Starting phenix.real_space_refine on Tue Feb 3 12:19:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8k_62176/02_2026/9k8k_62176.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8k_62176/02_2026/9k8k_62176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k8k_62176/02_2026/9k8k_62176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8k_62176/02_2026/9k8k_62176.map" model { file = "/net/cci-nas-00/data/ceres_data/9k8k_62176/02_2026/9k8k_62176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8k_62176/02_2026/9k8k_62176.cif" } resolution = 3.25 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= 0.003 sd= 0.167 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 2 5.16 5 C 550 2.51 5 N 134 2.21 5 O 158 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 846 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 422 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'TRANS': 54} Chain: "B" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 422 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'TRANS': 54} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.24, per 1000 atoms: 0.28 Number of scatterers: 846 At special positions: 0 Unit cell: (42.0147, 50.6331, 48.4785, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 2 16.00 O 158 8.00 N 134 7.00 C 550 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: 0.09 Conformation dependent library (CDL) restraints added in 23.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 240 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 247 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 240 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 247 " 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 208 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'A' and resid 197 through 210 removed outlier: 4.080A pdb=" N VAL A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 231 Processing helix chain 'A' and resid 234 through 250 removed outlier: 3.871A pdb=" N LYS A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 210 removed outlier: 3.576A pdb=" N ASP B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 231 Processing helix chain 'B' and resid 234 through 250 removed outlier: 3.708A pdb=" N LYS B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 189 hydrogen bond angles 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: 0.06 Time building geometry restraints manager: 0.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 264 1.34 - 1.46: 94 1.46 - 1.57: 488 1.57 - 1.69: 0 1.69 - 1.80: 4 Bond restraints: 850 Sorted by residual: bond pdb=" CB VAL A 219 " pdb=" CG2 VAL A 219 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.13e-01 bond pdb=" C GLU B 223 " pdb=" N LYS B 224 " ideal model delta sigma weight residual 1.335 1.326 0.009 1.36e-02 5.41e+03 4.61e-01 bond pdb=" CB VAL B 219 " pdb=" CG2 VAL B 219 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.56e-01 bond pdb=" CB VAL B 248 " pdb=" CG1 VAL B 248 " ideal model delta sigma weight residual 1.521 1.502 0.019 3.30e-02 9.18e+02 3.26e-01 bond pdb=" C LYS B 224 " pdb=" O LYS B 224 " ideal model delta sigma weight residual 1.237 1.230 0.007 1.19e-02 7.06e+03 3.05e-01 ... (remaining 845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 1062 1.06 - 2.13: 69 2.13 - 3.19: 7 3.19 - 4.25: 2 4.25 - 5.31: 2 Bond angle restraints: 1142 Sorted by residual: angle pdb=" N LYS B 224 " pdb=" CA LYS B 224 " pdb=" C LYS B 224 " ideal model delta sigma weight residual 111.36 108.93 2.43 1.09e+00 8.42e-01 4.98e+00 angle pdb=" C GLU A 212 " pdb=" N VAL A 213 " pdb=" CA VAL A 213 " ideal model delta sigma weight residual 121.97 118.26 3.71 1.80e+00 3.09e-01 4.24e+00 angle pdb=" C VAL A 228 " pdb=" N ALA A 229 " pdb=" CA ALA A 229 " ideal model delta sigma weight residual 120.31 122.68 -2.37 1.52e+00 4.33e-01 2.44e+00 angle pdb=" N LYS A 215 " pdb=" CA LYS A 215 " pdb=" C LYS A 215 " ideal model delta sigma weight residual 113.41 111.53 1.88 1.22e+00 6.72e-01 2.38e+00 angle pdb=" CA LEU A 237 " pdb=" CB LEU A 237 " pdb=" CG LEU A 237 " ideal model delta sigma weight residual 116.30 121.61 -5.31 3.50e+00 8.16e-02 2.31e+00 ... (remaining 1137 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.67: 432 16.67 - 33.33: 58 33.33 - 49.99: 28 49.99 - 66.66: 7 66.66 - 83.32: 3 Dihedral angle restraints: 528 sinusoidal: 208 harmonic: 320 Sorted by residual: dihedral pdb=" CA SER A 214 " pdb=" C SER A 214 " pdb=" N LYS A 215 " pdb=" CA LYS A 215 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB GLU B 223 " pdb=" CG GLU B 223 " pdb=" CD GLU B 223 " pdb=" OE1 GLU B 223 " ideal model delta sinusoidal sigma weight residual 0.00 -83.32 83.32 1 3.00e+01 1.11e-03 9.43e+00 dihedral pdb=" CB LYS B 224 " pdb=" CG LYS B 224 " pdb=" CD LYS B 224 " pdb=" CE LYS B 224 " ideal model delta sinusoidal sigma weight residual -60.00 -115.97 55.97 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.019: 54 0.019 - 0.039: 49 0.039 - 0.058: 29 0.058 - 0.077: 9 0.077 - 0.096: 5 Chirality restraints: 146 Sorted by residual: chirality pdb=" CA GLU A 212 " pdb=" N GLU A 212 " pdb=" C GLU A 212 " pdb=" CB GLU A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.33e-01 chirality pdb=" CA VAL B 213 " pdb=" N VAL B 213 " pdb=" C VAL B 213 " pdb=" CB VAL B 213 " both_signs ideal model delta sigma weight residual