Starting phenix.real_space_refine on Wed Jul 1 20:41:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z94_39854/07_2026/8z94_39854.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z94_39854/07_2026/8z94_39854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z94_39854/07_2026/8z94_39854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z94_39854/07_2026/8z94_39854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z94_39854/07_2026/8z94_39854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z94_39854/07_2026/8z94_39854.map" } resolution = 4.56 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 6 5.16 5 C 315 2.51 5 N 84 2.21 5 O 102 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: 507 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 169 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "A" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 169 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 169 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Time building chain proxies: 0.15, per 1000 atoms: 0.30 Number of scatterers: 507 At special positions: 0 Unit cell: (43.46, 39.22, 31.8, 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 6 16.00 O 102 8.00 N 84 7.00 C 315 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: 0.02 Conformation dependent library (CDL) restraints added in 11.5 milliseconds 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 120 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: 0.64 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: 0.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 171 1.34 - 1.46: 78 1.46 - 1.57: 255 1.57 - 1.69: 0 1.69 - 1.81: 9 Bond restraints: 513 Sorted by residual: bond pdb=" CB VAL B 458 " pdb=" CG1 VAL B 458 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.30e+00 bond pdb=" CA VAL C 458 " pdb=" CB VAL C 458 " ideal model delta sigma weight residual 1.553 1.540 0.013 7.40e-03 1.83e+04 2.94e+00 bond pdb=" CA VAL A 458 " pdb=" CB VAL A 458 " ideal model delta sigma weight residual 1.553 1.541 0.012 7.40e-03 1.83e+04 2.59e+00 bond pdb=" CA ASN B 464 " pdb=" C ASN B 464 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.88e+00 bond pdb=" CA ASN A 464 " pdb=" C ASN A 464 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.83e+00 ... (remaining 508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 611 1.78 - 3.55: 61 3.55 - 5.32: 17 5.32 - 7.10: 1 7.10 - 8.87: 6 Bond angle restraints: 696 Sorted by residual: angle pdb=" N VAL B 460 " pdb=" CA VAL B 460 " pdb=" C VAL B 460 " ideal model delta sigma weight residual 110.42 104.63 5.79 9.60e-01 1.09e+00 3.64e+01 angle pdb=" CA TYR C 453 " pdb=" CB TYR C 453 " pdb=" CG TYR C 453 " ideal model delta sigma weight residual 113.90 122.77 -8.87 1.80e+00 3.09e-01 2.43e+01 angle pdb=" CA TYR A 453 " pdb=" CB TYR A 453 " pdb=" CG TYR A 453 " ideal model delta sigma weight residual 113.90 122.74 -8.84 1.80e+00 3.09e-01 2.41e+01 angle pdb=" CA TYR B 453 " pdb=" CB TYR B 453 " pdb=" CG TYR B 453 " ideal model delta sigma weight residual 113.90 122.71 -8.81 1.80e+00 3.09e-01 2.39e+01 angle pdb=" C VAL A 458 " pdb=" CA VAL A 458 " pdb=" CB VAL A 458 " ideal model delta sigma weight residual 111.74 108.09 3.65 9.40e-01 1.13e+00 1.51e+01 ... (remaining 691 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.61: 272 17.61 - 35.21: 27 35.21 - 52.81: 0 52.81 - 70.41: 1 70.41 - 88.01: 3 Dihedral angle restraints: 303 sinusoidal: 114 harmonic: 189 Sorted by residual: dihedral pdb=" CA TYR A 465 " pdb=" C TYR A 465 " pdb=" N LEU A 466 " pdb=" CA LEU A 466 " ideal model delta harmonic sigma weight residual 180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA TYR B 465 " pdb=" C TYR B 465 " pdb=" N LEU B 466 " pdb=" CA LEU B 466 " ideal model delta harmonic sigma weight residual 180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA TYR C 465 " pdb=" C TYR C 465 " pdb=" N LEU C 466 " pdb=" CA LEU C 466 " ideal model delta harmonic sigma weight residual -180.00 -164.17 -15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 300 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 55 0.049 - 0.097: 12 0.097 - 0.146: 10 0.146 - 0.195: 0 0.195 - 0.243: 4 Chirality restraints: 81 Sorted by residual: chirality pdb=" CA TYR B 453 " pdb=" N TYR B 453 " pdb=" C TYR B 453 " pdb=" CB TYR B 453 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA TYR A 453 " pdb=" N TYR A 453 " pdb=" C TYR A 453 " pdb=" CB TYR A 453 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TYR C 453 " pdb=" N TYR C 453 " pdb=" C TYR C 453 " pdb=" CB TYR C 453 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 78 not shown) Planarity restraints: 90 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.019 2.00e-02 2.50e+03 1.59e-02 5.06e+00 pdb=" CG TYR A 453 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 453 " -0.019 2.00e-02 2.50e+03 1.58e-02 4.98e+00 pdb=" CG TYR C 453 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR C 453 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 453 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 453 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 453 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 453 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 453 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 453 " -0.019 2.00e-02 2.50e+03 1.57e-02 4.92e+00 pdb=" CG TYR B 453 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 453 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 453 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 453 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 453 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 453 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 453 " -0.000 2.00e-02 2.50e+03 ... (remaining 87 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 56 2.68 - 3.24: 661 3.24 - 3.79: 803 3.79 - 4.35: 1154 4.35 - 4.90: 1703 Nonbonded interactions: 4377 Sorted by model distance: nonbonded pdb=" N TYR B 453 " pdb=" O ILE C 452 " model vdw 2.126 3.120 nonbonded pdb=" OG SER C 456 " pdb=" N GLY C 457 " model vdw 2.210 3.120 nonbonded pdb=" OG SER A 456 " pdb=" N GLY A 457 " model vdw 2.211 3.120 nonbonded pdb=" OG SER B 456 " pdb=" N GLY B 457 " model vdw 2.212 3.120 nonbonded pdb=" NE2 GLN B 459 " pdb=" CB LEU B 466 " model vdw 2.241 3.520 ... (remaining 4372 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: 1.150 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: 1.740 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:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4619 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 : 0.007 0.095 513 Z= 0.372 Angle : 1.425 8.874 696 Z= 0.941 Chirality : 0.077 0.243 81 Planarity : 0.007 0.021 90 Dihedral : 16.605 88.012 183 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 146.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -7.88 (0.45), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.00 (0.34), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.040 0.007 TYR A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.37 ( 513) covalent geometry : angle 1.42476 / 0.94 ( 696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0177 time to fit residues: 0.1532 Evaluate side-chains 5 residues out of total 20 (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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.7320 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.164254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.140837 restraints weight = 427.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.143363 restraints weight = 249.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.144060 restraints weight = 184.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.144060 restraints weight = 169.