Starting phenix.real_space_refine on Tue Aug 4 11:45:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ve9_64995/08_2026/9ve9_64995_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ve9_64995/08_2026/9ve9_64995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ve9_64995/08_2026/9ve9_64995_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ve9_64995/08_2026/9ve9_64995_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ve9_64995/08_2026/9ve9_64995.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ve9_64995/08_2026/9ve9_64995.map" } resolution = 3.26 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= -0.000 sd= 1.000 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: 3 Type Number sf(0) Gaussians C 1270 2.51 5 N 315 2.21 5 O 315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1900 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 271 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 109 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 0.46, per 1000 atoms: 0.24 Number of scatterers: 1900 At special positions: 0 Unit cell: (69.9, 56.852, 39.144, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 315 8.00 N 315 7.00 C 1270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.13 Conformation dependent library (CDL) restraints added in 81.1 milliseconds 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 450 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 46.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 114 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 133 Processing sheet with id=AA3, first strand: chain 'B' and resid 107 through 111 92 hydrogen bonds defined for protein. 276 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: 0.28 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 310 1.28 - 1.35: 285 1.35 - 1.41: 150 1.41 - 1.48: 265 1.48 - 1.54: 910 Bond restraints: 1920 Sorted by residual: bond pdb=" C LEU C 105 " pdb=" N GLY C 106 " ideal model delta sigma weight residual 1.335 1.324 0.011 7.50e-03 1.78e+04 2.08e+00 bond pdb=" C LEU G 105 " pdb=" N GLY G 106 " ideal model delta sigma weight residual 1.335 1.324 0.011 7.50e-03 1.78e+04 2.05e+00 bond pdb=" C GLY G 106 " pdb=" O GLY G 106 " ideal model delta sigma weight residual 1.236 1.230 0.006 5.30e-03 3.56e+04 1.33e+00 bond pdb=" CA VAL I 133 " pdb=" CB VAL I 133 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.32e+00 bond pdb=" C GLY C 106 " pdb=" O GLY C 106 " ideal model delta sigma weight residual 1.236 1.230 0.006 5.30e-03 3.56e+04 1.30e+00 ... (remaining 1915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 2328 1.02 - 2.03: 202 2.03 - 3.05: 28 3.05 - 4.07: 22 4.07 - 5.08: 10 Bond angle restraints: 2590 Sorted by residual: angle pdb=" C LEU C 105 " pdb=" N GLY C 106 " pdb=" CA GLY C 106 " ideal model delta sigma weight residual 122.63 119.53 3.10 1.03e+00 9.43e-01 9.04e+00 angle pdb=" C LEU G 105 " pdb=" N GLY G 106 " pdb=" CA GLY G 106 " ideal model delta sigma weight residual 122.63 119.54 3.09 1.03e+00 9.43e-01 9.02e+00 angle pdb=" N GLY C 106 " pdb=" CA GLY C 106 " pdb=" C GLY C 106 " ideal model delta sigma weight residual 111.21 113.56 -2.35 1.04e+00 9.25e-01 5.10e+00 angle pdb=" N GLY G 106 " pdb=" CA GLY G 106 " pdb=" C GLY G 106 " ideal model delta sigma weight residual 111.21 113.53 -2.32 1.04e+00 9.25e-01 5.00e+00 angle pdb=" CA GLY C 106 " pdb=" C GLY C 106 " pdb=" N ASN C 107 " ideal model delta sigma weight residual 115.64 117.29 -1.65 7.90e-01 1.60e+00 4.39e+00 ... (remaining 2585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.05: 890 11.05 - 22.10: 95 22.10 - 33.15: 80 33.15 - 44.20: 25 44.20 - 55.26: 35 Dihedral angle restraints: 1125 sinusoidal: 440 harmonic: 685 Sorted by residual: dihedral pdb=" CA GLY C 118 " pdb=" C GLY C 118 " pdb=" N LYS C 119 " pdb=" CA LYS C 119 " ideal model delta harmonic sigma weight residual 180.00 161.77 18.23 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLY G 118 " pdb=" C GLY G 118 " pdb=" N LYS G 119 " pdb=" CA LYS G 119 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLY A 118 " pdb=" C GLY A 118 " pdb=" N LYS A 119 " pdb=" CA LYS A 119 " ideal model delta harmonic sigma weight residual 180.00 161.79 18.21 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 1122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 110 0.023 - 0.047: 120 0.047 - 0.070: 35 0.070 - 0.093: 20 0.093 - 0.116: 45 Chirality restraints: 330 Sorted by residual: chirality pdb=" CA VAL G 124 " pdb=" N VAL G 124 " pdb=" C VAL G 124 " pdb=" CB VAL G 124 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA VAL I 124 " pdb=" N VAL I 124 " pdb=" C VAL I 124 " pdb=" CB VAL I 124 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA VAL E 124 " pdb=" N VAL E 124 " pdb=" C VAL E 124 " pdb=" CB VAL E 124 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 327 not shown) Planarity restraints: 320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 117 " 0.004 2.00e-02 2.50e+03 8.18e-03 6.70e-01 pdb=" C PHE G 117 " -0.014 2.00e-02 2.50e+03 pdb=" O PHE G 117 " 0.005 2.00e-02 2.50e+03 pdb=" N GLY G 118 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE I 117 " 0.004 2.00e-02 2.50e+03 8.11e-03 6.57e-01 pdb=" C PHE I 117 " -0.014 2.00e-02 2.50e+03 pdb=" O PHE I 117 " 0.005 2.00e-02 2.50e+03 pdb=" N GLY I 118 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 117 " 0.004 2.00e-02 2.50e+03 7.97e-03 6.35e-01 pdb=" C PHE A 117 " -0.014 2.00e-02 2.50e+03 pdb=" O PHE A 117 " 0.005 2.00e-02 2.50e+03 pdb=" N GLY A 118 " 0.005 2.00e-02 2.50e+03 ... (remaining 317 not shown) Histogram of nonbonded interaction distances: 2.68 - 3.12: 1186 3.12 - 3.57: 1875 3.57 - 4.01: 2678 4.01 - 4.46: 3515 4.46 - 4.90: 6623 Nonbonded interactions: 15877 Sorted by model distance: nonbonded pdb=" N ASN I 116 " pdb=" O ASN I 116 " model vdw 2.676 2.496 nonbonded pdb=" N ASN C 116 " pdb=" O ASN C 116 " model vdw 2.677 2.496 nonbonded pdb=" N ASN A 116 " pdb=" O ASN A 116 " model vdw 2.677 2.496 nonbonded pdb=" N ASN E 116 " pdb=" O ASN E 116 " model vdw 2.677 2.496 nonbonded pdb=" N ASN G 116 " pdb=" O ASN G 116 " model vdw 2.678 2.496 ... (remaining 15872 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 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: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.830 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 0.026 1920 Z= 0.290 Angle : 0.730 5.083 2590 Z= 0.371 Chirality : 0.052 0.116 330 Planarity : 0.003 0.018 320 Dihedral : 18.204 55.256 675 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.38 % Allowed : 23.81 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.53), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 115 PHE 0.007 0.002 PHE E 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.29 ( 1920) covalent geometry : angle 0.72954 / 0.37 ( 2590) hydrogen bonds : bond 0.05407 / 3.16 ( 92) hydrogen bonds : angle 6.45479 / 4.51 ( 276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.068 Fit side-chains REVERT: A 115 ARG cc_start: 0.7699 (mtt-85) cc_final: 0.7309 (mtt-85) REVERT: C 115 ARG cc_start: 0.7237 (mtt-85) cc_final: 0.6788 (ttm110) REVERT: I 115 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7430 (mtt-85) outliers start: 5 outliers final: 0 residues processed: 28 average time/residue: 0.1383 time to fit residues: 4.1910 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.138601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.111035 restraints weight = 2192.516| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.44 r_work: 0.3921 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1920 Z= 0.130 Angle : 0.625 5.644 2590 Z= 0.296 Chirality : 0.049 0.122 330 Planarity : 0.003 0.011 320 Dihedral : 5.403 18.645 240 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 2.38 % Allowed : 22.86 % Favored : 74.76 % 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: -1.90 (0.55), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 115 PHE 0.024 0.002 PHE G 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 1920) covalent geometry : angle 0.62479 / 0.30 ( 2590) hydrogen bonds : bond 0.01607 / 1.01 ( 92) hydrogen bonds : angle 4.77752 / 3.34 ( 276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.075 Fit side-chains REVERT: A 115 ARG cc_start: 0.7783 (mtt-85) cc_final: 0.7555 (mtt-85) REVERT: C 115 ARG cc_start: 0.7473 (mtt-85) cc_final: 0.6939 (ttm110) outliers start: 5 outliers final: 0 residues processed: 22 average time/residue: 0.1188 time to fit residues: 2.9010 Evaluate side-chains 15 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.140847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.112304 restraints weight = 2192.627| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.46 r_work: 0.3777 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1920 Z= 0.149 Angle : 0.631 7.024 2590 Z= 0.295 Chirality : 0.049 0.123 330 Planarity : 0.002 0.009 320 Dihedral : 5.276 18.041 240 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 0.48 % Allowed : 22.86 % Favored : 76.67 % 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: -2.04 (0.57), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 115 PHE 0.013 0.002 PHE G 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 1920) covalent geometry : angle 0.63138 / 0.29 ( 2590) hydrogen bonds : bond 0.01517 / 0.95 ( 92) hydrogen bonds : angle 4.14864 / 2.84 ( 276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.088 Fit side-chains REVERT: A 115 ARG cc_start: 0.7830 (mtt-85) cc_final: 0.7509 (mtt-85) REVERT: C 115 ARG cc_start: 0.7637 (mtt-85) cc_final: 0.6975 (ttm110) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.1546 time to fit residues: 2.7249 Evaluate side-chains 14 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 126 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.130422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.101303 restraints weight = 2210.989| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.44 r_work: 0.3784 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1920 Z= 0.159 Angle : 0.623 6.436 2590 Z= 0.296 Chirality : 0.049 0.121 330 Planarity : 0.002 0.007 320 Dihedral : 5.285 18.228 240 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.95 % Allowed : 24.76 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.58), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 115 PHE 0.012 0.002 PHE G 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 1920) covalent geometry : angle 0.62313 / 0.30 ( 2590) hydrogen bonds : bond 0.01457 / 0.89 ( 92) hydrogen bonds : angle 3.98586 / 2.68 ( 276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.071 Fit side-chains REVERT: A 115 ARG cc_start: 0.8044 (mtt-85) cc_final: 0.7733 (mtt-85) outliers start: 2 outliers final: 0 residues processed: 21 average time/residue: 0.1163 time to fit residues: 2.7172 Evaluate side-chains 16 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.138424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.111482 restraints weight = 2170.044| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.39 r_work: 0.3772 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 1920 Z= 0.153 Angle : 0.612 6.923 2590 Z= 0.288 Chirality : 0.049 0.122 330 Planarity : 0.002 0.011 320 Dihedral : 5.246 18.301 240 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 0.48 % Allowed : 25.71 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.59), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 115 PHE 0.011 0.002 PHE G 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 1920) covalent geometry : angle 0.61188 / 0.29 ( 2590) hydrogen bonds : bond 0.01372 / 0.85 ( 92) hydrogen bonds : angle 3.87042 / 2.60 ( 276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.073 Fit side-chains REVERT: A 115 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7670 (mtt-85) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.1348 time to fit residues: 2.6770 Evaluate side-chains 17 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.137856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.110183 restraints weight = 2142.767| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.43 r_work: 0.3750 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 1920 Z= 0.200 Angle : 0.640 6.075 2590 Z= 0.302 Chirality : 0.049 0.125 330 Planarity : 0.002 0.013 320 Dihedral : 5.333 17.930 240 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 1.43 % Allowed : 24.29 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.59), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 115 PHE 0.017 0.002 PHE D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 ( 1920) covalent geometry : angle 0.64035 / 0.30 ( 2590) hydrogen bonds : bond 0.01484 / 0.92 ( 92) hydrogen bonds : angle 3.84626 / 2.60 ( 276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 18 time to evaluate : 0.074 Fit side-chains REVERT: A 115 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7748 (mtt-85) outliers start: 3 outliers final: 1 residues processed: 21 average time/residue: 0.1208 time to fit residues: 2.8154 Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 101 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 9 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.127105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.098722 restraints weight = 2227.458| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.40 r_work: 0.3787 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1920 Z= 0.140 Angle : 0.605 7.777 2590 Z= 0.285 Chirality : 0.049 0.123 330 Planarity : 0.002 0.010 320 Dihedral : 5.250 18.538 240 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 0.95 % Allowed : 25.24 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.59), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG I 115 PHE 0.022 0.002 PHE D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 1920) covalent geometry : angle 0.60543 / 0.28 ( 2590) hydrogen bonds : bond 0.01325 / 0.82 ( 92) hydrogen bonds : angle 3.81056 / 2.56 ( 276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.095 Fit side-chains REVERT: A 115 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7855 (mtt-85) outliers start: 2 outliers final: 0 residues processed: 18 average