Starting phenix.real_space_refine on Fri Aug 22 12:37:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z93_39853/08_2025/8z93_39853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z93_39853/08_2025/8z93_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_39853/08_2025/8z93_39853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z93_39853/08_2025/8z93_39853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z93_39853/08_2025/8z93_39853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z93_39853/08_2025/8z93_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-2.0-5787/lib/python3.9/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: 0.23, per 1000 atoms: 0.48 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 24.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.22 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: 0.07 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: 0.690 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: 0.010 Process input model: 3.000 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 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 aren 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 covalent geometry : bond 0.00639 ( 486) covalent geometry : angle 1.05252 ( 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: 0.0154 time to fit residues: 0.1182 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... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4035 r_free = 0.4035 target = 0.128854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115042 restraints weight = 524.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.117003 restraints weight = 290.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.118740 restraints weight = 218.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.120536 restraints weight = 158.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.121867 restraints weight = 119.756| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5105 moved from start: 0.6359 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 : 2.506 Molprobity Statistics. All-atom Clashscore : 45.75 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 aren 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 covalent geometry : bond 0.00744 ( 486) covalent geometry : angle 1.03234 ( 657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 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: 0.0153 time to fit residues: 0.0859 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: 2.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4112 r_free = 0.4112 target = 0.173894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.149411 restraints weight = 417.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.152711 restraints weight = 235.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.154108 restraints weight = 158.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.156286 restraints weight = 129.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.157229 restraints weight = 96.072| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 moved from start: 0.7456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 486 Z= 0.235 Angle : 0.943 5.699 657 Z= 0.531 Chirality : 0.080 0.179 69 Planarity : 0.006 0.011 81 Dihedral : 9.196 22.741 69 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 35.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 38.89 % Favored : 61.11 % Rotamer: Outliers : 6.25 % Allowed : 0.00 % 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 aren not related in a simple way. whole: -8.13 (0.48), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.19 (0.36), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.004 TYR C 534 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 486) covalent geometry : angle 0.94261 ( 657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 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: 1 poor density : 4 time to evaluate : 0.004 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 5 average time/residue: 0.0166 time to fit residues: 0.0921 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.6983 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.193847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.166744 restraints weight = 343.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170268 restraints weight = 176.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.172686 restraints weight = 107.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.174479 restraints weight = 71.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.175913 restraints weight = 50.761| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4900 moved from start: 0.8275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 486 Z= 0.280 Angle : 0.952 6.698 657 Z= 0.542 Chirality : 0.078 0.205 69 Planarity : 0.006 0.014 81 Dihedral : 7.714 16.807 69 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 34.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 44.44 % Favored : 55.56 % 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 aren not related in a simple way. whole: -8.01 (0.49), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.10 (0.37), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.004 TYR B 544 Details of bonding type rmsd covalent geometry : bond 0.00610 ( 486) covalent geometry : angle 0.95214 ( 657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 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 : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0140 time to fit residues: 0.0934 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.6650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.176749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.155641 restraints weight = 390.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.158342 restraints weight = 215.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.160348 restraints weight = 146.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.161797 restraints weight = 111.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.162404 restraints weight = 89.515| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 moved from start: 0.8050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 486 Z= 0.165 Angle : 0.790 5.603 657 Z= 0.443 Chirality : 0.066 0.143 69 Planarity : 0.005 0.012 81 Dihedral : 7.848 19.403 69 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 35.95 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 aren not related in a simple way. whole: -8.10 (0.46), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.17 (0.35), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.003 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 486) covalent geometry : angle 0.79043 ( 657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 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 REVERT: A 547 MET cc_start: 0.7879 (tmm) cc_final: 0.7514 (ttt) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0149 time to fit residues: 0.0847 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 : 0.005 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 0.0870 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.0870 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 overall best weight: 1.7243 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.148581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.124618 restraints weight = 358.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.127957 restraints weight = 227.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.129757 restraints weight = 165.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.131516 restraints weight = 137.