Starting phenix.real_space_refine on Wed Jul 1 20:41:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z93_39853/07_2026/8z93_39853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z93_39853/07_2026/8z93_39853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z93_39853/07_2026/8z93_39853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z93_39853/07_2026/8z93_39853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z93_39853/07_2026/8z93_39853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z93_39853/07_2026/8z93_39853.map" } resolution = 4.65 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= 0.002 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 S 3 5.16 5 C 309 2.51 5 N 69 2.21 5 O 96 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 477 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 159 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Restraints were copied for chains: B, C Time building chain proxies: 0.17, per 1000 atoms: 0.36 Number of scatterers: 477 At special positions: 0 Unit cell: (43.46, 40.28, 29.68, 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) S 3 16.00 O 96 8.00 N 69 7.00 C 309 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 26.7 milliseconds 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 102 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: 0.46 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: 0.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 132 1.33 - 1.45: 105 1.45 - 1.56: 243 1.56 - 1.67: 0 1.67 - 1.79: 6 Bond restraints: 486 Sorted by residual: bond pdb=" CA MET C 547 " pdb=" CB MET C 547 " ideal model delta sigma weight residual 1.534 1.517 0.017 1.64e-02 3.72e+03 1.05e+00 bond pdb=" CA MET A 547 " pdb=" CB MET A 547 " ideal model delta sigma weight residual 1.534 1.517 0.016 1.64e-02 3.72e+03 1.00e+00 bond pdb=" CA MET B 547 " pdb=" CB MET B 547 " ideal model delta sigma weight residual 1.534 1.518 0.016 1.64e-02 3.72e+03 9.55e-01 bond pdb=" N THR A 537 " pdb=" CA THR A 537 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.20e-02 6.94e+03 8.04e-01 bond pdb=" N THR C 537 " pdb=" CA THR C 537 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.20e-02 6.94e+03 8.02e-01 ... (remaining 481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 557 1.30 - 2.59: 82 2.59 - 3.88: 15 3.88 - 5.18: 0 5.18 - 6.47: 3 Bond angle restraints: 657 Sorted by residual: angle pdb=" CA TYR A 534 " pdb=" CB TYR A 534 " pdb=" CG TYR A 534 " ideal model delta sigma weight residual 113.90 120.37 -6.47 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA TYR C 534 " pdb=" CB TYR C 534 " pdb=" CG TYR C 534 " ideal model delta sigma weight residual 113.90 120.36 -6.46 1.80e+00 3.09e-01 1.29e+01 angle pdb=" CA TYR B 534 " pdb=" CB TYR B 534 " pdb=" CG TYR B 534 " ideal model delta sigma weight residual 113.90 120.34 -6.44 1.80e+00 3.09e-01 1.28e+01 angle pdb=" N GLY C 538 " pdb=" CA GLY C 538 " pdb=" C GLY C 538 " ideal model delta sigma weight residual 111.62 115.43 -3.81 1.77e+00 3.19e-01 4.62e+00 angle pdb=" N GLY A 538 " pdb=" CA GLY A 538 " pdb=" C GLY A 538 " ideal model delta sigma weight residual 111.62 115.41 -3.79 1.77e+00 3.19e-01 4.59e+00 ... (remaining 652 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 6.58: 178 6.58 - 13.15: 26 13.15 - 19.72: 39 19.72 - 26.29: 15 26.29 - 32.86: 9 Dihedral angle restraints: 267 sinusoidal: 96 harmonic: 171 Sorted by residual: dihedral pdb=" CA THR B 537 " pdb=" C THR B 537 " pdb=" N GLY B 538 " pdb=" CA GLY B 538 " ideal model delta harmonic sigma weight residual -180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA THR C 537 " pdb=" C THR C 537 " pdb=" N GLY C 538 " pdb=" CA GLY C 538 " ideal model delta harmonic sigma weight residual 180.00 -152.17 -27.83 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA THR A 537 " pdb=" C THR A 537 " pdb=" N GLY A 538 " pdb=" CA GLY A 538 " ideal model delta harmonic sigma weight residual 180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 264 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.038: 36 0.038 - 0.075: 18 0.075 - 0.112: 9 0.112 - 0.148: 3 0.148 - 0.185: 3 Chirality restraints: 69 Sorted by residual: chirality pdb=" CA TYR C 534 " pdb=" N TYR C 534 " pdb=" C TYR C 534 " pdb=" CB TYR C 534 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA TYR B 534 " pdb=" N TYR B 534 " pdb=" C TYR B 534 " pdb=" CB TYR B 534 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA TYR A 534 " pdb=" N TYR A 534 " pdb=" C TYR A 534 " pdb=" CB TYR A 534 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.38e-01 ... (remaining 66 not shown) Planarity restraints: 81 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 534 " 0.017 2.00e-02 2.50e+03 1.46e-02 4.25e+00 pdb=" CG TYR B 534 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 534 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 534 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 534 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 534 " 0.016 2.00e-02 2.50e+03 1.45e-02 4.23e+00 pdb=" CG TYR A 534 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 534 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 534 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 534 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 534 " 0.016 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR C 534 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR C 534 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 534 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 534 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 534 " -0.001 2.00e-02 2.50e+03 ... (remaining 78 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 27 2.63 - 3.20: 532 3.20 - 3.76: 702 3.76 - 4.33: 996 4.33 - 4.90: 1471 Nonbonded interactions: 3728 Sorted by model distance: nonbonded pdb=" N TYR B 531 " pdb=" OG1 THR C 532 " model vdw 2.060 3.120 nonbonded pdb=" N GLY B 550 " pdb=" O ILE C 549 " model vdw 2.232 3.120 nonbonded pdb=" O SER A 536 " pdb=" OG1 THR A 537 " model vdw 2.312 3.040 nonbonded pdb=" O SER C 536 " pdb=" OG1 THR C 537 " model vdw 2.313 3.040 nonbonded pdb=" O SER B 536 " pdb=" OG1 THR B 537 " model vdw 2.313 3.040 ... (remaining 3723 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' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 1.880 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 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 : 0.006 0.028 486 Z= 0.307 Angle : 1.053 6.472 657 Z= 0.609 Chirality : 0.065 0.185 69 Planarity : 0.005 0.015 81 Dihedral : 13.343 32.863 165 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 54.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -7.84 (0.52), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.40), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.036 0.004 TYR A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.31 ( 486) covalent geometry : angle 1.05252 / 0.61 ( 657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0144 time to fit residues: 0.1114 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 overall best weight: 3.3350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.128749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.114986 restraints weight = 523.