Starting phenix.real_space_refine on Tue Feb 3 12:19:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kzb_62658/02_2026/9kzb_62658.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kzb_62658/02_2026/9kzb_62658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kzb_62658/02_2026/9kzb_62658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kzb_62658/02_2026/9kzb_62658.map" model { file = "/net/cci-nas-00/data/ceres_data/9kzb_62658/02_2026/9kzb_62658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kzb_62658/02_2026/9kzb_62658.cif" } resolution = 3.27 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= 0.003 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 558 2.51 5 N 162 2.21 5 O 204 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 924 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 93 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 61 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Restraints were copied for chains: G, I, C, J, K, H, A, D, E, L Time building chain proxies: 0.13, per 1000 atoms: 0.14 Number of scatterers: 924 At special positions: 0 Unit cell: (68.89, 49.8, 29.05, 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 204 8.00 N 162 7.00 C 558 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: 0.04 Conformation dependent library (CDL) restraints added in 35.5 milliseconds 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 168 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 0.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 198 1.29 - 1.35: 150 1.35 - 1.42: 42 1.42 - 1.48: 155 1.48 - 1.55: 373 Bond restraints: 918 Sorted by residual: bond pdb=" CA GLY G 18 " pdb=" C GLY G 18 " ideal model delta sigma weight residual 1.517 1.506 0.011 7.00e-03 2.04e+04 2.65e+00 bond pdb=" CA GLY J 18 " pdb=" C GLY J 18 " ideal model delta sigma weight residual 1.517 1.506 0.011 7.00e-03 2.04e+04 2.52e+00 bond pdb=" CA GLY K 18 " pdb=" C GLY K 18 " ideal model delta sigma weight residual 1.517 1.506 0.011 7.00e-03 2.04e+04 2.45e+00 bond pdb=" CA GLY I 18 " pdb=" C GLY I 18 " ideal model delta sigma weight residual 1.517 1.507 0.011 7.00e-03 2.04e+04 2.41e+00 bond pdb=" CA GLY B 18 " pdb=" C GLY B 18 " ideal model delta sigma weight residual 1.517 1.507 0.011 7.00e-03 2.04e+04 2.28e+00 ... (remaining 913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 894 0.91 - 1.82: 247 1.82 - 2.74: 47 2.74 - 3.65: 12 3.65 - 4.56: 12 Bond angle restraints: 1212 Sorted by residual: angle pdb=" O GLY B 18 " pdb=" C GLY B 18 " pdb=" N GLN B 19 " ideal model delta sigma weight residual 123.61 122.10 1.51 7.70e-01 1.69e+00 3.83e+00 angle pdb=" CA GLY I 16 " pdb=" C GLY I 16 " pdb=" N ALA I 17 " ideal model delta sigma weight residual 114.88 117.75 -2.87 1.47e+00 4.63e-01 3.82e+00 angle pdb=" CA GLY C 16 " pdb=" C GLY C 16 " pdb=" N ALA C 17 " ideal model delta sigma weight residual 114.88 117.74 -2.86 1.47e+00 4.63e-01 3.79e+00 angle pdb=" CA GLY G 16 " pdb=" C GLY G 16 " pdb=" N ALA G 17 " ideal model delta sigma weight residual 114.88 117.73 -2.85 1.47e+00 4.63e-01 3.76e+00 angle pdb=" CA GLY G 18 " pdb=" C GLY G 18 " pdb=" N GLN G 19 " ideal model delta sigma weight residual 115.47 117.81 -2.34 1.21e+00 6.83e-01 3.74e+00 ... (remaining 1207 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 8.40: 342 8.40 - 16.79: 78 16.79 - 25.18: 18 25.18 - 33.58: 6 33.58 - 41.97: 12 Dihedral angle restraints: 456 sinusoidal: 144 harmonic: 312 Sorted by residual: dihedral pdb=" CA GLY B 18 " pdb=" C GLY B 18 " pdb=" N GLN B 19 " pdb=" CA GLN B 19 " ideal model delta harmonic sigma weight residual -180.00 -161.39 -18.61 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLY I 18 " pdb=" C GLY I 18 " pdb=" N GLN I 19 " pdb=" CA GLN I 19 " ideal model delta harmonic sigma weight residual -180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA GLY C 18 " pdb=" C GLY C 18 " pdb=" N GLN C 19 " pdb=" CA GLN C 19 " ideal model delta harmonic sigma weight residual 180.00 -161.40 -18.60 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 453 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.027: 61 0.027 - 0.048: 28 0.048 - 0.070: 1 0.070 - 0.091: 4 0.091 - 0.112: 26 Chirality restraints: 120 Sorted by residual: chirality pdb=" CA VAL K 14 " pdb=" N VAL K 14 " pdb=" C VAL K 14 " pdb=" CB VAL K 14 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA VAL B 11 " pdb=" N VAL B 11 " pdb=" C VAL B 11 " pdb=" CB VAL B 11 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA VAL C 14 " pdb=" N VAL C 14 " pdb=" C VAL C 14 " pdb=" CB VAL C 14 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.10e-01 ... (remaining 117 not shown) Planarity restraints: 174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 22 " 0.015 2.00e-02 2.50e+03 9.50e-03 1.80e+00 pdb=" CG TYR K 22 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR K 22 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR K 22 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR K 22 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR K 22 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR K 22 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR K 22 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 22 " 0.015 2.00e-02 2.50e+03 9.48e-03 1.80e+00 pdb=" CG TYR C 22 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR C 22 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 22 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 22 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C 22 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 22 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 22 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 22 " 0.015 2.00e-02 2.50e+03 9.48e-03 1.80e+00 pdb=" CG TYR B 22 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 22 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 22 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 22 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 22 