 0.379 1.781 240 Planarity : 0.001 0.005 216 Dihedral : 11.483 70.814 192 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 1.39 % Allowed : 12.50 % Favored : 86.11 % 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 are not related in a simple way. whole: -4.59 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE D 3 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 1380) covalent geometry : angle 1.24370 ( 1836) hydrogen bonds : bond 0.01265 ( 24) hydrogen bonds : angle 3.10387 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.108 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 13 average time/residue: 0.0827 time to fit residues: 1.3792 Evaluate side-chains 13 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 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 = 0.5082 r_free = 0.5082 target = 0.156876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.119795 restraints weight = 5286.972| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 3.75 r_work: 0.4533 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1380 Z= 0.179 Angle : 1.250 11.772 1836 Z= 0.458 Chirality : 0.381 1.760 240 Planarity : 0.001 0.005 216 Dihedral : 11.403 74.016 192 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 1.39 % Allowed : 11.81 % Favored : 86.81 % 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 are not related in a simple way. whole: -4.46 (0.57), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.004 0.001 PHE B 3 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 1380) covalent geometry : angle 1.25019 ( 1836) hydrogen bonds : bond 0.01456 ( 24) hydrogen bonds : angle 2.91338 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.087 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 17 average time/residue: 0.0743 time to fit residues: 1.6114 Evaluate side-chains 17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 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 = 0.5119 r_free = 0.5119 target = 0.158583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.122393 restraints weight = 5201.648| |-----------------------------------------------------------------------------| r_work (start): 0.4747 rms_B_bonded: 3.70 r_work: 0.4571 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1380 Z= 0.147 Angle : 1.240 11.361 1836 Z= 0.448 Chirality : 0.379 1.709 240 Planarity : 0.001 0.004 216 Dihedral : 11.193 72.132 192 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 13.19 % Favored : 86.81 % 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 are not related in a simple way. whole: -4.41 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE J 3 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 1380) covalent geometry : angle 1.23996 ( 1836) hydrogen bonds : bond 0.01045 ( 24) hydrogen bonds : angle 2.72169 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.091 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0711 time to fit residues: 1.4544 Evaluate side-chains 16 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.5214 r_free = 0.5214 target = 0.167428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4803 r_free = 0.4803 target = 0.130546 restraints weight = 5194.871| |-----------------------------------------------------------------------------| r_work (start): 0.4822 rms_B_bonded: 3.99 r_work: 0.4627 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1380 Z= 0.139 Angle : 1.240 11.313 1836 Z= 0.447 Chirality : 0.379 1.711 240 Planarity : 0.001 0.005 216 Dihedral : 10.659 69.514 192 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.69 % Allowed : 12.50 % Favored : 86.81 % 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 are not related in a simple way. whole: -4.34 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE L 3 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 1380) covalent geometry : angle 1.23978 ( 1836) hydrogen bonds : bond 0.00886 ( 24) hydrogen bonds : angle 2.53745 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.086 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.0777 time to fit residues: 1.3989 Evaluate side-chains 14 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.5134 r_free = 0.5134 target = 0.157520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.121935 restraints weight = 5225.137| |-----------------------------------------------------------------------------| r_work (start): 0.4794 rms_B_bonded: 3.81 r_work: 0.4603 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1380 Z= 0.159 Angle : 1.243 11.294 1836 Z= 0.452 Chirality : 0.379 1.708 240 Planarity : 0.001 0.004 216 Dihedral : 10.272 68.166 192 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % 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 are not related in a simple way. whole: -4.25 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE J 3 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 1380) covalent geometry : angle 1.24323 ( 1836) hydrogen bonds : bond 0.01344 ( 24) hydrogen bonds : angle 2.60054 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.059 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0547 time to fit residues: 1.1265 Evaluate side-chains 15 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 1 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.5199 r_free = 0.5199 target = 0.166265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.129727 restraints weight = 5059.922| |-----------------------------------------------------------------------------| r_work (start): 0.4787 rms_B_bonded: 4.04 r_work: 0.4589 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1380 Z= 0.135 Angle : 1.242 11.307 1836 Z= 0.448 Chirality : 0.380 1.706 240 Planarity : 0.001 0.006 216 Dihedral : 10.253 67.192 192 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.69 % Allowed : 13.89 % Favored : 85.42 % 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 are not related in a simple way. whole: -4.19 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE A 3 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 1380) covalent geometry : angle 1.24155 ( 1836) hydrogen bonds : bond 0.00763 ( 24) hydrogen bonds : angle 2.51203 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.089 Fit side-chains REVERT: L 16 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8732 (mt) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 0.0871 time to fit residues: 1.3391 Evaluate side-chains 13 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.5184 r_free = 0.5184 target = 0.164163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.127240 restraints weight = 5163.716| |-----------------------------------------------------------------------------| r_work (start): 0.4785 rms_B_bonded: 4.15 r_work: 0.4580 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 1380 Z= 0.158 Angle : 1.242 11.281 1836 Z= 0.451 Chirality : 0.380 1.709 240 Planarity : 0.001 0.005 216 Dihedral : 10.108 67.307 192 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 1.39 % Allowed : 13.19 % Favored : 85.42 % 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 are not related in a simple way. whole: -4.19 (0.56), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.000 PHE A 3 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 1380) covalent geometry : angle 1.24247 ( 1836) hydrogen bonds : bond 0.01298 ( 24) hydrogen bonds : angle 2.58039 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1092.59 seconds wall clock time: 19 minutes 13.50 seconds (1153.50 seconds total)