Starting phenix.real_space_refine on Tue Feb 3 12:20:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8h_62173/02_2026/9k8h_62173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8h_62173/02_2026/9k8h_62173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k8h_62173/02_2026/9k8h_62173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8h_62173/02_2026/9k8h_62173.map" model { file = "/net/cci-nas-00/data/ceres_data/9k8h_62173/02_2026/9k8h_62173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8h_62173/02_2026/9k8h_62173.cif" } resolution = 2.71 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= 0.002 sd= 0.221 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 946 2.51 5 N 232 2.21 5 O 278 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 1460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 729 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "B" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 729 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} 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: 0.52, per 1000 atoms: 0.36 Number of scatterers: 1460 At special positions: 0 Unit cell: (53.865, 58.1742, 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 278 8.00 N 232 7.00 C 946 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 62.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 175 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS B 195 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 175 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 195 " 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 352 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 141 through 164 Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.782A pdb=" N LYS A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 209 removed outlier: 3.586A pdb=" N ALA A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 3.532A pdb=" N LEU A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 164 removed outlier: 3.955A pdb=" N LYS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 188 removed outlier: 4.085A pdb=" N LYS B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU B 173 " --> pdb=" O GLU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 210 removed outlier: 3.826A pdb=" N ALA B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 230 removed outlier: 3.671A pdb=" N GLU B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) 124 hydrogen bonds defined for protein. 372 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: 0.16 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: 474 1.34 - 1.46: 86 1.46 - 1.57: 902 1.57 - 1.69: 0 1.69 - 1.80: 4 Bond restraints: 1466 Sorted by residual: bond pdb=" CA LEU A 188 " pdb=" C LEU A 188 " ideal model delta sigma weight residual 1.522 1.505 0.017 1.37e-02 5.33e+03 1.56e+00 bond pdb=" CB GLU B 216 " pdb=" CG GLU B 216 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CA LYS A 209 " pdb=" CB LYS A 209 " ideal model delta sigma weight residual 1.526 1.540 -0.014 1.36e-02 5.41e+03 1.02e+00 bond pdb=" CA LYS A 209 " pdb=" C LYS A 209 " ideal model delta sigma weight residual 1.526 1.538 -0.012 1.23e-02 6.61e+03 9.34e-01 bond pdb=" CB VAL B 159 " pdb=" CG2 VAL B 159 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.44e-01 ... (remaining 1461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 1908 1.73 - 3.46: 33 3.46 - 5.18: 6 5.18 - 6.91: 1 6.91 - 8.64: 2 Bond angle restraints: 1950 Sorted by residual: angle pdb=" CA LYS A 209 " pdb=" CB LYS A 209 " pdb=" CG LYS A 209 " ideal model delta sigma weight residual 114.10 122.34 -8.24 2.00e+00 2.50e-01 1.70e+01 angle pdb=" CA GLU B 216 " pdb=" CB GLU B 216 " pdb=" CG GLU B 216 " ideal model delta sigma weight residual 114.10 119.69 -5.59 2.00e+00 2.50e-01 7.82e+00 angle pdb=" N LYS B 168 " pdb=" CA LYS B 168 " pdb=" C LYS B 168 " ideal model delta sigma weight residual 114.56 111.08 3.48 1.27e+00 6.20e-01 7.50e+00 angle pdb=" CA LEU A 208 " pdb=" CB LEU A 208 " pdb=" CG LEU A 208 " ideal model delta sigma weight residual 116.30 124.94 -8.64 3.50e+00 8.16e-02 6.10e+00 angle pdb=" C LYS A 209 " pdb=" CA LYS A 209 " pdb=" CB LYS A 209 " ideal model delta sigma weight residual 111.23 115.24 -4.01 1.70e+00 3.46e-01 5.57e+00 ... (remaining 1945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 738 17.54 - 35.07: 128 35.07 - 52.60: 55 52.60 - 70.14: 10 70.14 - 87.67: 9 Dihedral angle restraints: 940 sinusoidal: 408 harmonic: 532 Sorted by residual: dihedral pdb=" CB GLU A 225 " pdb=" CG GLU A 225 " pdb=" CD GLU A 225 " pdb=" OE1 GLU A 225 " ideal model delta sinusoidal sigma weight residual 0.00 -87.67 87.67 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CA GLU B 225 " pdb=" CB GLU B 225 " pdb=" CG GLU B 225 " pdb=" CD GLU B 225 " ideal model delta sinusoidal