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 22 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 22 " 0.004 2.00e-02 2.50e+03 ... (remaining 171 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 615 3.06 - 3.52: 735 3.52 - 3.98: 1269 3.98 - 4.44: 1464 4.44 - 4.90: 3015 Nonbonded interactions: 7098 Sorted by model distance: nonbonded pdb=" N VAL G 14 " pdb=" O VAL G 14 " model vdw 2.601 2.496 nonbonded pdb=" N VAL C 14 " pdb=" O VAL C 14 " model vdw 2.601 2.496 nonbonded pdb=" N VAL I 14 " pdb=" O VAL I 14 " model vdw 2.601 2.496 nonbonded pdb=" N VAL K 14 " pdb=" O VAL K 14 " model vdw 2.601 2.496 nonbonded pdb=" N VAL J 14 " pdb=" O VAL J 14 " model vdw 2.601 2.496 ... (remaining 7093 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 'B' selection = chain 'G' selection = chain 'I' selection = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'A' selection = chain 'D' selection = chain 'E' 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: 1.540 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: 0.000 Process input model: 1.960 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.009 0.036 918 Z= 0.488 Angle : 0.966 4.560 1212 Z= 0.615 Chirality : 0.056 0.112 120 Planarity : 0.003 0.009 174 Dihedral : 12.212 41.969 288 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % 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: -6.01 (0.20), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.57 (0.15), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.022 0.006 TYR C 22 Details of bonding type rmsd covalent geometry : bond 0.00853 ( 918) covalent geometry : angle 0.96551 ( 1212) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0090 time to fit residues: 0.1084 Evaluate side-chains 7 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.019 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.0070 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.098943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.090433 restraints weight = 1625.219| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.25 r_work: 0.3541 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 918 Z= 0.241 Angle : 0.682 4.183 1212 Z= 0.374 Chirality : 0.059 0.137 120 Planarity : 0.002 0.007 174 Dihedral : 5.902 17.659 144 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 23.61 % Favored : 76.39 % 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: -4.48 (0.40), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.31), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR B 22 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 918) covalent geometry : angle 0.68163 ( 1212) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0075 time to fit residues: 0.0872 Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 0.0030 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 overall best weight: 1.0794 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.106471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.097907 restraints weight = 1629.092| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.32 r_work: 0.3667 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.002 0.013 918 Z= 0.114 Angle : 0.507 2.962 1212 Z= 0.275 Chirality : 0.059 0.135 120 Planarity : 0.001 0.003 174 Dihedral : 4.489 13.424 144 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.00 % Allowed : 23.61 % Favored : 76.39 % 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: -3.17 (0.57), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.44), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR B 22 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 918) covalent geometry : angle 0.50739 ( 1212) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.023 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0078 time to fit residues: 0.0896 Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.103087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.094224 restraints weight = 1612.596| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.37 r_work: 0.3557 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 918 Z= 0.201 Angle : 0.608 4.107 1212 Z= 0.328 Chirality : 0.055 0.127 120 Planarity : 0.002 0.007 174 Dihedral : 5.084 13.692 144 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 30.56 % Favored : 69.44 % 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: -2.91 (0.59), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.45), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR I 22 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 918) covalent geometry : angle 0.60817 ( 1212) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0129 time to fit residues: 0.1373 Evaluate side-chains 5 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.102869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.094046 restraints weight = 1620.993| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.39 r_work: 0.3623 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 918 Z= 0.130 Angle : 0.517 3.443 1212 Z= 0.276 Chirality : 0.056 0.129 120 Planarity : 0.001 0.004 174 Dihedral : 4.404 12.310 144 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % 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: -2.53 (0.61), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.47), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.003 TYR I 22 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 918) covalent geometry : angle 0.51689 ( 1212) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0078 time to fit residues: 0.0813 Evaluate side-chains 5 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.107028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.097736 restraints weight = 1551.113| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.46 r_work: 0.3641 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 918 Z= 0.103 Angle : 0.469 3.128 1212 Z= 0.249 Chirality : 0.056 0.128 120 Planarity : 0.001 0.003 174 Dihedral : 3.951 11.594 144 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % 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: -2.52 (0.58), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.44), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR G 22 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 918) covalent geometry : angle 0.46935 ( 1212) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0073 time to fit residues: 0.0764 Evaluate side-chains 5 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.018 ------------------------------------------------------------------------------- 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: 1.