False 2.44 2.53 -0.09 2.00e-01 2.50e+01 2.19e-01 chirality pdb=" CA ILE B 238 " pdb=" N ILE B 238 " pdb=" C ILE B 238 " pdb=" CB ILE B 238 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.09 2.00e-01 2.50e+01 2.16e-01 ... (remaining 143 not shown) Planarity restraints: 136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 223 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C GLU B 223 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU B 223 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS B 224 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 238 " 0.004 2.00e-02 2.50e+03 7.02e-03 4.93e-01 pdb=" C ILE B 238 " -0.012 2.00e-02 2.50e+03 pdb=" O ILE B 238 " 0.005 2.00e-02 2.50e+03 pdb=" N LYS B 239 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 213 " -0.003 2.00e-02 2.50e+03 6.51e-03 4.24e-01 pdb=" C VAL A 213 " 0.011 2.00e-02 2.50e+03 pdb=" O VAL A 213 " -0.004 2.00e-02 2.50e+03 pdb=" N SER A 214 " -0.004 2.00e-02 2.50e+03 ... (remaining 133 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 5 2.58 - 3.16: 638 3.16 - 3.74: 1236 3.74 - 4.32: 1652 4.32 - 4.90: 2888 Nonbonded interactions: 6419 Sorted by model distance: nonbonded pdb=" OD1 ASP B 202 " pdb="ZN ZN B 301 " model vdw 2.005 2.230 nonbonded pdb=" OD1 ASP A 202 " pdb="ZN ZN A 301 " model vdw 2.027 2.230 nonbonded pdb=" O VAL A 213 " pdb=" OG SER A 214 " model vdw 2.237 3.040 nonbonded pdb=" O GLY B 199 " pdb=" OG1 THR B 203 " model vdw 2.316 3.040 nonbonded pdb=" OD2 ASP A 251 " pdb=" NZ LYS B 239 " model vdw 2.430 3.120 ... (remaining 6414 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 2.100 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.012 0.213 854 Z= 0.426 Angle : 0.602 5.315 1142 Z= 0.337 Chirality : 0.036 0.096 146 Planarity : 0.003 0.019 136 Dihedral : 19.968 83.318 320 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.33 % Allowed : 28.89 % Favored : 67.78 % 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: -1.78 (0.72), residues: 106 helix: -0.64 (0.50), residues: 92 sheet: None (None), residues: 0 loop : -3.85 (0.80), residues: 14 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR A 208 HIS 0.002 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 850) covalent geometry : angle 0.60228 ( 1142) hydrogen bonds : bond 0.14652 ( 63) hydrogen bonds : angle 5.17933 ( 189) metal coordination : bond 0.16872 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.021 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 14 average time/residue: 0.0736 time to fit residues: 1.1136 Evaluate side-chains 15 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 250 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.172640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.158919 restraints weight = 624.801| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 0.89 r_work: 0.3612 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 854 Z= 0.138 Angle : 0.521 5.072 1142 Z= 0.280 Chirality : 0.034 0.096 146 Planarity : 0.002 0.012 136 Dihedral : 8.399 54.346 118 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.44 % Allowed : 25.56 % Favored : 70.00 % 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: -1.10 (0.79), residues: 106 helix: -0.22 (0.51), residues: 98 sheet: None (None), residues: 0 loop : -5.54 (0.97), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR A 208 HIS 0.001 0.000 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 850) covalent geometry : angle 0.52069 ( 1142) hydrogen bonds : bond 0.04626 ( 63) hydrogen bonds : angle 3.31917 ( 189) metal coordination : bond 0.00254 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.021 Fit side-chains REVERT: A 232 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7022 (tt) REVERT: A 250 MET cc_start: 0.7409 (mtt) cc_final: 0.6624 (mmm) outliers start: 4 outliers final: 1 residues processed: 15 average time/residue: 0.0588 time to fit residues: 0.9508 Evaluate side-chains 14 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 235 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.171334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.156835 restraints weight = 604.463| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 0.92 r_work: 0.3545 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 854 Z= 0.129 Angle : 0.506 4.823 1142 Z= 0.266 Chirality : 0.034 0.094 146 Planarity : 0.002 0.010 136 Dihedral : 8.170 52.527 114 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.33 % Allowed : 26.67 % Favored : 70.00 % 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: -0.69 (0.80), residues: 106 helix: 0.03 (0.52), residues: 98 sheet: None (None), residues: 0 loop : -5.19 (1.12), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 208 HIS 0.001 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 850) covalent geometry : angle 0.50612 ( 1142) hydrogen bonds : bond 0.04482 ( 63) hydrogen bonds : angle 3.10362 ( 189) metal coordination : bond 0.00139 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.020 Fit side-chains REVERT: A 250 MET cc_start: 0.7474 (mtt) cc_final: 0.6664 (mmm) outliers start: 3 outliers final: 2 residues processed: 14 average time/residue: 0.0795 time to fit residues: 1.2213 Evaluate side-chains 14 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain B residue 214 