Starting phenix.real_space_refine on Wed Sep 17 02:56:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z94_39854/09_2025/8z94_39854.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z94_39854/09_2025/8z94_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z94_39854/09_2025/8z94_39854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z94_39854/09_2025/8z94_39854.map" model { file = "/net/cci-nas-00/data/ceres_data/8z94_39854/09_2025/8z94_39854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z94_39854/09_2025/8z94_39854.cif" } 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-2.0-5805/lib/python3.9/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: 0.32, per 1000 atoms: 0.63 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: 0.03 Conformation dependent library (CDL) restraints added in 14.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.74 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: 1.140 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: 0.010 Extract box with map and model: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 2.060 Find NCS groups from input model: 0.020 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4737 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 aren 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 covalent geometry : bond 0.00748 ( 513) covalent geometry : angle 1.42476 ( 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 : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0187 time to fit residues: 0.1651 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 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: 0.4704 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 aren 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 covalent geometry : bond 0.01100 ( 513) covalent geometry : angle 1.75072 ( 696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 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 outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0122 time to fit residues: 0.1091 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 : 0.006 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.0030 overall best weight: 0.6670 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.177694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.148156 restraints weight = 451.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.151907 restraints weight = 253.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.153488 restraints weight = 182.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.155070 restraints weight = 153.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.155070 restraints weight = 136.414| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4402 moved from start: 1.0509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 513 Z= 0.331 Angle : 1.476 9.479 696 Z= 0.871 Chirality : 0.077 0.222 81 Planarity : 0.007 0.022 90 Dihedral : 11.079 23.066 69 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 61.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % Rotamer: Outliers : 5.00 % Allowed : 5.00 % 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 aren not related in a simple way. whole: -8.24 (0.33), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.27 (0.25), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.039 0.009 TYR C 453 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 513) covalent geometry : angle 1.47565 ( 696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 8 time to evaluate : 0.004 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.0115 time to fit residues: 0.1144 Evaluate side-chains 5 residues out of total 20 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 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: 4.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.9653 ------------------------------------------------------------------------------- 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 = 0.170089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.145685 restraints weight = 415.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.149185 restraints weight = 288.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.151635 restraints weight = 215.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.151635 restraints weight = 171.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.151634 restraints weight = 171.775| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4927 moved from start: 1.0680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.043 513 Z= 0.466 Angle : 1.608 9.617 696 Z= 0.926 Chirality : 0.077 0.249 81 Planarity : 0.008 0.025 90 Dihedral : 13.487 28.576 69 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 76.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 60.00 % Favored : 40.00 % 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 aren not related in a simple way. whole: -8.81 (0.31), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.71 (0.24), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.011 TYR A 453 Details of bonding type rmsd covalent geometry : bond 0.00990 ( 513) covalent geometry : angle 1.60806 ( 696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 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 : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0117 time to fit residues: 0.0793 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=3.50 ------------------------------------------------------------------------------- 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: 3.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 overall best weight: 1.3650 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.193657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.157434 restraints weight = 261.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.161212 restraints weight = 182.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.164060 restraints weight = 140.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.164993 restraints weight = 116.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.166187 restraints weight = 105.159| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4760 moved from start: 1.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 513 Z= 0.370 Angle : 1.472 9.749 696 Z= 0.840 Chirality : 0.071 0.235 81 Planarity : 0.007 0.023 90 Dihedral : 12.844 24.926 69 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 60.61 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 aren not related in a simple way. whole: -8.73 (0.26), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.65 (0.20), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.043 0.009 TYR A 453 Details of bonding type rmsd covalent geometry : bond 0.00773 ( 513) covalent geometry : angle 1.47237 ( 696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 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 : 0.004 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0178 time to fit residues: 0.1355 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 overall best weight: 0.1443 ------------------------------------------------------------------------------- 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 = 0.4513 r_free = 0.4513 target = 0.185374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.154884 restraints weight = 304.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.157707 restraints weight = 207.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.159795 restraints weight = 164.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.159795 restraints weight = 140.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.159795 restraints weight = 140.925| |-----------------------------------------------------------------------------| r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4456 moved from start: 1.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.023 513 Z= 0.310 Angle : 1.360 9.550 696 Z= 0.783 Chirality : 0.070 0.212 81 Planarity : 0.007 0.021 90 Dihedral : 12.255 25.970 69 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 48.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % 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 aren not related in a simple way. whole: -8.02 (0.41), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.10 (0.31), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.040 0.009 TYR B 453 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 513) covalent geometry : angle 1.36017 ( 696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 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 REVERT: A 469 GLN cc_start: 0.6114 (tp-100) cc_final: 0.5706 (tp-100) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0133 time to fit residues: 0.1199 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: 3.9990 chunk 1 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3777 ------------------------------------------------------------------------------- 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 = 0.4573 r_free = 0.4573 target = 0.181072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.167577 restraints weight = 393.