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 0.0870 chunk 4 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.0270 chunk 6 optimal weight: 1.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.110118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.100589 restraints weight = 1536.829| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.59 r_work: 0.3736 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 918 Z= 0.065 Angle : 0.387 2.509 1212 Z= 0.203 Chirality : 0.057 0.122 120 Planarity : 0.001 0.003 174 Dihedral : 3.163 8.851 144 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % 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: -2.47 (0.52), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.40), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR G 22 Details of bonding type rmsd covalent geometry : bond 0.00136 ( 918) covalent geometry : angle 0.38698 ( 1212) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.030 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0117 time to fit residues: 0.0919 Evaluate side-chains 3 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 0.0670 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.0010 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.3128 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.104623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095159 restraints weight = 1537.871| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.53 r_work: 0.3642 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 918 Z= 0.126 Angle : 0.483 3.598 1212 Z= 0.253 Chirality : 0.054 0.117 120 Planarity : 0.002 0.005 174 Dihedral : 3.791 11.517 144 Min Nonbonded Distance : 2.669 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % 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: -2.45 (0.54), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.41), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.003 TYR I 22 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 918) covalent geometry : angle 0.48306 ( 1212) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0117 time to fit residues: 0.0785 Evaluate side-chains 2 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.019 ------------------------------------------------------------------------------- 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: 7.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.107361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.097557 restraints weight = 1558.144| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.53 r_work: 0.3661 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 918 Z= 0.115 Angle : 0.460 3.335 1212 Z= 0.242 Chirality : 0.054 0.115 120 Planarity : 0.001 0.004 174 Dihedral : 3.757 11.240 144 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % 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: -2.32 (0.55), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.42), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR I 22 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 918) covalent geometry : angle 0.46009 ( 1212) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.018 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1 average time/residue: 0.0145 time to fit residues: 0.0681 Evaluate side-chains 1 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.108362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.098795 restraints weight = 1549.253| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.62 r_work: 0.3700 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 918 Z= 0.076 Angle : 0.402 2.870 1212 Z= 0.209 Chirality : 0.055 0.113 120 Planarity : 0.001 0.003 174 Dihedral : 3.260 9.889 144 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % 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: -2.26 (0.56), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.43), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR I 22 Details of bonding type rmsd covalent geometry : bond 0.00162 ( 918) covalent geometry : angle 0.40248 ( 1212) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 252 Ramachandran restraints generated. 126 Oldfield, 0 Emsley, 126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0334 Evaluate side-chains 0 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 9 optimal weight: 0.0010 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.0670 chunk 1 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 overall best weight: 2.2130 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.100889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.091153 restraints weight = 1522.032| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.48 r_work: 0.3580 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 918 Z= 0.206 Angle : 0.561 4.034 1212 Z= 0.298 Chirality : 0.051 0.108 120 Planarity : 0.002 0.008 174 Dihedral : 4.499 13.723 144 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % 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: -2.25 (0.59), residues: 126 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.45), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR I 22 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 918) covalent geometry : angle 0.56099 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 453.63 seconds wall clock time: 8 minutes 33.63 seconds (513.63 seconds total)