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.173350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.159854 restraints weight = 617.932| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 0.88 r_work: 0.3622 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 854 Z= 0.140 Angle : 0.518 4.654 1142 Z= 0.270 Chirality : 0.035 0.093 146 Planarity : 0.002 0.009 136 Dihedral : 8.199 52.882 114 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.44 % Allowed : 26.67 % Favored : 68.89 % 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: -0.63 (0.81), residues: 106 helix: 0.06 (0.52), residues: 98 sheet: None (None), residues: 0 loop : -5.05 (1.16), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 208 HIS 0.002 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 850) covalent geometry : angle 0.51797 ( 1142) hydrogen bonds : bond 0.04584 ( 63) hydrogen bonds : angle 3.10794 ( 189) metal coordination : bond 0.00171 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 13 time to evaluate : 0.034 Fit side-chains REVERT: A 250 MET cc_start: 0.7453 (mtt) cc_final: 0.6791 (mmm) REVERT: B 236 GLU cc_start: 0.7688 (mp0) cc_final: 0.7328 (mp0) outliers start: 4 outliers final: 2 residues processed: 15 average time/residue: 0.0801 time to fit residues: 1.3139 Evaluate side-chains 15 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain B residue 214 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.169602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.153140 restraints weight = 591.073| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 0.99 r_work: 0.3548 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 854 Z= 0.148 Angle : 0.535 4.710 1142 Z= 0.277 Chirality : 0.035 0.093 146 Planarity : 0.002 0.008 136 Dihedral : 8.235 53.540 114 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 6.67 % Allowed : 25.56 % Favored : 67.78 % 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: -0.71 (0.80), residues: 106 helix: 0.01 (0.52), residues: 98 sheet: None (None), residues: 0 loop : -5.05 (1.17), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 208 HIS 0.002 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 850) covalent geometry : angle 0.53490 ( 1142) hydrogen bonds : bond 0.04710 ( 63) hydrogen bonds : angle 3.14963 ( 189) metal coordination : bond 0.00180 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 12 time to evaluate : 0.032 Fit side-chains REVERT: A 206 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7114 (tp) REVERT: A 250 MET cc_start: 0.7142 (mtt) cc_final: 0.6552 (mmm) outliers start: 6 outliers final: 3 residues processed: 17 average time/residue: 0.0702 time to fit residues: 1.3083 Evaluate side-chains 16 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain B residue 214 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.0270 chunk 7 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.173301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.156980 restraints weight = 599.167| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.00 r_work: 0.3604 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 854 Z= 0.103 Angle : 0.494 5.915 1142 Z= 0.247 Chirality : 0.033 0.088 146 Planarity : 0.002 0.008 136 Dihedral : 7.795 50.920 114 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.44 % Allowed : 28.89 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.83), residues: 106 helix: 0.53 (0.54), residues: 98 sheet: None (None), residues: 0 loop : -4.95 (1.17), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 208 HIS 0.001 0.000 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 850) covalent geometry : angle 0.49368 ( 1142) hydrogen bonds : bond 0.04007 ( 63) hydrogen bonds : angle 2.77788 ( 189) metal coordination : bond 0.00110 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.043 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.7149 (mtt) cc_final: 0.6286 (mmm) REVERT: B 236 GLU cc_start: 0.7533 (mp0) cc_final: 0.7119 (mp0) outliers start: 4 outliers final: 2 residues processed: 14 average time/residue: 0.0798 time to fit residues: 1.2307 Evaluate side-chains 13 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 214 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.170252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.153802 restraints weight = 576.689| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 0.97 r_work: 0.3576 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 854 Z= 0.147 Angle : 0.527 5.067 1142 Z= 0.269 Chirality : 0.035 0.090 146 Planarity : 0.002 0.008 136 Dihedral : 8.226 54.989 114 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 6.67 % Allowed : 24.44 % Favored : 68.89 % 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: -0.47 (0.81), residues: 106 helix: 0.17 (0.52), residues: 98 sheet: None (None), residues: 0 loop : -5.08 (1.14), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 208 HIS 0.002 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 850) covalent geometry : angle 0.52678 ( 1142) hydrogen bonds : bond 0.04630 ( 63) hydrogen bonds : angle 3.08879 ( 189) metal coordination : bond 0.00177 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 11 time to evaluate : 0.038 Fit side-chains REVERT: A 250 MET cc_start: 0.7093 (mtt) cc_final: 0.6296 (mmm) outliers start: 6 outliers final: 4 