Starting phenix.real_space_refine on Wed Mar 5 14:17:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r23_4708/03_2025/6r23_4708.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r23_4708/03_2025/6r23_4708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r23_4708/03_2025/6r23_4708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r23_4708/03_2025/6r23_4708.map" model { file = "/net/cci-nas-00/data/ceres_data/6r23_4708/03_2025/6r23_4708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r23_4708/03_2025/6r23_4708.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.026 sd= 0.295 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 974 2.51 5 N 260 2.21 5 O 274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1518 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 759 Classifications: {'peptide': 91} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 83} Restraints were copied for chains: B Time building chain proxies: 1.81, per 1000 atoms: 1.19 Number of scatterers: 1518 At special positions: 0 Unit cell: (90.72, 56.16, 47.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 274 8.00 N 260 7.00 C 974 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: 0.42 Conformation dependent library (CDL) restraints added in 218.7 milliseconds 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: 356 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 68.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 109 through 119 removed outlier: 4.046A pdb=" N ILE A 113 " --> pdb=" O ASP A 109 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A 118 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 139 removed outlier: 4.323A pdb=" N ARG A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 removed outlier: 3.775A pdb=" N TYR A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 169 removed outlier: 3.743A pdb=" N MET A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 188 removed outlier: 3.545A pdb=" N THR A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 119 removed outlier: 4.046A pdb=" N ILE B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 139 removed outlier: 4.322A pdb=" N ARG B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU B 130 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B 139 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.775A pdb=" N TYR B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 169 removed outlier: 3.743A pdb=" N MET B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 188 removed outlier: 3.546A pdb=" N THR B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) 64 hydrogen bonds defined for protein. 192 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: 0.26 Time building geometry restraints manager: 0.50 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: 480 1.34 - 1.46: 268 1.46 - 1.57: 784 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 1552 Sorted by residual: bond pdb=" C ASP B 144 " pdb=" N PHE B 145 " ideal model delta sigma weight residual 1.332 1.350 -0.017 1.40e-02 5.10e+03 1.52e+00 bond pdb=" C ASP A 144 " pdb=" N PHE A 145 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.40e-02 5.10e+03 1.48e+00 bond pdb=" N PHE A 145 " pdb=" CA PHE A 145 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.39e+00 bond pdb=" N PHE B 145 " pdb=" CA PHE B 145 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.34e+00 bond pdb=" C PRO B 142 " pdb=" N PRO B 143 " ideal model delta sigma weight residual 1.334 1.307 0.027 2.34e-02 1.83e+03 1.29e+00 ... (remaining 1547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 1896 1.59 - 3.18: 153 3.18 - 4.77: 31 4.77 - 6.36: 10 6.36 - 7.95: 2 Bond angle restraints: 2092 Sorted by residual: angle pdb=" C ARG B 140 " pdb=" N MET B 141 " pdb=" CA MET B 141 " ideal model delta sigma weight residual 121.80 129.75 -7.95 2.44e+00 1.68e-01 1.06e+01 angle pdb=" C ARG A 140 " pdb=" N MET A 141 " pdb=" CA MET A 141 " ideal model delta sigma weight residual 121.80 129.72 -7.92 2.44e+00 1.68e-01 1.05e+01 angle pdb=" C ASP B 144 " pdb=" N PHE B 145 " pdb=" CA PHE B 145 " ideal model delta sigma weight residual 121.54 127.72 -6.18 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C ASP A 144 " pdb=" N PHE A 145 " pdb=" CA PHE A 145 " ideal model delta sigma weight residual 121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01 angle pdb=" N SER B 121 " pdb=" CA SER B 121 " pdb=" C SER B 121 " ideal model delta sigma weight residual 108.24 112.30 -4.06 1.32e+00 5.74e-01 9.45e+00 ... (remaining 2087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 820 16.66 - 33.32: 112 33.32 - 49.98: 28 49.98 - 66.63: 0 66.63 - 83.29: 6 Dihedral angle restraints: 966 sinusoidal: 422 harmonic: 544 Sorted by residual: dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N PHE B 192 " pdb=" CA PHE B 192 " ideal model delta harmonic sigma weight residual 180.00 142.43 37.57 0 5.00e+00 4.00e-02 5.65e+01 dihedral pdb=" CA ARG A 191 " pdb=" C ARG A 191 " pdb=" N PHE A 192 " pdb=" CA PHE A 192 " ideal model delta harmonic sigma weight residual 180.00 142.44 37.56 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA MET B 141 " pdb=" C MET B 141 " pdb=" N PRO B 142 " pdb=" CA PRO B 142 " ideal model