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.131516 restraints weight = 118.141| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5237 moved from start: 0.8194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 486 Z= 0.194 Angle : 0.835 4.968 657 Z= 0.457 Chirality : 0.068 0.153 69 Planarity : 0.005 0.011 81 Dihedral : 7.674 19.114 69 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 34.86 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 aren not related in a simple way. whole: -7.49 (0.51), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.70 (0.39), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.025 0.003 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 486) covalent geometry : angle 0.83542 ( 657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 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: 0.0129 time to fit residues: 0.0740 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: 0.0170 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.0170 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.6777 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.160829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.136910 restraints weight = 440.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.138090 restraints weight = 287.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.139877 restraints weight = 239.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.140501 restraints weight = 199.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.141438 restraints weight = 183.012| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5306 moved from start: 0.8622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 486 Z= 0.169 Angle : 0.769 5.014 657 Z= 0.434 Chirality : 0.066 0.143 69 Planarity : 0.005 0.011 81 Dihedral : 7.838 21.408 69 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 32.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 44.44 % Favored : 55.56 % 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 aren not related in a simple way. whole: -7.32 (0.55), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.58 (0.42), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.002 TYR A 534 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 486) covalent geometry : angle 0.76857 ( 657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 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 : 0.019 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0231 time to fit residues: 0.1314 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 : 0.007 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.219122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.164914 restraints weight = 344.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.167188 restraints weight = 231.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.169540 restraints weight = 191.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.170803 restraints weight = 162.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.172419 restraints weight = 145.954| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5487 moved from start: 0.8678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 486 Z= 0.231 Angle : 0.777 5.104 657 Z= 0.444 Chirality : 0.064 0.147 69 Planarity : 0.005 0.011 81 Dihedral : 8.458 22.296 69 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 39.22 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 aren not related in a simple way. whole: -6.66 (0.71), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.07 (0.54), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.003 TYR C 534 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 486) covalent geometry : angle 0.77749 ( 657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 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 : 0.007 Fit side-chains REVERT: A 534 TYR cc_start: 0.5318 (p90) cc_final: 0.4616 (m-10) outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0222 time to fit residues: 0.1720 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 : 0.007 ------------------------------------------------------------------------------- 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: 6.9990 chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.1317 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.162189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.139315 restraints weight = 328.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.142466 restraints weight = 213.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.144281 restraints weight = 157.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.145862 restraints weight = 128.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.145862 restraints weight = 109.340| |-----------------------------------------------------------------------------| r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5387 moved from start: 0.9229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 486 Z= 0.182 Angle : 0.816 5.567 657 Z= 0.465 Chirality : 0.067 0.164 69 Planarity : 0.005 0.017 81 Dihedral : 7.926 21.203 69 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 42.48 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 aren not related in a simple way. whole: -6.82 (0.69), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.19 (0.53), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.004 TYR C 534 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 486) covalent geometry : angle 0.81610 ( 657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 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 : 0.007 Fit side-chains REVERT: A 534 TYR cc_start: 0.5203 (p90) cc_final: 0.4564 (m-10) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0254 time to fit residues: 0.1428 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 : 0.007 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.154009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.131211 restraints weight = 488.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.134220 restraints weight = 312.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.135696 restraints weight = 225.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.137358 restraints weight = 186.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.138141 restraints weight = 153.204| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 moved from start: 0.9103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 486 Z= 0.392 Angle : 1.059 5.962 657 Z= 0.583 Chirality : 0.075 0.179 69 Planarity : 0.007 0.018 81 Dihedral : 10.055 25.827 69 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 45.75 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 aren not related in a simple way. whole: -6.74 (0.81), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.13 (0.62), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.044 0.004 TYR C 534 Details of bonding type rmsd covalent geometry : bond 0.00792 ( 486) covalent geometry : angle 1.05909 ( 657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 72 Ramachandran restraints generated. 36 Oldfield, 0 Emsley, 36 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 : 0.023 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0256 time to fit residues: 0.1877 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 : 0.007 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 overall best weight: 5.6657 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.151257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.131353 restraints weight = 488.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.133039 restraints weight = 351.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.133371 restraints weight = 281.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.133394 restraints weight = 269.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.133394 restraints weight = 268.432| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5798 moved from start: 0.9155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.030 486 Z= 0.371 Angle : 1.044 5.630 657 Z= 0.568 Chirality : 0.074 0.175 69 Planarity : 0.007 0.017 81 Dihedral : 10.478 26.294 69 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 46.84 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 aren not related in a simple way. whole: -6.57 (0.97), residues: 54 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.00 (0.74), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.005 TYR C 534 Details of bonding type rmsd covalent geometry : bond 0.00751 ( 486) covalent geometry : angle 1.04359 ( 657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 244.67 seconds wall clock time: 5 minutes 15.16 seconds (315.16 seconds total)