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.167578 restraints weight = 401.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.167578 restraints weight = 400.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.167578 restraints weight = 400.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.167578 restraints weight = 400.271| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4615 moved from start: 1.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.028 513 Z= 0.325 Angle : 1.401 9.824 696 Z= 0.797 Chirality : 0.067 0.232 81 Planarity : 0.007 0.024 90 Dihedral : 13.143 28.156 69 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 51.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % 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 aren not related in a simple way. whole: -7.99 (0.44), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.09 (0.33), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.038 0.008 TYR C 453 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 513) covalent geometry : angle 1.40102 ( 696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 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: 0.0138 time to fit residues: 0.1083 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 : 0.005 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 overall best weight: 1.4987 ------------------------------------------------------------------------------- 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 = 0.4496 r_free = 0.4496 target = 0.177866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.143523 restraints weight = 340.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.146056 restraints weight = 238.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.148848 restraints weight = 197.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.150268 restraints weight = 162.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.151117 restraints weight = 145.838| |-----------------------------------------------------------------------------| r_work (final): 0.4777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4218 moved from start: 1.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 513 Z= 0.315 Angle : 1.390 9.796 696 Z= 0.791 Chirality : 0.066 0.215 81 Planarity : 0.007 0.022 90 Dihedral : 13.347 28.092 69 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 53.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 50.00 % Favored : 50.00 % 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 aren not related in a simple way. whole: -7.82 (0.46), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.95 (0.35), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.048 0.009 TYR C 453 Details of bonding type rmsd covalent geometry : bond 0.00643 ( 513) covalent geometry : angle 1.38951 ( 696) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 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 : 0.005 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0173 time to fit residues: 0.1155 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.0270 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.0270 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.2840 ------------------------------------------------------------------------------- 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 = 0.4385 r_free = 0.4385 target = 0.171786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.142992 restraints weight = 371.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.147267 restraints weight = 203.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.150455 restraints weight = 139.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.153036 restraints weight = 105.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.154615 restraints weight = 85.370| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4275 moved from start: 1.2753 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= 0.288 Angle : 1.340 9.846 696 Z= 0.767 Chirality : 0.064 0.194 81 Planarity : 0.006 0.021 90 Dihedral : 12.579 26.700 69 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 42.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % 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 aren not related in a simple way. whole: -7.79 (0.45), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.94 (0.34), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.037 0.008 TYR C 453 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 513) covalent geometry : angle 1.33971 ( 696) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 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 outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0111 time to fit residues: 0.0996 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.0050 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.0050 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 overall best weight: 0.0357 ------------------------------------------------------------------------------- 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 = 0.4514 r_free = 0.4514 target = 0.187809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.160728 restraints weight = 446.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.163886 restraints weight = 255.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.166633 restraints weight = 184.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.167623 restraints weight = 147.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.167621 restraints weight = 134.062| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4346 moved from start: 1.4246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 513 Z= 0.270 Angle : 1.303 9.896 696 Z= 0.747 Chirality : 0.066 0.203 81 Planarity : 0.006 0.019 90 Dihedral : 11.476 24.466 69 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 39.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 45.00 % Favored : 55.00 % 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 aren not related in a simple way. whole: -7.43 (0.46), residues: 60 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.66 (0.35), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.032 0.008 TYR C 453 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 513) covalent geometry : angle 1.30298 ( 696) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 80 Ramachandran restraints generated. 40 Oldfield, 0 Emsley, 40 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 REVERT: A 469 GLN cc_start: 0.5594 (tp-100) cc_final: 0.4565 (tp-100) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0167 time to fit residues: 0.1456 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=1.00 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.3323 ------------------------------------------------------------------------------- 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 = 0.4589 r_free = 0.4589 target = 0.188942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.166755 restraints weight = 429.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.166359 restraints weight = 464.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.166359 restraints weight = 485.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.166359 restraints weight = 485.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.166359 restraints weight = 485.263| |-----------------------------------------------------------------------------| r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4751 moved from start: 1.2832 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= 0.368 Angle : 1.479 10.033 696 Z= 0.843 Chirality : 0.067 0.230 81 Planarity : 0.007 0.024 90 Dihedral : 13.626 25.831 69 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 53.54 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 aren not related in a simple way. whole: -8.01 (0.37), 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 0.008 TYR C 453 Details of bonding type rmsd covalent geometry : bond 0.00749 ( 513) covalent geometry : angle 1.47895 ( 696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 205.59 seconds wall clock time: 4 minutes 16.29 seconds (256.29 seconds total)