Starting phenix.real_space_refine on Tue Feb 3 12:26:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k8j_62175/02_2026/9k8j_62175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k8j_62175/02_2026/9k8j_62175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k8j_62175/02_2026/9k8j_62175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k8j_62175/02_2026/9k8j_62175.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k8j_62175/02_2026/9k8j_62175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k8j_62175/02_2026/9k8j_62175.map" } resolution = 3.12 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= 0.214 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 4 5.16 5 C 1277 2.51 5 N 315 2.21 5 O 383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 1981 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1979 Classifications: {'peptide': 249} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 245} 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: 0.63, per 1000 atoms: 0.32 Number of scatterers: 1981 At special positions: 0 Unit cell: (71.1018, 53.865, 66.7926, 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 4 16.00 O 383 8.00 N 315 7.00 C 1277 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: 0.17 Conformation dependent library (CDL) restraints added in 76.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 64 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 247 " 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 470 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 0 sheets defined 85.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 24 through 40 removed outlier: 3.581A pdb=" N LYS A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 60 removed outlier: 3.705A pdb=" N ASP A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 76 removed outlier: 3.722A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 98 removed outlier: 3.628A pdb=" N LYS A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.567A pdb=" N ALA A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 138 removed outlier: 3.512A pdb=" N ALA A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 160 through 178 removed outlier: 4.007A pdb=" N ILE A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.973A pdb=" N GLY A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 214 through 231 removed outlier: 3.525A pdb=" N ALA A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 141 hydrogen bonds defined for protein. 423 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: 0.30 Time building geometry restraints manager: 0.23 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: 647 1.34 - 1.46: 291 1.46 - 1.57: 1053 1.57 - 1.69: 0 1.69 - 1.80: 8 Bond restraints: 1999 Sorted by residual: bond pdb=" CA GLU A 115 " pdb=" CB GLU A 115 " ideal model delta sigma weight residual 1.524 1.545 -0.022 1.31e-02 5.83e+03 2.69e+00 bond pdb=" CB GLU A 93 " pdb=" CG GLU A 93 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.05e-01 bond pdb=" CG LEU A 184 " pdb=" CD1 LEU A 184 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.90e-01 bond pdb=" C ARG A 76 " pdb=" O ARG A 76 " ideal model delta sigma weight residual 1.244 1.238 0.007 1.00e-02 1.00e+04 4.56e-01 bond pdb=" CB PRO A 100 " pdb=" CG PRO A 100 " ideal model delta sigma weight residual 1.492 1.524 -0.032 5.00e-02 4.00e+02 4.00e-01 ... (remaining 1994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 2433 0.92 - 1.85: 182 1.85 - 2.77: 44 2.77 - 3.69: 24 3.69 - 4.62: 3 Bond angle restraints: 2686 Sorted by residual: angle pdb=" N VAL A 160 " pdb=" CA VAL A 160 " pdb=" C VAL A 160 " ideal model delta sigma weight residual 112.90 109.95 2.95 9.60e-01 1.09e+00 9.44e+00 angle pdb=" N GLY A 4 " pdb=" CA GLY A 4 " pdb=" C GLY A 4 " ideal model delta sigma weight residual 114.69 111.82 2.87 1.19e+00 7.06e-01 5.82e+00 angle pdb=" C GLU A 115 " pdb=" CA GLU A 115 " pdb=" CB GLU A 115 " ideal model delta sigma weight residual 111.50 114.54 -3.04 1.29e+00 6.01e-01 5.54e+00 angle pdb=" N GLU A 182 " pdb=" CA GLU A 182 " pdb=" C GLU A 182 " ideal model delta sigma weight residual 111.36 113.90 -2.54 1.09e+00 8.42e-01 5.43e+00 angle pdb=" CA GLU A 115 " pdb=" CB GLU A 115 " pdb=" CG GLU A 115 " ideal model delta sigma weight residual 114.10 118.72 -4.62 2.00e+00 2.50e-01 5.33e+00 ... (remaining 2681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 1027 17.59 - 35.18: 149 35.18 - 52.78: 65 52.78 - 70.37: 5 70.37 - 87.96: 2 Dihedral angle restraints: 1248 sinusoidal: 521 harmonic: 727 Sorted by residual: dihedral pdb=" CA GLY A 195 " pdb=" C GLY A 195 " pdb=" N ASP A 196 " pdb=" CA ASP A 196 " ideal model delta harmonic sigma weight residual 180.00 -161.92 -18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CB GLU A 235 " pdb=" CG GLU A 235 " pdb=" CD GLU A 235 " pdb=" OE1 GLU A 235 " ideal model delta sinusoidal sigma weight residual 0.00 87.96 -87.96 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CG ARG A 58 " pdb=" CD ARG A 58 " pdb=" NE ARG A 58 " pdb=" CZ ARG A 58 " ideal model delta sinusoidal sigma weight residual 90.00 131.92 -41.92 2 1.50e+01 4.44e-03 9.52e+00 ... (remaining 1245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 156 0.021 - 0.041: 93 0.041 - 0.062: 48 0.062 - 0.082: 18 0.082 - 0.103: 7 Chirality restraints: 322 Sorted by residual: chirality pdb=" CA VAL A 213 " pdb=" N VAL A 213 " pdb=" C VAL A 213 " pdb=" CB VAL A 213 " both_signs ideal model delta sigma weight residual False 2.44 2.54 -0.10 2.00e-01 2.50e+01 2.65e-01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.36e-01 chirality pdb=" CB VAL A 66 " pdb=" CA VAL A 66 " pdb=" CG1 