Starting phenix.real_space_refine on Tue Feb 3 12:18:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vyi_65454/02_2026/9vyi_65454.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vyi_65454/02_2026/9vyi_65454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vyi_65454/02_2026/9vyi_65454.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vyi_65454/02_2026/9vyi_65454.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vyi_65454/02_2026/9vyi_65454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vyi_65454/02_2026/9vyi_65454.map" } resolution = 3.7 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= 0.004 sd= 0.062 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 3 5.16 5 C 404 2.51 5 N 117 2.21 5 O 134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 658 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 658 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 87} Time building chain proxies: 0.23, per 1000 atoms: 0.35 Number of scatterers: 658 At special positions: 0 Unit cell: (36.72, 38.08, 54.4, 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 3 16.00 O 134 8.00 N 117 7.00 C 404 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: 0.03 Conformation dependent library (CDL) restraints added in 18.1 milliseconds 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 158 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.779A pdb=" N ILE A 4 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 31 removed outlier: 6.828A pdb=" N LEU A 29 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 66 removed outlier: 7.033A pdb=" N PHE A 64 " --> pdb=" O ILE A 71 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 71 " --> pdb=" O PHE A 64 " (cutoff:3.500A) 8 hydrogen bonds defined for protein. 12 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: 0.04 Time building geometry restraints manager: 0.04 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: 228 1.34 - 1.46: 137 1.46 - 1.58: 302 1.58 - 1.69: 0 1.69 - 1.81: 3 Bond restraints: 670 Sorted by residual: bond pdb=" CA ASN A 67 " pdb=" C ASN A 67 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.49e-02 4.50e+03 4.48e-01 bond pdb=" CG PRO A 21 " pdb=" CD PRO A 21 " ideal model delta sigma weight residual 1.503 1.523 -0.020 3.40e-02 8.65e+02 3.47e-01 bond pdb=" CG PRO A 77 " pdb=" CD PRO A 77 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.48e-01 bond pdb=" CA ASN A 50 " pdb=" C ASN A 50 " ideal model delta sigma weight residual 1.519 1.524 -0.006 1.19e-02 7.06e+03 2.28e-01 bond pdb=" CA VAL A 84 " pdb=" CB VAL A 84 " ideal model delta sigma weight residual 1.538 1.533 0.005 1.13e-02 7.83e+03 2.01e-01 ... (remaining 665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.74: 773 0.74 - 1.48: 105 1.48 - 2.23: 24 2.23 - 2.97: 7 2.97 - 3.71: 3 Bond angle restraints: 912 Sorted by residual: angle pdb=" N ASN A 67 " pdb=" CA ASN A 67 " pdb=" C ASN A 67 " ideal model delta sigma weight residual 113.38 110.08 3.30 1.17e+00 7.31e-01 7.93e+00 angle pdb=" N ASN A 50 " pdb=" CA ASN A 50 " pdb=" C ASN A 50 " ideal model delta sigma weight residual 113.43 110.13 3.30 1.26e+00 6.30e-01 6.88e+00 angle pdb=" CA ASN A 67 " pdb=" C ASN A 67 " pdb=" O ASN A 67 " ideal model delta sigma weight residual 119.78 122.12 -2.34 1.07e+00 8.73e-01 4.79e+00 angle pdb=" CA GLY A 13 " pdb=" C GLY A 13 " pdb=" O GLY A 13 " ideal model delta sigma weight residual 122.59 120.37 2.22 1.04e+00 9.25e-01 4.54e+00 angle pdb=" CA ASN A 67 " pdb=" C ASN A 67 " pdb=" N GLY A 68 " ideal model delta sigma weight residual 118.08 115.81 2.27 1.31e+00 5.83e-01 3.01e+00 ... (remaining 907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.57: 331 11.57 - 23.13: 31 23.13 - 34.70: 15 34.70 - 46.26: 13 46.26 - 57.82: 1 Dihedral angle restraints: 391 sinusoidal: 140 harmonic: 251 Sorted by residual: dihedral pdb=" N LEU A 29 " pdb=" CA LEU A 29 " pdb=" CB LEU A 29 " pdb=" CG LEU A 29 " ideal model delta sinusoidal sigma weight residual -60.00 -104.11 44.11 3 1.50e+01 4.44e-03 7.93e+00 dihedral pdb=" CA LYS A 41 " pdb=" C LYS A 41 " pdb=" N GLN A 42 " pdb=" CA GLN A 42 " ideal model delta harmonic sigma weight residual 180.00 -165.96 -14.04 0 5.00e+00 4.00e-02 7.88e+00 dihedral pdb=" N ASP A 88 " pdb=" CA ASP A 88 " pdb=" CB ASP A 88 " pdb=" CG ASP A 88 " ideal model delta sinusoidal sigma weight residual -180.00 -136.97 -43.03 3 1.50e+01 4.44e-03 7.73e+00 ... (remaining 388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 64 0.029 - 0.059: 22 0.059 - 0.088: 7 0.088 - 0.117: 9 0.117 - 0.146: 3 Chirality restraints: 105 Sorted by residual: chirality pdb=" CB VAL A 38 " pdb=" CA VAL A 38 " pdb=" CG1 VAL A 38 " pdb=" CG2 VAL A 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL A 78 " pdb=" N VAL A 78 " pdb=" C VAL A 78 " pdb=" CB VAL A 78 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA ILE A 58 " pdb=" N ILE A 58 " pdb=" C ILE A 58 " pdb=" CB ILE A 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 ... (remaining 102 not shown) Planarity restraints: 122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 76 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO A 77 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 77 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 77 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 20 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 21 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 21 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 21 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 26 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO A 27 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.016 5.00e-02 4.00e+02 ... (remaining 119 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 156 2.79 - 3.32: 651 3.32 - 3.84: 1126 3.84 - 4.37: 1260 4.37 - 4.90: 2164 Nonbonded interactions: 5357 Sorted by model distance: nonbonded pdb=" OG SER A 59 " pdb=" O ILE A 71 " model vdw 2.261 3.040 nonbonded pdb=" N ALA A 2 " pdb=" O VAL A 93 " model vdw 2.439 3.120 nonbonded pdb=" O PRO A 18 " pdb=" ND1 HIS A 46 " model vdw 2.441 3.120 nonbonded pdb=" OG SER A 12 " pdb=" OG1 THR A 83 " model vdw 2.490 3.040 nonbonded pdb=" NH2 ARG A 61 " pdb=" O SER A 94 " model vdw 2.542 3.120 ... (remaining 5352 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 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: 1.410 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 1.960 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 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 : 0.002 0.020 670 Z= 0.126 Angle : 0.612 3.711 912 Z= 0.389 Chirality : 0.047 0.146 105 Planarity : 0.006 0.049 122 Dihedral : 14.630 57.825 233 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 22.22 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.88), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.18 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.004 0.002 TYR A 43 PHE 0.002 0.001 PHE A 17 TRP 0.002 0.001 TRP A 63 HIS 0.002 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 670) covalent geometry : angle 0.61166 ( 912) hydrogen bonds : bond 0.26852 ( 8) hydrogen bonds : angle 9.95486 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.016 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0471 time to fit residues: 0.3198 Evaluate side-chains 5 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 8 optimal weight: 30.0000 overall best weight: 4.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.039796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.034428 restraints weight = 7589.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.035148 restraints weight = 5536.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.035664 restraints weight = 4381.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.036099 restraints weight = 3674.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.036386 restraints weight = 3158.579| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 670 Z= 0.111 Angle : 0.498 3.953 912 Z= 0.271 Chirality : 0.045 0.113 105 Planarity : 0.007 0.053 122 Dihedral : 4.340 13.734 96 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.78 % Allowed : 25.00 % Favored : 72.22 % 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: -0.02 (0.88), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.00 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.005 0.002 TYR A 43 PHE 0.003 0.001 PHE A 64 TRP 0.006 0.002 TRP A 63 HIS 0.001 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 670) covalent geometry : angle 0.49843 ( 912) hydrogen bonds : bond 0.03409 ( 8) hydrogen bonds : angle 5.69072 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.018 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 7 average time/residue: 0.0397 time to fit residues: 0.3160 Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 5 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 50.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 40.0000 chunk 8 optimal weight: 10.0000 overall best weight: 6.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.039616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.034622 restraints weight = 7567.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.035362 restraints weight = 5349.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.035850 restraints weight = 4129.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.036244 restraints weight = 3438.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.036532 restraints weight = 2918.595| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 670 Z= 0.142 Angle : 0.524 4.092 912 Z= 0.276 Chirality : 0.045 0.117 105 Planarity : 0.007 0.050 122 Dihedral : 4.422 13.442 96 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.17 % Allowed : 25.00 % Favored : 70.83 % 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: -0.30 (0.86), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.22 (0.65), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.008 0.003 TYR A 43 PHE 0.002 0.001 PHE A 64 TRP 0.008 0.003 TRP A 63 HIS 0.001 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 670) covalent geometry : angle 0.52413 ( 912) hydrogen bonds : bond 0.02687 ( 8) hydrogen bonds : angle 5.46763 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.016 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 8 average time/residue: 0.0328 time to fit residues: 0.3009 Evaluate side-chains 9 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 40.0000 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 40.0000 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 overall best weight: 7.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.039318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.034068 restraints weight = 7828.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.034817 restraints weight = 5562.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.035411 restraints weight = 4333.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.035823 restraints weight = 3509.