time/residue: 0.1359 time to fit residues: 2.7113 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.138629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.111194 restraints weight = 2139.431| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.39 r_work: 0.3844 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 1920 Z= 0.161 Angle : 0.626 7.358 2590 Z= 0.292 Chirality : 0.049 0.123 330 Planarity : 0.002 0.012 320 Dihedral : 5.250 17.856 240 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.44 % Favored : 87.56 % Rotamer: Outliers : 0.95 % Allowed : 25.24 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.59), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 115 PHE 0.016 0.002 PHE D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 1920) covalent geometry : angle 0.62641 / 0.29 ( 2590) hydrogen bonds : bond 0.01377 / 0.86 ( 92) hydrogen bonds : angle 3.76422 / 2.54 ( 276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.071 Fit side-chains REVERT: A 115 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7765 (mtt-85) REVERT: F 100 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6943 (mt-10) outliers start: 2 outliers final: 0 residues processed: 19 average time/residue: 0.1330 time to fit residues: 2.7877 Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.129089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.100765 restraints weight = 2193.072| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.37 r_work: 0.3845 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1920 Z= 0.154 Angle : 0.626 7.447 2590 Z= 0.293 Chirality : 0.049 0.123 330 Planarity : 0.002 0.015 320 Dihedral : 5.238 18.317 240 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 1.90 % Allowed : 24.76 % Favored : 73.33 % 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: -1.92 (0.60), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 115 PHE 0.024 0.002 PHE D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 1920) covalent geometry : angle 0.62573 / 0.29 ( 2590) hydrogen bonds : bond 0.01363 / 0.85 ( 92) hydrogen bonds : angle 3.75798 / 2.54 ( 276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.076 Fit side-chains REVERT: A 115 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7874 (mtt-85) REVERT: F 100 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6958 (mt-10) outliers start: 4 outliers final: 0 residues processed: 21 average time/residue: 0.1188 time to fit residues: 2.7689 Evaluate side-chains 19 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 16 optimal weight: 0.1980 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.128042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.099936 restraints weight = 2235.805| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.39 r_work: 0.3766 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 1920 Z= 0.181 Angle : 0.659 8.444 2590 Z= 0.305 Chirality : 0.050 0.124 330 Planarity : 0.002 0.015 320 Dihedral : 5.277 17.720 240 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 0.48 % Allowed : 26.19 % Favored : 73.33 % 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: -1.96 (0.60), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 115 PHE 0.031 0.002 PHE D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 1920) covalent geometry : angle 0.65861 / 0.31 ( 2590) hydrogen bonds : bond 0.01399 / 0.87 ( 92) hydrogen bonds : angle 3.65408 / 2.42 ( 276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.073 Fit side-chains REVERT: A 115 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7901 (mtt-85) REVERT: F 100 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6919 (mt-10) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.1392 time to fit residues: 2.6022 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.126021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.098486 restraints weight = 2297.800| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.35 r_work: 0.3740 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1920 Z= 0.229 Angle : 0.694 8.466 2590 Z= 0.324 Chirality : 0.050 0.126 330 Planarity : 0.003 0.013 320 Dihedral : 5.400 17.902 240 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.00 % Favored : 84.00 % Rotamer: Outliers : 0.48 % Allowed : 26.19 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.60), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 115 PHE 0.026 0.003 PHE D 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 ( 1920) covalent geometry : angle 0.69358 / 0.32 ( 2590) hydrogen bonds : bond 0.01475 / 0.91 ( 92) hydrogen bonds : angle 3.61499 / 2.39 ( 276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 803.84 seconds wall clock time: 14 minutes 28.55 seconds (868.55 seconds total)