VAL A 66 " pdb=" CG2 VAL A 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.53 -0.10 2.00e-01 2.50e+01 2.31e-01 ... (remaining 319 not shown) Planarity restraints: 336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 158 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 159 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 159 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 159 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 115 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C GLU A 115 " -0.025 2.00e-02 2.50e+03 pdb=" O GLU A 115 " 0.009 2.00e-02 2.50e+03 pdb=" N THR A 116 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 126 " 0.006 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" C ASP A 126 " -0.019 2.00e-02 2.50e+03 pdb=" O ASP A 126 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE A 127 " 0.006 2.00e-02 2.50e+03 ... (remaining 333 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 389 2.78 - 3.31: 1845 3.31 - 3.84: 3108 3.84 - 4.37: 3641 4.37 - 4.90: 6418 Nonbonded interactions: 15401 Sorted by model distance: nonbonded pdb=" OD2 ASP A 68 " pdb="ZN ZN A 301 " model vdw 2.244 2.230 nonbonded pdb=" OD1 ASP A 32 " pdb=" NH2 ARG A 35 " model vdw 2.264 3.120 nonbonded pdb=" ND2 ASN A 22 " pdb=" OE1 GLU A 25 " model vdw 2.365 3.120 nonbonded pdb=" N ASP A 81 " pdb=" OD1 ASP A 81 " model vdw 2.438 3.120 nonbonded pdb=" OH TYR A 208 " pdb=" NZ LYS A 215 " model vdw 2.464 3.120 ... (remaining 15396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.500 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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 : 0.003 0.068 2001 Z= 0.162 Angle : 0.641 4.618 2686 Z= 0.404 Chirality : 0.034 0.103 322 Planarity : 0.004 0.052 336 Dihedral : 18.922 87.960 778 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.67 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 25.94 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.52), residues: 247 helix: 0.58 (0.37), residues: 204 sheet: None (None), residues: 0 loop : -3.56 (0.57), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.003 0.001 TYR A 123 PHE 0.008 0.001 PHE A 149 HIS 0.001 0.000 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 1999) covalent geometry : angle 0.64083 ( 2686) hydrogen bonds : bond 0.17606 ( 141) hydrogen bonds : angle 5.33581 ( 423) metal coordination : bond 0.05814 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0355 time to fit residues: 1.0643 Evaluate side-chains 19 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 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 51 HIS A 247 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.168558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.139321 restraints weight = 1797.028| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.93 r_work: 0.3365 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 2001 Z= 0.181 Angle : 0.572 5.601 2686 Z= 0.302 Chirality : 0.034 0.110 322 Planarity : 0.003 0.035 336 Dihedral : 4.761 33.942 267 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.67 % Favored : 93.93 % Rotamer: Outliers : 2.83 % Allowed : 23.58 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.52), residues: 247 helix: 0.71 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -2.73 (0.87), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.011 0.001 TYR A 38 PHE 0.004 0.001 PHE A 142 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 1999) covalent geometry : angle 0.57208 ( 2686) hydrogen bonds : bond 0.05161 ( 141) hydrogen bonds : angle 3.74684 ( 423) metal coordination : bond 0.08890 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.080 Fit side-chains REVERT: A 131 MET cc_start: 0.8109 (mtt) cc_final: 0.7900 (mtp) outliers start: 6 outliers final: 2 residues processed: 26 average time/residue: 0.0883 time to fit residues: 2.6390 Evaluate side-chains 19 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 130 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 13 optimal weight: 0.1980 chunk 8 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 overall best weight: 0.2518 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.175643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146016 restraints weight = 1811.702| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.00 r_work: 0.3414 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2001 Z= 0.108 Angle : 0.498 4.787 2686 Z= 0.263 Chirality : 0.032 0.100 322 Planarity : 0.002 0.027 336 Dihedral : 4.428 28.054 267 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.67 % Favored : 93.93 % Rotamer: Outliers : 1.89 % Allowed : 22.17 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.53), residues: 247 helix: 1.09 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.59 (0.88), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 19 TYR 0.009 0.001 TYR A 150 PHE 0.002 0.001 PHE A 142 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 1999) covalent geometry : angle 0.49848 ( 2686) hydrogen bonds : bond 0.03961 ( 141) hydrogen bonds : angle 3.35847 ( 423) metal coordination : bond 0.00181 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.047 Fit side-chains REVERT: A 153 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.6908 (tp) outliers start: 4 outliers final: 1 residues processed: 24 average time/residue: 0.0466 time to fit residues: 1.3514 Evaluate side-chains 20 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 153 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.0570 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.3925 r_free = 0.3925 target = 0.173983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144846 