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.036103 restraints weight = 2979.237| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 670 Z= 0.157 Angle : 0.541 4.366 912 Z= 0.286 Chirality : 0.045 0.119 105 Planarity : 0.007 0.053 122 Dihedral : 4.595 11.883 96 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.94 % Allowed : 26.39 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.88), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.19 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.008 0.003 TYR A 43 PHE 0.002 0.001 PHE A 64 TRP 0.007 0.003 TRP A 63 HIS 0.001 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 670) covalent geometry : angle 0.54052 ( 912) hydrogen bonds : bond 0.02835 ( 8) hydrogen bonds : angle 5.04838 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 6 time to evaluate : 0.015 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 9 average time/residue: 0.0278 time to fit residues: 0.2905 Evaluate side-chains 7 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 3 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 40.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 overall best weight: 7.7490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.038750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.032641 restraints weight = 8226.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.033658 restraints weight = 5294.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.034386 restraints weight = 3825.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.034929 restraints weight = 2965.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.035301 restraints weight = 2424.175| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 670 Z= 0.166 Angle : 0.566 4.452 912 Z= 0.295 Chirality : 0.045 0.116 105 Planarity : 0.006 0.044 122 Dihedral : 4.598 12.337 96 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 8.33 % Allowed : 27.78 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.87), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.66), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.010 0.003 TYR A 43 PHE 0.002 0.001 PHE A 64 TRP 0.008 0.003 TRP A 63 HIS 0.001 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 670) covalent geometry : angle 0.56596 ( 912) hydrogen bonds : bond 0.02891 ( 8) hydrogen bonds : angle 4.86627 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 3 time to evaluate : 0.016 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 8 average time/residue: 0.0160 time to fit residues: 0.1683 Evaluate side-chains 8 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 3 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 40.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 0.0770 chunk 8 optimal weight: 40.0000 overall best weight: 4.4685 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.039690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.034103 restraints weight = 8148.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.034869 restraints weight = 5781.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.035442 restraints weight = 4457.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.035877 restraints weight = 3642.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.036084 restraints weight = 3089.156| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 670 Z= 0.107 Angle : 0.499 4.315 912 Z= 0.264 Chirality : 0.044 0.114 105 Planarity : 0.005 0.037 122 Dihedral : 4.221 10.970 96 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.94 % Allowed : 27.78 % Favored : 65.28 % 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: -0.33 (0.88), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.24 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 20 TYR 0.007 0.002 TYR A 43 PHE 0.003 0.001 PHE A 64 TRP 0.006 0.002 TRP A 63 HIS 0.001 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 670) covalent geometry : angle 0.49934 ( 912) hydrogen bonds : bond 0.02391 ( 8) hydrogen bonds : angle 4.44451 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 4 time to evaluate : 0.051 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 8 average time/residue: 0.0412 time to fit residues: 0.3800 Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 3 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 overall best weight: 7.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.039387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.033747 restraints weight = 8098.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.034522 restraints weight = 5821.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.035113 restraints weight = 4510.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.035525 restraints weight = 3679.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.035794 restraints weight = 3106.708| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 670 Z= 0.159 Angle : 0.541 4.404 912 Z= 0.283 Chirality : 0.044 0.120 105 Planarity : 0.005 0.039 122 Dihedral : 4.605 15.292 96 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 6.94 % Allowed : 29.17 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.88), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.35 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 20 TYR 0.008 0.003 TYR A 43 PHE 0.003 0.001 PHE A 64 TRP 0.009 0.003 TRP A 63 HIS 0.002 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 670) covalent geometry : angle 0.54137 ( 912) hydrogen bonds : bond 0.02813 ( 8) hydrogen bonds : angle 5.08147 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 2 time to evaluate : 0.028 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 7 average time/residue: 0.0244 time to fit residues: 0.2305 Evaluate side-chains 5 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 2 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 30.0000 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 overall best weight: 5.1488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.039872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.034443 restraints weight = 7418.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.035165 restraints weight = 5475.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.035656 restraints weight = 4306.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.036059 restraints weight = 3608.