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.117844 restraints weight = 293.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.119578 restraints weight = 191.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.121287 restraints weight = 139.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.122026 restraints weight = 104.928| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5004 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 486 Z= 0.346 Angle : 1.032 5.126 657 Z= 0.586 Chirality : 0.082 0.195 69 Planarity : 0.008 0.018 81 Dihedral : 11.181 27.786 69 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 41.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % 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: -8.37 (0.44), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.37 (0.34), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.006 TYR C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.35 ( 486) covalent geometry : angle 1.03234 / 0.59 ( 657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0150 time to fit residues: 0.0843 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 5.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.180369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.147728 restraints weight = 423.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.149700 restraints weight = 271.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.152268 restraints weight = 209.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.153369 restraints weight = 159.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.154441 restraints weight = 134.734| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5029 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 486 Z= 0.359 Angle : 1.183 7.360 657 Z= 0.656 Chirality : 0.084 0.189 69 Planarity : 0.007 0.014 81 Dihedral : 11.629 29.804 69 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 40.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 6.25 % Allowed : 6.25 % 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: -8.02 (0.50), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.11 (0.39), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.004 TYR C 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00722 / 0.36 ( 486) covalent geometry : angle 1.18329 / 0.66 ( 657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.004 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 6 average time/residue: 0.0141 time to fit residues: 0.0944 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.141179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.121978 restraints weight = 392.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.124855 restraints weight = 222.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.126848 restraints weight = 153.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.127829 restraints weight = 117.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.127834 restraints weight = 100.118| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5273 moved from start: 0.8174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 486 Z= 0.365 Angle : 1.108 6.810 657 Z= 0.625 Chirality : 0.084 0.204 69 Planarity : 0.008 0.025 81 Dihedral : 11.965 26.861 69 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 40.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -8.22 (0.45), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.26 (0.34), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.005 TYR A 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.37 ( 486) covalent geometry : angle 1.10822 / 0.62 ( 657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0134 time to fit residues: 0.0767 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.0010 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.0060 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0050 overall best weight: 0.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.214208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.184354 restraints weight = 314.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.188838 restraints weight = 204.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.192219 restraints weight = 143.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.194814 restraints weight = 110.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.196460 restraints weight = 89.669| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5096 moved from start: 0.8857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 486 Z= 0.222 Angle : 0.908 6.069 657 Z= 0.501 Chirality : 0.078 0.188 69 Planarity : 0.006 0.019 81 Dihedral : 9.061 20.847 69 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 42.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 27.78 % Favored : 72.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.91 (0.47), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.02 (0.36), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.004 TYR B 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 ( 486) covalent geometry : angle 0.90789 / 0.50 ( 657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0124 time to fit residues: 0.0842 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.0670 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.4210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 545 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.157827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.135821 restraints weight = 339.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.138959 restraints weight = 214.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.141169 restraints weight = 155.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.142445 restraints weight = 121.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.142748 restraints weight = 102.796| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4955 moved from start: 0.9361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 486 Z= 0.197 Angle : 0.893 5.419 657 Z= 0.504 Chirality : 0.071 0.162 69 Planarity : 0.005 0.011 81 Dihedral : 9.093 21.863 69 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 40.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.82 (0.46), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.96 (0.35), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.004 TYR A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 ( 486) covalent geometry : angle 0.89303 / 0.50 ( 657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0123 time to fit residues: 0.0705 Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 overall best weight: 1.3647 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.174879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.147872 restraints weight = 345.