restraints weight = 1780.362| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.96 r_work: 0.3390 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2001 Z= 0.118 Angle : 0.508 5.200 2686 Z= 0.265 Chirality : 0.033 0.101 322 Planarity : 0.002 0.019 336 Dihedral : 4.460 30.605 267 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.67 % Favored : 93.93 % Rotamer: Outliers : 3.30 % Allowed : 21.70 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.53), residues: 247 helix: 1.13 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -3.22 (0.65), residues: 34 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 TYR 0.009 0.001 TYR A 38 PHE 0.002 0.001 PHE A 99 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 1999) covalent geometry : angle 0.50819 ( 2686) hydrogen bonds : bond 0.04177 ( 141) hydrogen bonds : angle 3.30484 ( 423) metal coordination : bond 0.00166 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.045 Fit side-chains REVERT: A 153 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.6926 (tp) REVERT: A 179 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5645 (mp0) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.0366 time to fit residues: 1.2477 Evaluate side-chains 25 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.168638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139350 restraints weight = 1790.945| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.95 r_work: 0.3346 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2001 Z= 0.161 Angle : 0.567 4.645 2686 Z= 0.292 Chirality : 0.035 0.117 322 Planarity : 0.003 0.021 336 Dihedral : 4.942 41.744 267 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.67 % Favored : 93.93 % Rotamer: Outliers : 3.30 % Allowed : 22.17 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.52), residues: 247 helix: 0.83 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -3.19 (0.68), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.012 0.001 TYR A 38 PHE 0.003 0.001 PHE A 142 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 1999) covalent geometry : angle 0.56737 ( 2686) hydrogen bonds : bond 0.05034 ( 141) hydrogen bonds : angle 3.49673 ( 423) metal coordination : bond 0.00227 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.055 Fit side-chains REVERT: A 131 MET cc_start: 0.8326 (mtm) cc_final: 0.8085 (mtp) REVERT: A 153 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7157 (tp) REVERT: A 179 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.5773 (mp0) outliers start: 7 outliers final: 4 residues processed: 27 average time/residue: 0.0392 time to fit residues: 1.3204 Evaluate side-chains 25 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 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 = 0.3871 r_free = 0.3871 target = 0.169511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139972 restraints weight = 1786.518| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.98 r_work: 0.3456 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2001 Z= 0.136 Angle : 0.541 4.747 2686 Z= 0.279 Chirality : 0.034 0.103 322 Planarity : 0.002 0.017 336 Dihedral : 4.879 41.128 267 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.67 % Favored : 93.93 % Rotamer: Outliers : 4.25 % Allowed : 21.23 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.52), residues: 247 helix: 0.96 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -3.12 (0.69), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 35 TYR 0.010 0.001 TYR A 38 PHE 0.002 0.001 PHE A 142 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 1999) covalent geometry : angle 0.54138 ( 2686) hydrogen bonds : bond 0.04499 ( 141) hydrogen bonds : angle 3.35732 ( 423) metal coordination : bond 0.00151 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.046 Fit side-chains REVERT: A 153 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.6953 (tp) REVERT: A 179 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5629 (mp0) outliers start: 9 outliers final: 4 residues processed: 26 average time/residue: 0.0338 time to fit residues: 1.0884 Evaluate side-chains 24 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 1 optimal weight: 0.0050 chunk 2 optimal weight: 0.6980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.169973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141463 restraints weight = 1796.137| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.89 r_work: 0.3381 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2001 Z= 0.118 Angle : 0.514 4.371 2686 Z= 0.272 Chirality : 0.033 0.103 322 Planarity : 0.002 0.015 336 Dihedral : 4.856 36.665 267 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.83 % Allowed : 22.64 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.53), residues: 247 helix: 1.17 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -3.11 (0.73), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 35 TYR 0.009 0.001 TYR A 38 PHE 0.003 0.001 PHE A 113 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 1999) covalent geometry : angle 0.51376 ( 2686) hydrogen bonds : bond 0.04111 ( 141) hydrogen bonds : angle 3.27700 ( 423) metal coordination : bond 0.00128 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.048 Fit side-chains REVERT: A 131 MET cc_start: 0.8230 (mtm) cc_final: 0.8021 (mtp) REVERT: A 153 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.6940 (tp) REVERT: A 179 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.5595 (mp0) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.0462 time to fit residues: 1.3659 Evaluate side-chains 26 