delta harmonic sigma weight residual 180.00 149.42 30.58 0 5.00e+00 4.00e-02 3.74e+01 ... (remaining 963 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.034: 148 0.034 - 0.068: 56 0.068 - 0.102: 14 0.102 - 0.136: 4 0.136 - 0.169: 6 Chirality restraints: 228 Sorted by residual: chirality pdb=" CA PRO A 108 " pdb=" N PRO A 108 " pdb=" C PRO A 108 " pdb=" CB PRO A 108 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA PRO B 108 " pdb=" N PRO B 108 " pdb=" C PRO B 108 " pdb=" CB PRO B 108 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CB ILE A 127 " pdb=" CA ILE A 127 " pdb=" CG1 ILE A 127 " pdb=" CG2 ILE A 127 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 225 not shown) Planarity restraints: 266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 106 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO A 107 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 106 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO B 107 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 166 " -0.007 2.00e-02 2.50e+03 1.43e-02 2.05e+00 pdb=" C ILE A 166 " 0.025 2.00e-02 2.50e+03 pdb=" O ILE A 166 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL A 167 " -0.008 2.00e-02 2.50e+03 ... (remaining 263 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 491 2.85 - 3.36: 1529 3.36 - 3.87: 2170 3.87 - 4.39: 2419 4.39 - 4.90: 3859 Nonbonded interactions: 10468 Sorted by model distance: nonbonded pdb=" O ILE B 152 " pdb=" OG1 THR B 156 " model vdw 2.332 3.040 nonbonded pdb=" O ILE A 152 " pdb=" OG1 THR A 156 " model vdw 2.333 3.040 nonbonded pdb=" O PHE A 114 " pdb=" OG1 THR A 118 " model vdw 2.353 3.040 nonbonded pdb=" O PHE B 114 " pdb=" OG1 THR B 118 " model vdw 2.353 3.040 nonbonded pdb=" OE1 GLU A 122 " pdb=" OG1 THR A 160 " model vdw 2.395 3.040 ... (remaining 10463 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.640 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: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 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 : 0.006 0.029 1552 Z= 0.368 Angle : 1.069 7.947 2092 Z= 0.635 Chirality : 0.046 0.169 228 Planarity : 0.007 0.042 266 Dihedral : 16.555 83.293 610 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 16.67 % Twisted General : 1.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.61 (0.51), residues: 178 helix: -3.06 (0.33), residues: 100 sheet: None (None), residues: 0 loop : -2.93 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 138 HIS 0.004 0.002 HIS A 170 PHE 0.023 0.003 PHE B 145 TYR 0.009 0.002 TYR A 164 ARG 0.004 0.001 ARG B 191 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.078 Fit side-chains REVERT: A 161 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8325 (mmtt) REVERT: A 169 MET cc_start: 0.8189 (ptp) cc_final: 0.7835 (ptm) REVERT: A 176 LYS cc_start: 0.8705 (mppt) cc_final: 0.8321 (mtpp) REVERT: A 179 MET cc_start: 0.8828 (mtt) cc_final: 0.8601 (mpp) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2154 time to fit residues: 5.6674 Evaluate side-chains 13 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.061466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055364 restraints weight = 3484.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.056929 restraints weight = 1984.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.057833 restraints weight = 1265.280| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1552 Z= 0.209 Angle : 0.684 5.939 2092 Z= 0.356 Chirality : 0.037 0.119 228 Planarity : 0.005 0.028 266 Dihedral : 6.182 27.162 202 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 1.12 % Allowed : 5.62 % Favored : 93.26 % Rotamer: Outliers : 1.22 % Allowed : 1.22 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.63), residues: 178 helix: -0.57 (0.47), residues: 104 sheet: None (None), residues: 0 loop : -1.89 (0.83), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 138 HIS 0.001 0.001 HIS A 170 PHE 0.022 0.003 PHE B 114 TYR 0.004 0.001 TYR A 155 ARG 0.004 0.001 ARG A 133 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.098 Fit side-chains REVERT: A 115 ASN cc_start: 0.8718 (t0) cc_final: 0.8472 (t0) REVERT: A 161 LYS cc_start: 0.8770 (tttm) cc_final: 0.8361 (mmtt) REVERT: A 175 LEU cc_start: 0.8283 (mm) cc_final: 0.7991 (pp) REVERT: A 176 LYS cc_start: 0.8741 (mppt) cc_final: 0.8409 (mtpp) REVERT: A 179 MET cc_start: 0.8855 (mtt) cc_final: 0.8374 (mtm) outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1556 time to fit residues: 4.0457 Evaluate side-chains 12 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 4 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.062430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056814 restraints weight = 3503.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.058252 restraints weight = 2008.