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.144060 restraints weight = 169.278| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4575 moved from start: 1.0109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.059 513 Z= 0.591 Angle : 1.751 9.496 696 Z= 1.040 Chirality : 0.095 0.332 81 Planarity : 0.010 0.032 90 Dihedral : 11.465 26.244 69 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 98.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % 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: -8.51 (0.29), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.48 (0.22), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.031 0.006 TYR A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.01100 / 0.59 ( 513) covalent geometry : angle 1.75072 / 1.04 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.006 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0134 time to fit residues: 0.1195 Evaluate side-chains 5 residues out of total 20 (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: 3.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0010 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.0030 overall best weight: 0.3343 ------------------------------------------------------------------------------- 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 = 0.4525 r_free = 0.4525 target = 0.186395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.152175 restraints weight = 389.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.156034 restraints weight = 227.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.158526 restraints weight = 164.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.159494 restraints weight = 133.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.159494 restraints weight = 121.063| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4274 moved from start: 1.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 513 Z= 0.327 Angle : 1.487 9.337 696 Z= 0.883 Chirality : 0.077 0.230 81 Planarity : 0.007 0.022 90 Dihedral : 10.979 24.341 69 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 59.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 40.00 % Favored : 60.00 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -8.01 (0.36), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.10 (0.28), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.039 0.009 TYR A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.33 ( 513) covalent geometry : angle 1.48679 / 0.88 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0133 time to fit residues: 0.1205 Evaluate side-chains 5 residues out of total 20 (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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.8647 ------------------------------------------------------------------------------- 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 = 0.4433 r_free = 0.4433 target = 0.179739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.151107 restraints weight = 308.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.153990 restraints weight = 214.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.155477 restraints weight = 167.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.156655 restraints weight = 144.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.156655 restraints weight = 130.627| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4500 moved from start: 1.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 513 Z= 0.377 Angle : 1.586 9.591 696 Z= 0.915 Chirality : 0.075 0.226 81 Planarity : 0.007 0.022 90 Dihedral : 12.272 26.942 69 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 64.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % 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: -8.14 (0.39), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.20 (0.30), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.040 0.008 TYR B 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00741 / 0.38 ( 513) covalent geometry : angle 1.58606 / 0.91 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0138 time to fit residues: 0.1220 Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 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: 3.9990 chunk 1 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0470 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.3980 overall best weight: 0.1500 ------------------------------------------------------------------------------- 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 = 0.4480 r_free = 0.4480 target = 0.179520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.152130 restraints weight = 367.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.155868 restraints weight = 218.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.157757 restraints weight = 156.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.159474 restraints weight = 130.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.160239 restraints weight = 113.273| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4190 moved from start: 1.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.024 513 Z= 0.314 Angle : 1.412 9.394 696 Z= 0.816 Chirality : 0.072 0.220 81 Planarity : 0.007 0.023 90 Dihedral : 11.899 26.539 69 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 55.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 40.00 % Favored : 60.00 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -7.83 (0.45), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.96 (0.34), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.041 0.009 TYR A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.31 ( 513) covalent geometry : angle 1.41237 / 0.82 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0140 time to fit residues: 0.1089 Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 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: 4.9990 chunk 1 optimal weight: 0.0170 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 overall best weight: 1.0177 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.181151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.169608 restraints weight = 357.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.168702 restraints weight = 399.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.168584 restraints weight = 440.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.168581 restraints weight = 448.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.168581 restraints weight = 448.462| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4201 moved from start: 1.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 513 Z= 0.336 Angle : 1.402 9.992 696 Z= 0.800 Chirality : 0.068 0.228 81 Planarity : 0.007 0.023 90 Dihedral : 12.108 23.885 69 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 61.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -7.83 (0.43), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.96 (0.33), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.039 0.009 TYR C 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.34 ( 513) covalent geometry : angle 1.40156 / 0.80 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0149 time to fit residues: 0.1309 Evaluate side-chains 7 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 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: 4.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.3320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 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 = 0.4411 r_free = 0.4411 target = 0.169434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.144708 restraints weight = 398.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.149033 restraints weight = 225.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.151414 restraints weight = 149.