Starting phenix.real_space_refine on Tue Feb 3 12:20:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9je7_61409/02_2026/9je7_61409.cif Found real_map, /net/cci-nas-00/data/ceres_data/9je7_61409/02_2026/9je7_61409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9je7_61409/02_2026/9je7_61409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9je7_61409/02_2026/9je7_61409.map" model { file = "/net/cci-nas-00/data/ceres_data/9je7_61409/02_2026/9je7_61409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9je7_61409/02_2026/9je7_61409.cif" } resolution = 3.36 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= 0.002 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 870 2.51 5 N 240 2.21 5 O 285 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: 1395 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 465 Classifications: {'peptide': 66} Link IDs: {'TRANS': 65} Restraints were copied for chains: C, E Time building chain proxies: 0.40, per 1000 atoms: 0.29 Number of scatterers: 1395 At special positions: 0 Unit cell: (69.72, 60.59, 28.22, 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 285 8.00 N 240 7.00 C 870 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: 0.10 Conformation dependent library (CDL) restraints added in 62.3 milliseconds 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 342 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 63.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.549A pdb=" N VAL C 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL E 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR C 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 48 removed outlier: 6.824A pdb=" N VAL E 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR C 44 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLY E 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N GLU C 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 58 removed outlier: 6.550A pdb=" N THR A 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA E 56 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LYS E 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN A 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.539A pdb=" N GLU C 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N THR E 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL E 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN C 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.779A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 83 removed outlier: 6.439A pdb=" N THR A 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA E 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N LYS E 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N GLN A 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL E 82 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N THR A 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR E 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 82 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU E 83 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 96 removed outlier: 8.132A pdb=" N ALA A 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR E 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ALA A 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE E 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY A 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LYS E 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA E 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 96 removed outlier: 8.132A pdb=" N ALA A 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR E 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ALA A 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE E 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY A 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LYS E 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL A 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE C 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 26 hydrogen bonds defined for protein. 78 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: 0.10 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 249 1.29 - 1.35: 216 1.35 - 1.42: 54 1.42 - 1.48: 225 1.48 - 1.54: 657 Bond restraints: 1401 Sorted by residual: bond pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta sigma weight residual 1.466 1.458 0.008 1.36e-02 5.41e+03 3.80e-01 bond pdb=" CA GLN E 99 " pdb=" C GLN E 99 " ideal model delta sigma weight residual 1.528 1.521 0.007 1.18e-02 7.18e+03 3.39e-01 bond pdb=" N GLN C 99 " pdb=" CA GLN C 99 " ideal model delta sigma weight residual 1.466 1.459 0.008 1.36e-02 5.41e+03 3.23e-01 bond pdb=" N GLN E 99 " pdb=" CA GLN E 99 " ideal model delta sigma weight residual 1.466 1.459 0.008 1.36e-02 5.41e+03 3.20e-01 bond pdb=" CA GLN A 99 " pdb=" C GLN A 99 " ideal model delta sigma weight residual 1.528 1.522 0.007 1.18e-02 7.18e+03 3.09e-01 ... (remaining 1396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 1818 1.16 - 2.31: 66 2.31 - 3.47: 3 3.47 - 4.62: 3 4.62 - 5.78: 6 Bond angle restraints: 1896 Sorted by residual: angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 