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.036368 restraints weight = 3086.178| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 670 Z= 0.119 Angle : 0.513 4.314 912 Z= 0.273 Chirality : 0.045 0.123 105 Planarity : 0.005 0.037 122 Dihedral : 4.455 15.304 96 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.94 % Allowed : 27.78 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.86), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.66), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 20 TYR 0.008 0.002 TYR A 43 PHE 0.002 0.001 PHE A 17 TRP 0.006 0.002 TRP A 63 HIS 0.001 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 670) covalent geometry : angle 0.51257 ( 912) hydrogen bonds : bond 0.02437 ( 8) hydrogen bonds : angle 4.73998 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 3 time to evaluate : 0.027 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 8 average time/residue: 0.0279 time to fit residues: 0.2884 Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 2 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 40.0000 chunk 2 optimal weight: 0.3980 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 overall best weight: 5.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.039274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.032621 restraints weight = 8262.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.033597 restraints weight = 5444.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.034318 restraints weight = 4063.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.034825 restraints weight = 3250.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.035207 restraints weight = 2735.256| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 670 Z= 0.120 Angle : 0.494 4.279 912 Z= 0.259 Chirality : 0.045 0.121 105 Planarity : 0.005 0.036 122 Dihedral : 4.514 16.060 96 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.56 % Allowed : 27.78 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.88), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.43 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.004 0.002 TYR A 43 PHE 0.001 0.001 PHE A 17 TRP 0.007 0.003 TRP A 63 HIS 0.001 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 670) covalent geometry : angle 0.49391 ( 912) hydrogen bonds : bond 0.02508 ( 8) hydrogen bonds : angle 4.83400 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 2 time to evaluate : 0.027 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 6 average time/residue: 0.0284 time to fit residues: 0.2278 Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 2 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 5.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.039314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.032664 restraints weight = 8003.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.033622 restraints weight = 5350.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.034345 restraints weight = 4009.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.034877 restraints weight = 3224.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.035174 restraints weight = 2700.802| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 670 Z= 0.122 Angle : 0.496 4.313 912 Z= 0.261 Chirality : 0.045 0.114 105 Planarity : 0.005 0.036 122 Dihedral : 4.628 18.385 96 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 5.56 % Allowed : 27.78 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.89), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.45 (0.68), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 20 TYR 0.003 0.002 TYR A 43 PHE 0.002 0.001 PHE A 17 TRP 0.007 0.002 TRP A 63 HIS 0.001 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 670) covalent geometry : angle 0.49621 ( 912) hydrogen bonds : bond 0.02681 ( 8) hydrogen bonds : angle 4.79517 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 182 Ramachandran restraints generated. 91 Oldfield, 0 Emsley, 91 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 2 time to evaluate : 0.016 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 6 average time/residue: 0.0175 time to fit residues: 0.1407 Evaluate side-chains 6 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 2 time to evaluate : 0.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 63 TRP Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 90 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 overall best weight: 7.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.040342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.033767 restraints weight = 8323.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.034762 restraints weight = 5448.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.035508 restraints weight = 3993.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.036025 restraints weight = 3171.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.036389 restraints weight = 2623.860| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 670 Z= 0.155 Angle : 0.525 4.376 912 Z= 0.276 Chirality : 0.045 0.113 105 Planarity : 0.005 0.040 122 Dihedral : 5.171 23.951 96 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.56 % Allowed : 27.78 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.90), residues: 91 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.69), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 20 TYR 0.005 0.002 TYR A 43 PHE 0.002 0.001 PHE A 64 TRP 0.008 0.003 TRP A 63 HIS 0.001 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 670) covalent geometry : angle 0.52529 ( 912) hydrogen bonds : bond 0.02871 ( 8) hydrogen bonds : angle 4.92328 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 303.83 seconds wall clock time: 5 minutes 51.07 seconds (351.07 seconds total)