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.153310 restraints weight = 114.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.154666 restraints weight = 92.931| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4209 moved from start: 1.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 513 Z= 0.331 Angle : 1.394 9.806 696 Z= 0.803 Chirality : 0.067 0.228 81 Planarity : 0.007 0.023 90 Dihedral : 12.811 26.130 69 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 55.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % Rotamer: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % 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: -7.73 (0.46), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.89 (0.35), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.044 0.009 TYR C 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.33 ( 513) covalent geometry : angle 1.39377 / 0.80 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0130 time to fit residues: 0.1026 Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 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: 4.9990 chunk 3 optimal weight: 0.0060 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0040 overall best weight: 1.6697 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.167589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.140960 restraints weight = 332.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.144537 restraints weight = 203.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.147195 restraints weight = 146.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.148936 restraints weight = 114.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.150663 restraints weight = 97.654| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4732 moved from start: 1.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 513 Z= 0.344 Angle : 1.397 9.671 696 Z= 0.803 Chirality : 0.068 0.227 81 Planarity : 0.007 0.023 90 Dihedral : 13.147 25.519 69 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 67.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -7.99 (0.40), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.08 (0.30), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.042 0.009 TYR A 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.34 ( 513) covalent geometry : angle 1.39700 / 0.80 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.010 Fit side-chains REVERT: A 469 GLN cc_start: 0.5773 (tp-100) cc_final: 0.5518 (tp-100) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0172 time to fit residues: 0.1520 Evaluate side-chains 7 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.004 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 0.0020 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0070 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0050 overall best weight: 0.0047 ------------------------------------------------------------------------------- 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 = 0.4632 r_free = 0.4632 target = 0.200671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.171094 restraints weight = 401.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.174598 restraints weight = 222.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.176293 restraints weight = 165.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.178535 restraints weight = 145.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.178548 restraints weight = 128.902| |-----------------------------------------------------------------------------| r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4025 moved from start: 1.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 513 Z= 0.309 Angle : 1.321 9.281 696 Z= 0.774 Chirality : 0.068 0.195 81 Planarity : 0.006 0.019 90 Dihedral : 11.459 25.963 69 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 47.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 40.00 % Favored : 60.00 % 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: -7.85 (0.42), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.97 (0.32), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.040 0.009 TYR C 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.31 ( 513) covalent geometry : angle 1.32128 / 0.77 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.004 Fit side-chains REVERT: A 469 GLN cc_start: 0.5575 (tp-100) cc_final: 0.4461 (tp-100) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0213 time to fit residues: 0.1827 Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.004 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.5610 ------------------------------------------------------------------------------- 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 = 0.4926 r_free = 0.4926 target = 0.299012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.253614 restraints weight = 420.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.256057 restraints weight = 274.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.257129 restraints weight = 222.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.257129 restraints weight = 203.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.257129 restraints weight = 203.442| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4209 moved from start: 1.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 513 Z= 0.283 Angle : 1.326 9.938 696 Z= 0.757 Chirality : 0.064 0.197 81 Planarity : 0.006 0.020 90 Dihedral : 11.800 25.121 69 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 39.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % 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: -7.60 (0.48), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.79 (0.37), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.037 0.008 TYR C 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.28 ( 513) covalent geometry : angle 1.32591 / 0.76 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 120 Ramachandran restraints generated. 60 Oldfield, 0 Emsley, 60 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0173 time to fit residues: 0.1205 Evaluate side-chains 6 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 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: 2.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0070 overall best weight: 1.3350 ------------------------------------------------------------------------------- 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 = 0.4565 r_free = 0.4565 target = 0.179681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.151268 restraints weight = 345.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.155232 restraints weight = 202.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.157458 restraints weight = 143.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.159547 restraints weight = 117.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.159762 restraints weight = 98.602| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4639 moved from start: 1.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 513 Z= 0.314 Angle : 1.384 10.069 696 Z= 0.790 Chirality : 0.066 0.216 81 Planarity : 0.007 0.023 90 Dihedral : 12.858 27.479 69 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 39.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 40.00 % Favored : 60.00 % 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: -7.45 (0.50), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.67 (0.38), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.009 TYR C 453 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.31 ( 513) covalent geometry : angle 1.38428 / 0.79 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 257.54 seconds wall clock time: 5 minutes 27.57 seconds (327.57 seconds total)