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.152365 restraints weight = 203.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.154972 restraints weight = 140.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.157163 restraints weight = 108.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.157150 restraints weight = 88.707| |-----------------------------------------------------------------------------| r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5012 moved from start: 1.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 486 Z= 0.267 Angle : 1.114 7.096 657 Z= 0.610 Chirality : 0.077 0.152 69 Planarity : 0.006 0.013 81 Dihedral : 11.705 35.375 69 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 51.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 5.26 % 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: -7.72 (0.49), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.88 (0.37), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.031 0.005 TYR C 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.27 ( 486) covalent geometry : angle 1.11368 / 0.61 ( 657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.004 Fit side-chains REVERT: A 534 TYR cc_start: 0.5499 (p90) cc_final: 0.4988 (m-80) outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0123 time to fit residues: 0.0967 Evaluate side-chains 5 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 3.5987 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 540 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.183924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.166216 restraints weight = 473.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.166643 restraints weight = 422.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.166741 restraints weight = 396.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.166741 restraints weight = 392.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.166741 restraints weight = 392.071| |-----------------------------------------------------------------------------| r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5223 moved from start: 1.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 486 Z= 0.306 Angle : 1.216 7.676 657 Z= 0.623 Chirality : 0.080 0.150 69 Planarity : 0.007 0.015 81 Dihedral : 11.601 25.299 69 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 49.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 33.33 % Favored : 66.67 % Rotamer: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % 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: -7.85 (0.46), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.98 (0.35), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.037 0.006 TYR C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.31 ( 486) covalent geometry : angle 1.21570 / 0.62 ( 657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.0244 time to fit residues: 0.0862 Evaluate side-chains 2 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 5.6657 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.173901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.156704 restraints weight = 449.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.157443 restraints weight = 397.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.157443 restraints weight = 365.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.157443 restraints weight = 365.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.157443 restraints weight = 365.051| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 moved from start: 1.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.039 486 Z= 0.430 Angle : 1.257 5.867 657 Z= 0.680 Chirality : 0.079 0.167 69 Planarity : 0.007 0.019 81 Dihedral : 12.643 27.317 69 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 47.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.93 (0.46), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.04 (0.35), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.046 0.007 TYR B 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00928 / 0.43 ( 486) covalent geometry : angle 1.25652 / 0.68 ( 657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0199 time to fit residues: 0.0919 Evaluate side-chains 3 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 4.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.158813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.146348 restraints weight = 501.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.147067 restraints weight = 401.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.147750 restraints weight = 350.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.147747 restraints weight = 311.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.147747 restraints weight = 311.038| |-----------------------------------------------------------------------------| r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5746 moved from start: 1.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 486 Z= 0.359 Angle : 1.226 6.003 657 Z= 0.665 Chirality : 0.074 0.156 69 Planarity : 0.007 0.020 81 Dihedral : 12.260 27.087 69 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 47.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.86 (0.47), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.99 (0.36), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.049 0.007 TYR B 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00792 / 0.36 ( 486) covalent geometry : angle 1.22577 / 0.66 ( 657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 108 Ramachandran restraints generated. 54 Oldfield, 0 Emsley, 54 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0204 time to fit residues: 0.0943 Evaluate side-chains 3 residues out of total 16 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.172984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.156292 restraints weight = 468.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.156740 restraints weight = 414.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.157200 restraints weight = 385.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.157200 restraints weight = 362.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.157200 restraints weight = 362.051| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 1.0658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.039 486 Z= 0.391 Angle : 1.218 5.390 657 Z= 0.659 Chirality : 0.075 0.159 69 Planarity : 0.007 0.019 81 Dihedral : 12.762 27.611 69 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 53.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -7.76 (0.49), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.91 (0.37), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.046 0.006 TYR C 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00855 / 0.39 ( 486) covalent geometry : angle 1.21815 / 0.66 ( 657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 222.26 seconds wall clock time: 4 minutes 45.39 seconds (285.39 seconds total)