Starting phenix.real_space_refine on Tue Feb 3 12:20:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8c_62168/02_2026/9k8c_62168.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8c_62168/02_2026/9k8c_62168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k8c_62168/02_2026/9k8c_62168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8c_62168/02_2026/9k8c_62168.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k8c_62168/02_2026/9k8c_62168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8c_62168/02_2026/9k8c_62168.map" } resolution = 3.15 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= 0.204 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 958 2.51 5 N 250 2.21 5 O 282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 1494 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 746 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'TRANS': 89} Chain: "B" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 746 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'TRANS': 89} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.49, per 1000 atoms: 0.33 Number of scatterers: 1494 At special positions: 0 Unit cell: (54.9423, 54.9423, 57.0969, 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 282 8.00 N 250 7.00 C 958 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: 0.13 Conformation dependent library (CDL) restraints added in 69.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 166 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 220 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS B 166 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 220 " 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 344 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 90.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'A' and resid 135 through 156 Processing helix chain 'A' and resid 159 through 179 removed outlier: 4.153A pdb=" N GLU A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 201 removed outlier: 3.633A pdb=" N LEU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 224 removed outlier: 3.836A pdb=" N LEU A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 157 Processing helix chain 'B' and resid 160 through 179 removed outlier: 3.791A pdb=" N LYS B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.562A pdb=" N LYS B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 224 removed outlier: 3.530A pdb=" N ALA B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 357 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: 0.20 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 346 1.33 - 1.45: 224 1.45 - 1.57: 930 1.57 - 1.68: 0 1.68 - 1.80: 4 Bond restraints: 1504 Sorted by residual: bond pdb=" CA GLY B 179 " pdb=" C GLY B 179 " ideal model delta sigma weight residual 1.514 1.444 0.070 1.41e-02 5.03e+03 2.49e+01 bond pdb=" CA ILE B 178 " pdb=" C ILE B 178 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.27e-02 6.20e+03 5.27e+00 bond pdb=" N GLY B 179 " pdb=" CA GLY B 179 " ideal model delta sigma weight residual 1.449 1.418 0.031 1.45e-02 4.76e+03 4.51e+00 bond pdb=" C GLY B 179 " pdb=" O GLY B 179 " ideal model delta sigma weight residual 1.235 1.216 0.019 1.35e-02 5.49e+03 1.90e+00 bond pdb=" C GLY B 179 " pdb=" N ASP B 180 " ideal model delta sigma weight residual 1.330 1.315 0.015 1.32e-02 5.74e+03 1.22e+00 ... (remaining 1499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 1900 1.01 - 2.02: 66 2.02 - 3.03: 19 3.03 - 4.04: 5 4.04 - 5.04: 6 Bond angle restraints: 1996 Sorted by residual: angle pdb=" N ASP B 180 " pdb=" CA ASP B 180 " pdb=" C ASP B 180 " ideal model delta sigma weight residual 109.07 114.11 -5.04 1.61e+00 3.86e-01 9.82e+00 angle pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" O GLY B 179 " ideal model delta sigma weight residual 120.57 116.05 4.52 1.74e+00 3.30e-01 6.76e+00 angle pdb=" C LYS A 181 " pdb=" N GLU A 182 " pdb=" CA GLU A 182 " ideal model delta sigma weight residual 121.54 125.79 -4.25 1.91e+00 2.74e-01 4.96e+00 angle pdb=" CA GLY B 179 " pdb=" C GLY B 179 " pdb=" N ASP B 180 " ideal model delta sigma weight residual 116.69 121.00 -4.31 2.04e+00 2.40e-01 4.47e+00 angle pdb=" N ILE B 178 " pdb=" CA ILE B 178 " pdb=" C ILE B 178 " ideal model delta sigma weight residual 109.34 105.16 4.18 2.08e+00 2.31e-01 4.04e+00 ... (remaining 1991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 750 16.88 - 33.76: 133 33.76 - 50.64: 60 50.64 - 67.51: 15 67.51 - 84.39: 2 Dihedral angle restraints: 960 sinusoidal: 438 harmonic: 522 Sorted by residual: dihedral pdb=" CA ASP B 180 " pdb=" CB ASP B 180 " pdb=" CG ASP B 180 " pdb=" OD1 ASP B 180 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA GLY A 158 " pdb=" C