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.059097 restraints weight = 1279.818| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1552 Z= 0.178 Angle : 0.600 5.989 2092 Z= 0.307 Chirality : 0.035 0.120 228 Planarity : 0.004 0.022 266 Dihedral : 5.174 23.668 202 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.68), residues: 178 helix: 0.60 (0.50), residues: 106 sheet: None (None), residues: 0 loop : -1.72 (0.88), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 138 HIS 0.001 0.000 HIS A 170 PHE 0.014 0.002 PHE A 192 TYR 0.015 0.002 TYR A 183 ARG 0.003 0.000 ARG B 129 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.096 Fit side-chains REVERT: A 141 MET cc_start: 0.4569 (ptm) cc_final: 0.4171 (mtt) REVERT: A 153 MET cc_start: 0.8670 (tmm) cc_final: 0.8348 (tmm) REVERT: A 161 LYS cc_start: 0.8757 (tttm) cc_final: 0.8371 (mmtt) REVERT: A 176 LYS cc_start: 0.8671 (mppt) cc_final: 0.8432 (mtpp) REVERT: A 177 ASP cc_start: 0.9313 (m-30) cc_final: 0.9069 (m-30) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.1844 time to fit residues: 3.9679 Evaluate side-chains 12 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056399 restraints weight = 3959.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057703 restraints weight = 2367.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058540 restraints weight = 1568.416| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1552 Z= 0.174 Angle : 0.579 5.864 2092 Z= 0.291 Chirality : 0.035 0.106 228 Planarity : 0.004 0.020 266 Dihedral : 4.890 22.278 202 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.70), residues: 178 helix: 1.19 (0.51), residues: 106 sheet: None (None), residues: 0 loop : -1.48 (0.89), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 138 HIS 0.001 0.001 HIS A 170 PHE 0.014 0.002 PHE A 192 TYR 0.003 0.001 TYR A 155 ARG 0.003 0.001 ARG B 129 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.099 Fit side-chains REVERT: A 141 MET cc_start: 0.4485 (ptm) cc_final: 0.4268 (mtt) REVERT: A 161 LYS cc_start: 0.8716 (tttm) cc_final: 0.8324 (mmtt) REVERT: A 176 LYS cc_start: 0.8775 (mppt) cc_final: 0.8572 (mtpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1591 time to fit residues: 2.8100 Evaluate side-chains 11 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 3 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.063680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057539 restraints weight = 3919.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058869 restraints weight = 2483.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059816 restraints weight = 1722.249| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 1552 Z= 0.195 Angle : 0.642 6.713 2092 Z= 0.312 Chirality : 0.036 0.118 228 Planarity : 0.004 0.020 266 Dihedral : 4.829 20.378 202 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.69), residues: 178 helix: 0.99 (0.51), residues: 106 sheet: None (None), residues: 0 loop : -1.36 (0.90), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 138 HIS 0.001 0.000 HIS A 170 PHE 0.020 0.003 PHE B 114 TYR 0.023 0.003 TYR B 155 ARG 0.002 0.000 ARG B 129 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.092 Fit side-chains REVERT: A 161 LYS cc_start: 0.8601 (tttm) cc_final: 0.8161 (mmtt) REVERT: A 176 LYS cc_start: 0.8759 (mppt) cc_final: 0.8437 (mtpp) REVERT: A 177 ASP cc_start: 0.9261 (m-30) cc_final: 0.8999 (m-30) REVERT: A 179 MET cc_start: 0.8893 (mmp) cc_final: 0.7720 (mmp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1585 time to fit residues: 2.7995 Evaluate side-chains 12 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 0.0970 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.058342 restraints weight = 3811.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.059686 restraints weight = 2415.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060567 restraints weight = 1672.188| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1552 Z= 0.183 Angle : 0.564 5.722 2092 Z= 0.282 Chirality : 0.033 0.094 228 Planarity : 0.003 0.017 266 Dihedral : 4.561 19.106 202 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.70), residues: 178 helix: 1.34 (0.52), residues: 106 sheet: None (None), residues: 0 loop : -1.25 (0.89), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 138 HIS 0.000 0.000 HIS B 170 PHE 0.015 0.002 PHE A 192 TYR 0.014 0.002 TYR B 183 ARG 0.002 0.000 ARG B 129 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8468 (tttm) cc_final: 0.7950 (mmtt) REVERT: A 176 LYS cc_start: 0.8771 (mppt) cc_final: 0.8469 (mtpp) REVERT: A 177 ASP cc_start: 0.9099 (m-30) cc_final: 0.8879 (m-30) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1607 time to fit residues: 2.4873 Evaluate side-chains 12 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.0050 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057889 restraints weight = 3688.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059276 restraints weight = 2306.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.060286 restraints weight = 1559.384| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 1552 Z= 0.188 Angle : 0.616 6.246 2092 Z= 0.294 Chirality : 0.033 0.092 228 Planarity : 0.003 0.020 266 Dihedral : 4.356 15.473 202 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.71), residues: 178 helix: 1.31 (0.53), residues: 106 sheet: None (None), residues: 0 loop : -1.28 (0.91), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 138 HIS 0.001 0.000 HIS B 170 PHE 0.010 0.001 PHE B 114 TYR 0.014 0.002 TYR B 183 ARG 0.002 0.000 ARG A 129 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8315 (tttm) cc_final: 0.7839 (mmtt) REVERT: A 176 LYS cc_start: 0.8635 (mppt) cc_final: 0.8423 (mtpp) REVERT: A 177 ASP cc_start: 0.9156 (m-30) cc_final: 0.8847 (m-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1837 time to fit residues: 3.3842 Evaluate side-chains 13 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 3 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 5 optimal weight: 0.0000 chunk 14 optimal weight: 0.0000 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.063957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057947 restraints weight = 3684.