residues processed: 16 average time/residue: 0.0729 time to fit residues: 1.2834 Evaluate side-chains 15 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 214 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.169952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.153034 restraints weight = 595.579| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.00 r_work: 0.3508 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 854 Z= 0.141 Angle : 0.555 5.115 1142 Z= 0.278 Chirality : 0.035 0.089 146 Planarity : 0.002 0.008 136 Dihedral : 8.179 54.772 114 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.44 % Allowed : 27.78 % Favored : 67.78 % 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: -0.44 (0.81), residues: 106 helix: 0.19 (0.52), residues: 98 sheet: None (None), residues: 0 loop : -5.04 (1.17), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 208 HIS 0.002 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 850) covalent geometry : angle 0.55517 ( 1142) hydrogen bonds : bond 0.04607 ( 63) hydrogen bonds : angle 3.09227 ( 189) metal coordination : bond 0.00152 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.7189 (mtt) cc_final: 0.6408 (mmm) outliers start: 4 outliers final: 4 residues processed: 15 average time/residue: 0.0787 time to fit residues: 1.2884 Evaluate side-chains 15 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 11 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 214 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.0070 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.173087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157865 restraints weight = 596.413| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 0.92 r_work: 0.3537 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 854 Z= 0.100 Angle : 0.487 5.005 1142 Z= 0.244 Chirality : 0.033 0.084 146 Planarity : 0.002 0.008 136 Dihedral : 7.627 50.021 114 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.33 % Allowed : 27.78 % Favored : 68.89 % 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: 0.49 (0.84), residues: 106 helix: 0.75 (0.54), residues: 98 sheet: None (None), residues: 0 loop : -4.09 (1.57), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 208 HIS 0.001 0.000 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 850) covalent geometry : angle 0.48733 ( 1142) hydrogen bonds : bond 0.03911 ( 63) hydrogen bonds : angle 2.76737 ( 189) metal coordination : bond 0.00109 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.7164 (mtt) cc_final: 0.6415 (mmm) outliers start: 3 outliers final: 2 residues processed: 13 average time/residue: 0.0908 time to fit residues: 1.2816 Evaluate side-chains 12 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 214 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.170125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.153830 restraints weight = 577.267| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 0.98 r_work: 0.3518 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 854 Z= 0.135 Angle : 0.530 4.763 1142 Z= 0.267 Chirality : 0.035 0.088 146 Planarity : 0.002 0.008 136 Dihedral : 8.025 53.797 114 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.33 % Allowed : 26.67 % Favored : 70.00 % 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: 0.07 (0.81), residues: 106 helix: 0.46 (0.52), residues: 98 sheet: None (None), residues: 0 loop : -3.98 (1.65), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 208 HIS 0.002 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 850) covalent geometry : angle 0.52962 ( 1142) hydrogen bonds : bond 0.04475 ( 63) hydrogen bonds : angle 3.00723 ( 189) metal coordination : bond 0.00164 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 212 Ramachandran restraints generated. 106 Oldfield, 0 Emsley, 106 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: A 250 MET cc_start: 0.7124 (mtt) cc_final: 0.6395 (mmm) outliers start: 3 outliers final: 3 residues processed: 14 average time/residue: 0.0793 time to fit residues: 1.2161 Evaluate side-chains 14 residues out of total 90 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 214 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 10 random chunks: chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.168860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.151846 restraints weight = 583.299| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.01 r_work: 0.3566 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 854 Z= 0.165 Angle : 0.567 4.834 1142 Z= 0.287 Chirality : 0.036 0.089 146 Planarity : 0.002 0.008 136 Dihedral : 8.375 56.695 114 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.56 % Allowed : 24.44 % Favored : 70.00 % 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: -0.42 (0.80), residues: 106 helix: 0.14 (0.51), residues: 98 sheet: None (None), residues: 0 loop : -4.13 (1.63), residues: 8 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 208 HIS 0.002 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 850) covalent geometry : angle 0.56718 ( 1142) hydrogen bonds : bond 0.04859 ( 63) hydrogen bonds : angle 3.22568 ( 189) metal coordination : bond 0.00208 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 504.94 seconds wall clock time: 9 minutes 29.59 seconds (569.59 seconds total)