sigma weight residual 180.00 -123.52 -56.48 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" N LEU A 199 " pdb=" CA LEU A 199 " pdb=" CB LEU A 199 " pdb=" CG LEU A 199 " ideal model delta sinusoidal sigma weight residual -180.00 -123.60 -56.40 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 937 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 181 0.038 - 0.075: 53 0.075 - 0.113: 1 0.113 - 0.151: 0 0.151 - 0.189: 1 Chirality restraints: 236 Sorted by residual: chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CB ILE B 230 " pdb=" CA ILE B 230 " pdb=" CG1 ILE B 230 " pdb=" CG2 ILE B 230 " both_signs ideal model delta sigma weight residual False 2.64 2.57 0.08 2.00e-01 2.50e+01 1.47e-01 chirality pdb=" CA GLU A 186 " pdb=" N GLU A 186 " pdb=" C GLU A 186 " pdb=" CB GLU A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.44 0.07 2.00e-01 2.50e+01 1.35e-01 ... (remaining 233 not shown) Planarity restraints: 240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 143 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" CD GLU A 143 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU A 143 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU A 143 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 185 " 0.010 2.00e-02 2.50e+03 7.42e-03 9.63e-01 pdb=" CG PHE A 185 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 185 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE A 185 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 185 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 185 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 185 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 221 " 0.004 2.00e-02 2.50e+03 7.72e-03 5.96e-01 pdb=" C ILE A 221 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE A 221 " 0.005 2.00e-02 2.50e+03 pdb=" N ALA A 222 " 0.004 2.00e-02 2.50e+03 ... (remaining 237 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 9 2.61 - 3.18: 1177 3.18 - 3.75: 2358 3.75 - 4.33: 2977 4.33 - 4.90: 5072 Nonbonded interactions: 11593 Sorted by model distance: nonbonded pdb=" OD2 ASP A 191 " pdb="ZN ZN B 301 " model vdw 2.036 2.230 nonbonded pdb=" OD2 ASP B 191 " pdb="ZN ZN A 301 " model vdw 2.062 2.230 nonbonded pdb=" OD2 ASP A 179 " pdb="ZN ZN A 301 " model vdw 2.083 2.230 nonbonded pdb=" OE2 GLU A 157 " pdb=" NH2 ARG A 161 " model vdw 2.258 3.120 nonbonded pdb=" OD2 ASP B 179 " pdb="ZN ZN B 301 " model vdw 2.395 2.230 ... (remaining 11588 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: 1.120 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.710 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.152 1470 Z= 0.255 Angle : 0.653 8.642 1950 Z= 0.371 Chirality : 0.033 0.189 236 Planarity : 0.003 0.016 240 Dihedral : 22.502 87.669 588 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.25 % Allowed : 38.31 % Favored : 58.44 % 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: 2.48 (0.61), residues: 178 helix: 2.27 (0.39), residues: 160 sheet: None (None), residues: 0 loop : -4.53 (0.39), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 161 PHE 0.016 0.002 PHE A 185 HIS 0.002 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 1466) covalent geometry : angle 0.65267 ( 1950) hydrogen bonds : bond 0.08493 ( 124) hydrogen bonds : angle 3.85641 ( 372) metal coordination : bond 0.11039 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.040 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 25 average time/residue: 0.9754 time to fit residues: 24.6194 Evaluate side-chains 23 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 ASP 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: 1.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.183772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.149431 restraints weight = 1268.629| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.27 r_work: 0.3507 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1470 Z= 0.150 Angle : 0.537 6.688 1950 Z= 0.280 Chirality : 0.030 0.076 236 Planarity : 0.003 0.020 240 Dihedral : 7.793 55.052 196 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.25 % Allowed : 33.77 % Favored : 62.99 % 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: 2.86 (0.61), residues: 178 helix: 2.44 (0.39), residues: 162 sheet: None (None), residues: 0 loop : -4.41 (0.49), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 161 PHE 0.011 0.002 PHE A 185 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 1466) covalent geometry : angle 0.53665 ( 1950) hydrogen bonds : bond 0.05088 ( 124) hydrogen bonds : angle 3.28361 ( 372) metal coordination : bond 0.00168 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.037 Fit side-chains REVERT: A 167 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7468 (t0) REVERT: B 141 