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059396 restraints weight = 2281.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.060363 restraints weight = 1523.047| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.6307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 1552 Z= 0.190 Angle : 0.596 6.434 2092 Z= 0.289 Chirality : 0.035 0.123 228 Planarity : 0.003 0.018 266 Dihedral : 4.096 12.546 202 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.72), residues: 178 helix: 1.52 (0.53), residues: 106 sheet: None (None), residues: 0 loop : -1.35 (0.91), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 138 HIS 0.000 0.000 HIS A 170 PHE 0.009 0.001 PHE B 114 TYR 0.015 0.002 TYR B 183 ARG 0.002 0.000 ARG A 129 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8347 (tttm) cc_final: 0.7800 (mmtt) REVERT: A 175 LEU cc_start: 0.8564 (mm) cc_final: 0.8219 (pp) REVERT: A 176 LYS cc_start: 0.8647 (mppt) cc_final: 0.8415 (mtpp) REVERT: A 177 ASP cc_start: 0.9128 (m-30) cc_final: 0.8903 (m-30) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1524 time to fit residues: 2.5394 Evaluate side-chains 13 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.0170 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.0470 chunk 12 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 0.2980 chunk 14 optimal weight: 0.0670 overall best weight: 0.1454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.059649 restraints weight = 3753.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.061243 restraints weight = 2422.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.062341 restraints weight = 1641.650| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 1552 Z= 0.191 Angle : 0.595 6.673 2092 Z= 0.287 Chirality : 0.035 0.103 228 Planarity : 0.003 0.013 266 Dihedral : 3.748 13.058 202 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.70), residues: 178 helix: 1.43 (0.52), residues: 106 sheet: None (None), residues: 0 loop : -1.45 (0.88), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 138 HIS 0.000 0.000 HIS A 170 PHE 0.006 0.001 PHE B 114 TYR 0.016 0.001 TYR B 183 ARG 0.002 0.000 ARG B 129 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.101 Fit side-chains REVERT: A 161 LYS cc_start: 0.8200 (tttm) cc_final: 0.7647 (mmtt) REVERT: A 175 LEU cc_start: 0.8503 (mm) cc_final: 0.8062 (pp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.2133 time to fit residues: 3.9171 Evaluate side-chains 13 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 0.0070 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059402 restraints weight = 3902.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060946 restraints weight = 2440.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061974 restraints weight = 1618.259| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1552 Z= 0.198 Angle : 0.630 6.688 2092 Z= 0.301 Chirality : 0.034 0.096 228 Planarity : 0.003 0.017 266 Dihedral : 3.800 12.641 202 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.71), residues: 178 helix: 1.50 (0.54), residues: 106 sheet: None (None), residues: 0 loop : -1.61 (0.85), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 138 HIS 0.000 0.000 HIS A 170 PHE 0.007 0.001 PHE B 114 TYR 0.016 0.002 TYR A 183 ARG 0.001 0.000 ARG A 133 ********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 161 LYS cc_start: 0.8197 (tttm) cc_final: 0.7641 (mmtt) REVERT: A 175 LEU cc_start: 0.8558 (mm) cc_final: 0.8063 (pp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.2190 time to fit residues: 3.9893 Evaluate side-chains 13 residues out of total 82 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.0070 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.065694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059597 restraints weight = 3916.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.061027 restraints weight = 2447.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.061995 restraints weight = 1651.472| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1552 Z= 0.192 Angle : 0.618 6.738 2092 Z= 0.296 Chirality : 0.034 0.098 228 Planarity : 0.003 0.019 266 Dihedral : 3.642 12.275 202 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.71), residues: 178 helix: 1.52 (0.53), residues: 106 sheet: None (None), residues: 0 loop : -1.37 (0.89), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 138 HIS 0.000 0.000 HIS A 170 PHE 0.005 0.001 PHE A 145 TYR 0.016 0.001 TYR B 183 ARG 0.001 0.000 ARG A 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 912.19 seconds wall clock time: 16 minutes 20.09 seconds (980.09 seconds total)