GLY A 158 " pdb=" N LYS A 159 " pdb=" CA LYS A 159 " ideal model delta harmonic sigma weight residual -180.00 -163.67 -16.33 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU A 204 " pdb=" CG GLU A 204 " pdb=" CD GLU A 204 " pdb=" OE1 GLU A 204 " ideal model delta sinusoidal sigma weight residual 0.00 -84.39 84.39 1 3.00e+01 1.11e-03 9.62e+00 ... (remaining 957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 159 0.032 - 0.064: 56 0.064 - 0.096: 9 0.096 - 0.129: 1 0.129 - 0.161: 1 Chirality restraints: 226 Sorted by residual: chirality pdb=" CA ILE B 178 " pdb=" N ILE B 178 " pdb=" C ILE B 178 " pdb=" CB ILE B 178 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA ASP B 180 " pdb=" N ASP B 180 " pdb=" C ASP B 180 " pdb=" CB ASP B 180 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.56e-01 chirality pdb=" CA GLU A 182 " pdb=" N GLU A 182 " pdb=" C GLU A 182 " pdb=" CB GLU A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.43 0.08 2.00e-01 2.50e+01 1.66e-01 ... (remaining 223 not shown) Planarity restraints: 250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 177 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C GLU B 177 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU B 177 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE B 178 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 200 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C LYS B 200 " 0.025 2.00e-02 2.50e+03 pdb=" O LYS B 200 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA B 201 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 179 " 0.005 2.00e-02 2.50e+03 9.72e-03 9.45e-01 pdb=" C GLY B 179 " -0.017 2.00e-02 2.50e+03 pdb=" O GLY B 179 " 0.006 2.00e-02 2.50e+03 pdb=" N ASP B 180 " 0.006 2.00e-02 2.50e+03 ... (remaining 247 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 10 2.56 - 3.15: 1058 3.15 - 3.73: 2230 3.73 - 4.32: 2863 4.32 - 4.90: 5063 Nonbonded interactions: 11224 Sorted by model distance: nonbonded pdb=" OD1 ASP A 216 " pdb="ZN ZN A 302 " model vdw 1.978 2.230 nonbonded pdb=" OD2 ASP B 162 " pdb="ZN ZN A 302 " model vdw 1.991 2.230 nonbonded pdb=" OD2 ASP A 162 " pdb="ZN ZN A 301 " model vdw 2.036 2.230 nonbonded pdb=" OD1 ASP B 216 " pdb="ZN ZN A 301 " model vdw 2.036 2.230 nonbonded pdb=" OD2 ASP B 216 " pdb="ZN ZN A 301 " model vdw 2.275 2.230 ... (remaining 11219 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' and resid 135 through 224) 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: 1.840 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.090 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.011 0.260 1508 Z= 0.413 Angle : 0.563 5.045 1996 Z= 0.315 Chirality : 0.033 0.161 226 Planarity : 0.003 0.023 250 Dihedral : 20.571 84.393 616 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 1.14 % Allowed : 5.68 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 31.88 % Favored : 68.12 % 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: 2.43 (0.61), residues: 176 helix: 2.42 (0.39), residues: 154 sheet: None (None), residues: 0 loop : -4.79 (0.36), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 153 PHE 0.007 0.002 PHE B 168 TRP 0.010 0.001 TRP A 151 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 1504) covalent geometry : angle 0.56344 ( 1996) hydrogen bonds : bond 0.07689 ( 119) hydrogen bonds : angle 3.47281 ( 357) metal coordination : bond 0.20594 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0980 time to fit residues: 1.2475 Evaluate side-chains 11 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.181755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.159031 restraints weight = 1206.760| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.42 r_work: 0.3527 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.778 1508 Z= 0.681 Angle : 0.456 4.418 1996 Z= 0.249 Chirality : 0.029 0.089 226 Planarity : 0.002 0.011 250 Dihedral : 4.346 15.613 190 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.50 % Allowed : 30.00 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.61), residues: 176 helix: 2.60 (0.39), residues: 154 sheet: None (None), residues: 0 loop : -4.75 (0.38), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 153 PHE 0.006 0.001 PHE B 168 TRP 0.009 0.001 TRP A 151 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 1504) covalent geometry : angle 0.45626 ( 1996) hydrogen bonds : bond 0.04264 ( 119) hydrogen bonds : angle 3.12050 ( 357) metal coordination : bond 0.38909 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 14 time to evaluate : 0.067 Fit side-chains REVERT: A 224 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6451 (tt) REVERT: B 145 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7044 (mm-30) outliers start: 4 outliers final: 0 residues processed: 17 average time/residue: 0.0709 time to fit residues: 1.4194 Evaluate side-chains 12 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 10 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 145 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.175400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150577 restraints weight = 1176.810| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.64 r_work: 0.3705 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1508 Z= 0.147 Angle : 0.473 4.532 1996 Z= 0.253 Chirality : 0.030 0.086 226 Planarity : 0.002 0.019 250 Dihedral : 4.322 16.229 190 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.25 % Allowed : 30.62 % Favored : 68.12 % 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: 2.67 (0.60), residues: 176 helix: 2.50 (0.38), residues: 156 sheet: None (None), residues: 0 loop : -4.73 (0.42), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 PHE 0.006 0.001 PHE B 168 TRP 0.009 0.001 TRP A 151 HIS 0.003 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 1504) covalent geometry : angle 0.47283 ( 1996) hydrogen bonds : bond 0.04429 ( 119) hydrogen bonds : angle 3.11788 ( 357) metal coordination : bond 0.00248 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.072 Fit side-chains REVERT: A 224 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6554 (tt) REVERT: B 145 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7116 (mm-30) outliers start: 2 outliers final: 0 residues processed: 14 average time/residue: 0.0788 time to fit residues: 1.2786 Evaluate side-chains 14 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 145 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.184921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.160287 restraints weight = 1189.150| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.74 r_work: 0.3696 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1508 Z= 0.125 Angle : 0.442 4.518 1996 Z= 0.239 Chirality : 0.029 0.085 226 Planarity : 0.002 0.010 250 Dihedral : 4.178 15.261 190 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.12 % Allowed : 30.62 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.61), residues: 176 helix: 2.61 (0.38), residues: 156 sheet: None (None), residues: 0 loop : -4.71 (0.43), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 PHE 0.005 0.001 PHE B 168 TRP 0.010 0.001 TRP A 151 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 1504) covalent geometry : angle 0.44225 ( 1996) hydrogen bonds : bond 0.04195 ( 119) hydrogen bonds : angle 3.03858 ( 357) metal coordination : bond 0.00158 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 13 time to evaluate : 0.036 Fit side-chains REVERT: A 224 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6539 (tt) REVERT: B 145 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7003 (mm-30) outliers start: 5 outliers final: 2 residues processed: 18 average time/residue: 0.0511 time to fit residues: 1.1138 Evaluate side-chains 16 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 145 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.177164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.151660 restraints weight = 1183.132| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.71 r_work: 0.3738 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1508 Z= 0.116 Angle : 0.432 4.553 1996 Z= 0.234 Chirality : 0.029 0.097 226 Planarity : 0.002 0.016 250 Dihedral : 4.113 14.753 190 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.50 % Allowed : 32.50 % Favored : 65.00 % 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: 3.09 (0.61), residues: 176 helix: 2.87 (0.38), residues: 154 sheet: None (None), residues: 0 loop : -4.65 (0.39), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 PHE 0.005 0.001 PHE B 168 TRP 0.010 0.001 TRP A 151 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 1504) covalent geometry : angle 0.43210 ( 1996) hydrogen bonds : bond 0.03993 ( 119) hydrogen bonds : angle 2.94594 ( 357) metal coordination : bond 0.00155 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.059 Fit side-chains REVERT: A 224 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6550 (tt) outliers start: 4 outliers final: 2 residues processed: 19 average time/residue: 0.0799 time to fit residues: 1.7308 Evaluate side-chains 13 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 10 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 224 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 11 optimal weight: 0.0030 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 overall best weight: 0.3168 