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6727 (mttm) outliers start: 5 outliers final: 1 residues processed: 25 average time/residue: 0.9627 time to fit residues: 24.2867 Evaluate side-chains 20 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 153 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 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 = 0.3992 r_free = 0.3992 target = 0.182107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.147103 restraints weight = 1265.038| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.28 r_work: 0.3389 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1470 Z= 0.146 Angle : 0.484 5.556 1950 Z= 0.256 Chirality : 0.030 0.089 236 Planarity : 0.003 0.023 240 Dihedral : 4.511 32.863 186 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.90 % Allowed : 35.71 % Favored : 60.39 % 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: 3.03 (0.60), residues: 178 helix: 2.63 (0.38), residues: 160 sheet: None (None), residues: 0 loop : -4.45 (0.48), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 PHE 0.010 0.002 PHE A 185 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 1466) covalent geometry : angle 0.48436 ( 1950) hydrogen bonds : bond 0.05075 ( 124) hydrogen bonds : angle 3.21931 ( 372) metal coordination : bond 0.00216 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.065 Fit side-chains REVERT: B 141 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6742 (mttm) REVERT: B 211 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.6270 (mttt) outliers start: 6 outliers final: 2 residues processed: 25 average time/residue: 1.0073 time to fit residues: 25.4386 Evaluate side-chains 21 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 17 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 211 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 chunk 3 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.184896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.149924 restraints weight = 1283.705| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.29 r_work: 0.3417 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1470 Z= 0.123 Angle : 0.436 5.226 1950 Z= 0.233 Chirality : 0.029 0.100 236 Planarity : 0.002 0.014 240 Dihedral : 3.615 10.615 184 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.25 % Allowed : 36.36 % Favored : 60.39 % 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: 3.30 (0.61), residues: 178 helix: 2.81 (0.38), residues: 160 sheet: None (None), residues: 0 loop : -4.34 (0.50), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 161 PHE 0.006 0.001 PHE A 185 HIS 0.003 0.001 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 1466) covalent geometry : angle 0.43582 ( 1950) hydrogen bonds : bond 0.04441 ( 124) hydrogen bonds : angle 3.14268 ( 372) metal coordination : bond 0.00147 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.065 Fit side-chains REVERT: A 161 ARG cc_start: 0.7468 (ttm170) cc_final: 0.7248 (ttm170) REVERT: A 209 LYS cc_start: 0.6883 (ttpm) cc_final: 0.6429 (ttpp) REVERT: B 141 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6604 (mttm) REVERT: B 211 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.6242 (mttt) outliers start: 5 outliers final: 1 residues processed: 25 average time/residue: 1.0384 time to fit residues: 26.2092 Evaluate side-chains 20 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 211 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 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 = 0.4014 r_free = 0.4014 target = 0.184395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.149084 restraints weight = 1285.561| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.29 r_work: 0.3434 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1470 Z= 0.129 Angle : 0.444 5.497 1950 Z= 0.236 Chirality : 0.030 0.099 236 Planarity : 0.002 0.017 240 Dihedral : 3.650 10.236 184 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 3.90 % Allowed : 34.42 % Favored : 61.69 % 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: 3.29 (0.60), residues: 178 helix: 2.80 (0.38), residues: 160 sheet: None (None), residues: 0 loop : -4.32 (0.51), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 198 PHE 0.007 0.001 PHE A 185 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 1466) covalent geometry : angle 0.44370 ( 1950) hydrogen bonds : bond 0.04644 ( 124) hydrogen bonds : angle 3.13321 ( 372) metal coordination : bond 0.00183 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.064 Fit side-chains REVERT: A 208 LEU cc_start: 0.7441 (tp) cc_final: 0.7204 (tt) REVERT: A 209 LYS cc_start: 0.6785 (ttpm) cc_final: 0.6369 (ttpt) REVERT: A 211 LYS cc_start: 0.7283 (mtmm) cc_final: 0.6845 (pttt) REVERT: B 141 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6660 (mttm) REVERT: B 211 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.6200 (mttt) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 1.0208 time to fit residues: 25.8161 Evaluate side-chains 23 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 211 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 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 = 0.4018 r_free = 0.4018 target = 0.184802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.149784 restraints weight = 1246.025| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.26 r_work: 0.3419 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1470 Z= 0.131 Angle : 0.450 5.454 1950 Z= 0.239 Chirality : 0.030 0.098 236 Planarity : 0.002 0.018 240 Dihedral : 3.606 9.878 184 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.90 % Allowed : 38.31 % Favored : 57.79 % 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: 3.29 (0.60), residues: 178 helix: 2.79 (0.38), residues: 160 sheet: None (None), residues: 0 loop : -4.25 (0.52), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 198 PHE 0.007 0.001 PHE A 185 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 1466) covalent geometry : angle 0.44989 ( 1950) hydrogen bonds : bond 0.04624 ( 124) hydrogen bonds : angle 3.14742 ( 372) metal coordination : bond 0.00181 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.065 Fit side-chains REVERT: A 161 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7405 (ttm170) REVERT: A 208 LEU cc_start: 0.7209 (tp) cc_final: 0.6954 (tt) REVERT: A 209 LYS cc_start: 0.6813 (ttpm) cc_final: 0.6379 (ttpt) REVERT: A 211 LYS cc_start: 0.7241 (mtmm) cc_final: 0.6794 (pttt) REVERT: B 141 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6583 (mttm) REVERT: B 211 LYS cc_start: 0.6451 (OUTLIER) cc_final: 0.6191 (mttt) outliers start: 6 outliers final: 3 residues processed: 25 average time/residue: 0.9691 time to fit residues: 24.4795 Evaluate side-chains 22 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 17 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 211 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.184070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.149024 restraints weight = 1279.872| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.28 r_work: 0.3431 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1470 Z= 0.140 Angle : 0.463 5.621 1950 Z= 0.244 Chirality : 0.030 0.094 236 Planarity : 0.002 0.022 240 Dihedral : 3.626 9.484 184 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.90 % Allowed : 38.31 % Favored : 57.79 % 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: 3.21 (0.60), residues: 178 helix: 2.73 (0.38), residues: 160 sheet: None (None), residues: 0 loop : -4.19 (0.54), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 PHE 0.007 0.001 PHE A 185 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 1466) covalent geometry : angle 0.46297 ( 1950) hydrogen bonds : bond 0.04879 ( 124) hydrogen bonds : angle 3.15465 ( 372) metal coordination : bond 0.00205 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.065 Fit side-chains REVERT: A 208 LEU cc_start: 0.7314 (tp) cc_final: 0.7049 (tt) REVERT: A 209 LYS cc_start: 0.6908 (ttpm) cc_final: 0.6457 (ttpp) REVERT: B 141 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6650 (mttm) REVERT: B 211 LYS cc_start: 0.6491 (OUTLIER) cc_final: 0.6246 (mttt) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 1.0264 time to fit residues: 24.9092 Evaluate side-chains 23 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 211 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.185543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.150620 restraints weight = 1255.115| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.27 r_work: 0.3459 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 0.026 1470 Z= 0.126 Angle : 0.436 5.262 1950 Z= 0.232 Chirality : 0.030 0.104 236 Planarity : 0.002 0.016 240 Dihedral : 3.550 9.559 184 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.90 % Allowed : 37.66 % Favored : 58.44 % 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: 3.30 (0.60), residues: 178 helix: 2.79 (0.38), residues: 160 sheet: None (None), residues: 0 loop : -4.15 (0.55), residues: 18 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 PHE 0.006 0.001 PHE A 185 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 1466) covalent geometry : angle 0.43560 ( 1950) hydrogen bonds : bond 0.04544 ( 124) hydrogen bonds : angle 3.13878 ( 372) metal coordination : bond 0.00174 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.063 Fit side-chains REVERT: A 208 LEU cc_start: 0.7324 (tp) cc_final: 0.7011 (tt) REVERT: A 209 LYS cc_start: 0.6882 (ttpm) cc_final: 0.6469 (ttpp) REVERT: B 211 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6187 (mttt) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.8075 time to fit residues: 19.5814 Evaluate side-chains 22 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 211 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.184518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.150549 restraints weight = 1315.409| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.31 r_work: 0.3419 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1470 Z= 0.164 Angle : 0.506 6.021 1950 Z= 0.264 Chirality : 0.031 0.088 236 Planarity : 0.003 0.032 240 Dihedral : 3.729 9.631 184 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.90 % Allowed : 37.66 % Favored : 58.44 % 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: 3.01 (0.59), residues: 178 helix: 2.50 (0.38), residues: 162 sheet: None (None), residues: 0 loop : -3.99 (0.60), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 PHE 0.004 0.001 PHE A 219 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 1466) covalent geometry : angle 0.50595 ( 1950) hydrogen bonds : bond 0.05423 ( 124) hydrogen bonds : angle 3.21446 ( 372) metal coordination : bond 0.00287 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.050 Fit side-chains REVERT: A 185 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: A 208 LEU cc_start: 0.7458 (tp) cc_final: 0.7128 (tt) REVERT: A 209 LYS cc_start: 0.6908 (ttpm) cc_final: 0.6487 (ttpp) REVERT: B 168 LYS cc_start: 0.6501 (mptm) cc_final: 0.6221 (mptt) REVERT: B 211 LYS cc_start: 0.6535 (OUTLIER) cc_final: 0.6237 (mttt) outliers start: 6 outliers final: 3 residues processed: 24 average time/residue: 0.6402 time to fit residues: 15.5360 Evaluate side-chains 23 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 211 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.185079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.150537 restraints weight = 1311.374| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.33 r_work: 0.3394 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1470 Z= 0.136 Angle : 0.455 5.566 1950 Z= 0.241 Chirality : 0.030 0.096 236 Planarity : 0.002 0.020 240 Dihedral : 3.589 9.076 184 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.25 % Allowed : 38.31 % Favored : 58.44 % 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: 3.18 (0.60), residues: 178 helix: 2.62 (0.38), residues: 162 sheet: None (None), residues: 0 loop : -3.92 (0.60), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 PHE 0.004 0.001 PHE A 185 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 1466) covalent geometry : angle 0.45481 ( 1950) hydrogen bonds : bond 0.04808 ( 124) hydrogen bonds : angle 3.16950 ( 372) metal coordination : bond 0.00159 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 356 Ramachandran restraints generated. 178 Oldfield, 0 Emsley, 178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.036 Fit side-chains REVERT: A 185 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: A 208 LEU cc_start: 0.7397 (tp) cc_final: 0.7130 (tt) REVERT: A 209 LYS cc_start: 0.7034 (ttpm) cc_final: 0.6793 (ttpt) REVERT: A 211 LYS cc_start: 0.7085 (mtmm) cc_final: 0.6704 (pttt) REVERT: B 168 LYS cc_start: 0.6568 (mptm) cc_final: 0.6293 (mptt) REVERT: B 211 LYS cc_start: 0.6482 (OUTLIER) cc_final: 0.6222 (mttt) outliers start: 5 outliers final: 3 residues processed: 23 average time/residue: 0.5910 time to fit residues: 13.7404 Evaluate side-chains 23 residues out of total 154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 PHE Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 211 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 15 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 = 0.4025 r_free = 0.4025 target = 0.185461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.150967 restraints weight = 1295.594| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.31 r_work: 0.3481 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1470 Z= 0.129 Angle : 0.443 5.409 1950 Z= 0.235 Chirality : 0.030 0.100 236 Planarity : 0.002 0.018 240 Dihedral : 3.537 9.036 184 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.25 % Allowed : 38.31 % Favored : 58.44 % 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: 3.25 (0.60), residues: 178 helix: 2.66 (0.38), residues: 162 sheet: None (None), residues: 0 loop : -3.90 (0.59), residues: 16 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 PHE 0.004 0.001 PHE A 185 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 1466) covalent geometry : angle 0.44300 ( 1950) hydrogen bonds : bond 0.04667 ( 124) hydrogen bonds : angle 3.14336 ( 372) metal coordination : bond 0.00165 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 804.31 seconds wall clock time: 14 minutes 50.42 seconds (890.42 seconds total)