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.166928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.137677 restraints weight = 1818.654| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.95 r_work: 0.3342 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2001 Z= 0.146 Angle : 0.541 4.118 2686 Z= 0.280 Chirality : 0.035 0.110 322 Planarity : 0.003 0.019 336 Dihedral : 4.889 40.249 267 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.30 % Allowed : 22.64 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.52), residues: 247 helix: 1.05 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -2.94 (0.75), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.010 0.001 TYR A 38 PHE 0.003 0.001 PHE A 142 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 1999) covalent geometry : angle 0.54133 ( 2686) hydrogen bonds : bond 0.04743 ( 141) hydrogen bonds : angle 3.38078 ( 423) metal coordination : bond 0.00176 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.046 Fit side-chains REVERT: A 131 MET cc_start: 0.8278 (mtm) cc_final: 0.8053 (mtp) REVERT: A 153 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7045 (tp) REVERT: A 179 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.5717 (mp0) outliers start: 7 outliers final: 4 residues processed: 28 average time/residue: 0.0423 time to fit residues: 1.4023 Evaluate side-chains 25 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 12 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.167378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.138432 restraints weight = 1781.356| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.89 r_work: 0.3343 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2001 Z= 0.138 Angle : 0.540 4.045 2686 Z= 0.280 Chirality : 0.034 0.107 322 Planarity : 0.002 0.019 336 Dihedral : 4.877 40.859 267 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.77 % Allowed : 22.64 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.52), residues: 247 helix: 1.09 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -2.75 (0.82), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.010 0.001 TYR A 38 PHE 0.003 0.001 PHE A 142 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 1999) covalent geometry : angle 0.53980 ( 2686) hydrogen bonds : bond 0.04559 ( 141) hydrogen bonds : angle 3.31963 ( 423) metal coordination : bond 0.00167 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.057 Fit side-chains REVERT: A 131 MET cc_start: 0.8254 (mtm) cc_final: 0.8032 (mtp) REVERT: A 153 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.6975 (tp) REVERT: A 175 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7709 (tp) REVERT: A 179 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5612 (mp0) outliers start: 8 outliers final: 5 residues processed: 26 average time/residue: 0.0740 time to fit residues: 2.2202 Evaluate side-chains 27 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 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 = 0.3836 r_free = 0.3836 target = 0.166718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.137212 restraints weight = 1844.781| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.96 r_work: 0.3328 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2001 Z= 0.140 Angle : 0.541 4.047 2686 Z= 0.279 Chirality : 0.034 0.108 322 Planarity : 0.003 0.019 336 Dihedral : 4.850 40.706 267 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.77 % Allowed : 22.64 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.52), residues: 247 helix: 1.06 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -2.68 (0.88), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.010 0.001 TYR A 38 PHE 0.003 0.001 PHE A 142 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 1999) covalent geometry : angle 0.54098 ( 2686) hydrogen bonds : bond 0.04603 ( 141) hydrogen bonds : angle 3.31303 ( 423) metal coordination : bond 0.00174 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 494 Ramachandran restraints generated. 247 Oldfield, 0 Emsley, 247 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.047 Fit side-chains REVERT: A 131 MET cc_start: 0.8259 (mtm) cc_final: 0.8034 (mtp) REVERT: A 153 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.6980 (tp) REVERT: A 179 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5649 (mp0) outliers start: 8 outliers final: 5 residues processed: 29 average time/residue: 0.0412 time to fit residues: 1.4206 Evaluate side-chains 27 residues out of total 212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 179 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3837 r_free = 0.3837 target = 0.166215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137421 restraints weight = 1830.969| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.90 r_work: 0.3329 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2001 Z= 0.151 Angle : 0.574 7.958 2686 Z= 0.290 Chirality : 0.035 0.114 322 Planarity : 0.003 0.019 336 Dihedral : 4.956 43.136 267 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.30 % Allowed : 23.11 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.53), residues: 247 helix: 0.96 (0.35), residues: 216 sheet: None (None), residues: 0 loop : -2.60 (0.94), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.011 0.001 TYR A 38 PHE 0.003 0.001 PHE A 142 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 1999) covalent geometry : angle 0.57353 ( 2686) hydrogen bonds : bond 0.04755 ( 141) hydrogen bonds : angle 3.33119 ( 423) metal coordination : bond 0.00189 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 571.23 seconds wall clock time: 10 minutes 23.54 seconds (623.54 seconds total)