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.178666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.154883 restraints weight = 1190.853| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.60 r_work: 0.3558 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1508 Z= 0.093 Angle : 0.409 4.744 1996 Z= 0.219 Chirality : 0.028 0.097 226 Planarity : 0.002 0.015 250 Dihedral : 3.924 15.085 190 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.12 % Allowed : 28.75 % Favored : 68.12 % 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: 3.44 (0.61), residues: 176 helix: 3.10 (0.39), residues: 154 sheet: None (None), residues: 0 loop : -4.56 (0.43), residues: 22 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 153 PHE 0.004 0.001 PHE B 168 TRP 0.010 0.001 TRP A 151 HIS 0.001 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 1504) covalent geometry : angle 0.40917 ( 1996) hydrogen bonds : bond 0.03513 ( 119) hydrogen bonds : angle 2.79508 ( 357) metal coordination : bond 0.00086 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 12 time to evaluate : 0.064 Fit side-chains REVERT: A 153 ARG cc_start: 0.7475 (ttp80) cc_final: 0.7131 (ttp80) REVERT: A 224 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6357 (tt) REVERT: B 145 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6858 (mm-30) REVERT: B 205 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7342 (mt-10) outliers start: 5 outliers final: 1 residues processed: 17 average time/residue: 0.0912 time to fit residues: 1.7863 Evaluate side-chains 14 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 145 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.0270 chunk 11 optimal weight: 0.0270 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4296 ------------------------------------------------------------------------------- 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 = 0.4013 r_free = 0.4013 target = 0.179895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.155449 restraints weight = 1202.294| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.70 r_work: 0.3717 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1508 Z= 0.100 Angle : 0.403 4.554 1996 Z= 0.218 Chirality : 0.028 0.099 226 Planarity : 0.002 0.015 250 Dihedral : 3.881 15.502 190 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.88 % Allowed : 29.38 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.56 (0.61), residues: 176 helix: 3.08 (0.39), residues: 156 sheet: None (None), residues: 0 loop : -4.42 (0.51), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 153 PHE 0.004 0.001 PHE B 168 TRP 0.008 0.001 TRP A 151 HIS 0.001 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 1504) covalent geometry : angle 0.40337 ( 1996) hydrogen bonds : bond 0.03636 ( 119) hydrogen bonds : angle 2.74393 ( 357) metal coordination : bond 0.00121 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.057 Fit side-chains REVERT: A 224 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6540 (tt) REVERT: B 145 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6940 (mm-30) REVERT: B 205 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7386 (mt-10) outliers start: 3 outliers final: 1 residues processed: 15 average time/residue: 0.0697 time to fit residues: 1.2339 Evaluate side-chains 15 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 145 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.0000 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.187229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.164006 restraints weight = 1202.090| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.63 r_work: 0.3509 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1508 Z= 0.120 Angle : 0.438 4.718 1996 Z= 0.235 Chirality : 0.029 0.101 226 Planarity : 0.002 0.015 250 Dihedral : 3.995 15.522 190 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.50 % Allowed : 30.62 % Favored : 66.88 % 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: 3.41 (0.61), residues: 176 helix: 2.98 (0.38), residues: 156 sheet: None (None), residues: 0 loop : -4.44 (0.55), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 153 PHE 0.004 0.001 PHE B 168 TRP 0.008 0.001 TRP A 151 HIS 0.001 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 1504) covalent geometry : angle 0.43835 ( 1996) hydrogen bonds : bond 0.04000 ( 119) hydrogen bonds : angle 2.84450 ( 357) metal coordination : bond 0.00170 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.067 Fit side-chains REVERT: A 153 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7007 (ttp80) REVERT: A 224 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6367 (tt) REVERT: B 145 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.6936 (mm-30) REVERT: B 205 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7371 (mt-10) outliers start: 4 outliers final: 1 residues processed: 16 average time/residue: 0.1022 time to fit residues: 1.8345 Evaluate side-chains 14 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 145 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.175320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151221 restraints weight = 1187.789| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.57 r_work: 0.3513 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1508 Z= 0.119 Angle : 0.432 4.723 1996 Z= 0.232 Chirality : 0.029 0.101 226 Planarity : 0.002 0.016 250 Dihedral : 3.980 15.245 190 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.88 % Allowed : 31.25 % Favored : 66.88 % 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: 3.38 (0.61), residues: 176 helix: 2.96 (0.38), residues: 156 sheet: None (None), residues: 0 loop : -4.43 (0.57), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 153 PHE 0.004 0.001 PHE B 168 TRP 0.007 0.001 TRP A 151 HIS 0.001 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 1504) covalent geometry : angle 0.43210 ( 1996) hydrogen bonds : bond 0.03980 ( 119) hydrogen bonds : angle 2.85184 ( 357) metal coordination : bond 0.00162 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.040 Fit side-chains REVERT: A 224 LEU cc_start: 0.6712 (OUTLIER) cc_final: 0.6386 (tt) REVERT: B 145 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6953 (mm-30) REVERT: B 205 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7358 (mt-10) outliers start: 3 outliers final: 1 residues processed: 14 average time/residue: 0.0478 time to fit residues: 0.7906 Evaluate side-chains 14 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 145 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 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 = 0.4108 r_free = 0.4108 target = 0.187519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164333 restraints weight = 1213.443| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.64 r_work: 0.3505 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1508 Z= 0.117 Angle : 0.429 4.704 1996 Z= 0.231 Chirality : 0.029 0.103 226 Planarity : 0.002 0.016 250 Dihedral : 3.962 15.019 190 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.88 % Allowed : 31.25 % Favored : 66.88 % 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: 3.39 (0.61), residues: 176 helix: 2.97 (0.38), residues: 156 sheet: None (None), residues: 0 loop : -4.43 (0.57), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 153 PHE 0.004 0.001 PHE B 168 TRP 0.007 0.001 TRP A 151 HIS 0.001 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 1504) covalent geometry : angle 0.42887 ( 1996) hydrogen bonds : bond 0.03965 ( 119) hydrogen bonds : angle 2.84990 ( 357) metal coordination : bond 0.00159 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 352 Ramachandran restraints generated. 176 Oldfield, 0 Emsley, 176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.063 Fit side-chains REVERT: A 224 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6367 (tt) REVERT: B 145 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: B 205 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7362 (mt-10) outliers start: 3 outliers final: 1 residues processed: 15 average time/residue: 0.0728 time to fit residues: 1.2846 Evaluate side-chains 15 residues out of total 160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 12 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 145 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.174478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150621 restraints weight = 1169.561| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.55 r_work: 0.3507 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1508 Z= 0.126 Angle : 0.440 4.754 1996 Z= 0.236 Chirality : 0.029 0.105 226 Planarity : 0.002 0.016 250 Dihedral : 4.006 15.349 190 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.88 % Allowed : 31.25 % Favored : 66.88 % 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: 3.35 (0.61), residues: 176 helix: 2.94 (0.38), residues: 156 sheet: None (None), residues: 0 loop : -4.43 (0.56), residues: 20 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 153 PHE 0.005 0.001 PHE B 168 TRP 0.007 0.001 TRP A 151 HIS 0.002 0.001 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 1504) covalent geometry : angle 0.43975 ( 1996) hydrogen bonds : bond 0.04088 ( 119) hydrogen bonds : angle 2.88627 ( 357) metal coordination : bond 0.00183 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 617.19 seconds wall clock time: 11 minutes 35.30 seconds (695.30 seconds total)