122.29 116.64 5.65 1.56e+00 4.11e-01 1.31e+01 angle pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta sigma weight residual 122.29 116.67 5.62 1.56e+00 4.11e-01 1.30e+01 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 122.29 116.70 5.59 1.56e+00 4.11e-01 1.28e+01 angle pdb=" CA HIS E 50 " pdb=" CB HIS E 50 " pdb=" CG HIS E 50 " ideal model delta sigma weight residual 113.80 115.49 -1.69 1.00e+00 1.00e+00 2.85e+00 angle pdb=" CA HIS C 50 " pdb=" CB HIS C 50 " pdb=" CG HIS C 50 " ideal model delta sigma weight residual 113.80 115.48 -1.68 1.00e+00 1.00e+00 2.82e+00 ... (remaining 1891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 771 16.34 - 32.68: 48 32.68 - 49.03: 3 49.03 - 65.37: 0 65.37 - 81.71: 3 Dihedral angle restraints: 825 sinusoidal: 285 harmonic: 540 Sorted by residual: dihedral pdb=" CA VAL C 49 " pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta harmonic sigma weight residual -180.00 -159.14 -20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA VAL E 49 " pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA VAL A 49 " pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta harmonic sigma weight residual 180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 148 0.036 - 0.071: 50 0.071 - 0.107: 31 0.107 - 0.143: 14 0.143 - 0.179: 6 Chirality restraints: 249 Sorted by residual: chirality pdb=" CA HIS A 50 " pdb=" N HIS A 50 " pdb=" C HIS A 50 " pdb=" CB HIS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.98e-01 chirality pdb=" CA HIS C 50 " pdb=" N HIS C 50 " pdb=" C HIS C 50 " pdb=" CB HIS C 50 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA HIS E 50 " pdb=" N HIS E 50 " pdb=" C HIS E 50 " pdb=" CB HIS E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 246 not shown) Planarity restraints: 237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " 0.017 2.00e-02 2.50e+03 1.56e-02 3.66e+00 pdb=" CG HIS C 50 " -0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " 0.016 2.00e-02 2.50e+03 1.56e-02 3.63e+00 pdb=" CG HIS E 50 " -0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.016 2.00e-02 2.50e+03 1.53e-02 3.53e+00 pdb=" CG HIS A 50 " -0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.008 2.00e-02 2.50e+03 ... (remaining 234 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 133 2.77 - 3.30: 1205 3.30 - 3.83: 2143 3.83 - 4.37: 2378 4.37 - 4.90: 4800 Nonbonded interactions: 10659 Sorted by model distance: nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS E 80 " model vdw 2.238 3.120 nonbonded pdb=" NZ LYS C 80 " pdb=" OE1 GLU E 46 " model vdw 2.274 3.120 nonbonded pdb=" ND2 ASN A 65 " pdb=" O GLY A 68 " model vdw 2.361 3.120 nonbonded pdb=" ND2 ASN E 65 " pdb=" O GLY E 68 " model vdw 2.361 3.120 nonbonded pdb=" ND2 ASN C 65 " pdb=" O GLY C 68 " model vdw 2.361 3.120 ... (remaining 10654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } 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: 3.740 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.610 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.014 1401 Z= 0.129 Angle : 0.612 5.775 1896 Z= 0.352 Chirality : 0.057 0.179 249 Planarity : 0.002 0.016 237 Dihedral : 11.781 81.708 483 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: -4.15 (0.42), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.32), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.008 0.002 PHE E 94 HIS 0.014 0.009 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 1401) covalent geometry : angle 0.61188 ( 1896) hydrogen bonds : bond 0.12165 ( 26) hydrogen bonds : angle 7.19637 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.057 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0900 time to fit residues: 2.0980 Evaluate side-chains 16 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.0270 chunk 6 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.151774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.136050 restraints weight = 1508.077| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.42 r_work: 0.3839 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 1401 Z= 0.089 Angle : 0.459 4.200 1896 Z= 0.264 Chirality : 0.055 0.159 249 Planarity : 0.002 0.010 237 Dihedral : 4.902 22.436 198 Min Nonbonded Distance : 2.688 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR A 39 PHE 0.005 0.001 PHE A 94 HIS 0.009 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00179 ( 1401) covalent geometry : angle 0.45933 ( 1896) hydrogen bonds : bond 0.01945 ( 26) hydrogen bonds : angle 5.02255 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.054 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1096 time to fit residues: 1.8118 Evaluate side-chains 15 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN E 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.142802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.127054 restraints weight = 1559.286| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 2.52 r_work: 0.3714 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1401 Z= 0.137 Angle : 0.524 4.146 1896 Z= 0.306 Chirality : 0.057 0.205 249 Planarity : 0.002 0.013 237 Dihedral : 5.150 23.761 198 Min Nonbonded Distance : 2.688 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.68 % Allowed : 6.80 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.47), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.36), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR E 39 PHE 0.006 0.002 PHE E 94 HIS 0.013 0.006 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 1401) covalent geometry : angle 0.52376 ( 1896) hydrogen bonds : bond 0.01610 ( 26) hydrogen bonds : angle 4.79883 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.032 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 12 average time/residue: 0.0814 time to fit residues: 1.0720 Evaluate side-chains 12 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN E 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.126049 restraints weight = 1596.793| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.29 r_work: 0.3648 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 1401 Z= 0.216 Angle : 0.613 4.843 1896 Z= 0.357 Chirality : 0.059 0.237 249 Planarity : 0.003 0.016 237 Dihedral : 5.535 23.387 198 Min Nonbonded Distance : 2.685 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.72 % Allowed : 7.48 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.46), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.35), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.004 TYR E 39 PHE 0.008 0.002 PHE E 94 HIS 0.014 0.007 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 1401) covalent geometry : angle 0.61318 ( 1896) hydrogen bonds : bond 0.01601 ( 26) hydrogen bonds : angle 4.85979 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.052 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 16 average time/residue: 0.0937 time to fit residues: 1.6697 Evaluate side-chains 19 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 0.0060 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.148473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.133586 restraints weight = 1542.353| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.37 r_work: 0.3746 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1401 Z= 0.100 Angle : 0.451 3.307 1896 Z= 0.267 Chirality : 0.055 0.190 249 Planarity : 0.002 0.010 237 Dihedral : 4.900 21.647 198 Min Nonbonded Distance : 2.692 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.72 % Allowed : 8.84 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.40 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.37), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 39 PHE 0.005 0.001 PHE E 94 HIS 0.008 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 1401) covalent geometry : angle 0.45132 ( 1896) hydrogen bonds : bond 0.01249 ( 26) hydrogen bonds : angle 4.56130 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 15 time to evaluate : 0.047 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 16 average time/residue: 0.0759 time to fit residues: 1.3614 Evaluate side-chains 17 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.146284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.131831 restraints weight = 1538.464| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 2.31 r_work: 0.3737 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 1401 Z= 0.111 Angle : 0.462 3.318 1896 Z= 0.271 Chirality : 0.055 0.194 249 Planarity : 0.002 0.011 237 Dihedral : 4.789 20.672 198 Min Nonbonded Distance : 2.689 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.04 % Allowed : 10.20 % Favored : 87.76 % 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: -3.39 (0.49), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR E 39 PHE 0.005 0.001 PHE A 94 HIS 0.009 0.004 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 1401) covalent geometry : angle 0.46182 ( 1896) hydrogen bonds : bond 0.01170 ( 26) hydrogen bonds : angle 4.49666 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.055 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 14 average time/residue: 0.0784 time to fit residues: 1.2654 Evaluate side-chains 16 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 chunk 1 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.150296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.135554 restraints weight = 1603.087| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.50 r_work: 0.3815 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 1401 Z= 0.065 Angle : 0.393 3.616 1896 Z= 0.229 Chirality : 0.054 0.164 249 Planarity : 0.001 0.007 237 Dihedral : 4.402 19.262 198 Min Nonbonded Distance : 2.691 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.72 % Allowed : 10.20 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.51), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 39 PHE 0.003 0.001 PHE A 94 HIS 0.006 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00128 ( 1401) covalent geometry : angle 0.39345 ( 1896) hydrogen bonds : bond 0.01028 ( 26) hydrogen bonds : angle 4.19864 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 12 time to evaluate : 0.040 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 14 average time/residue: 0.0520 time to fit residues: 0.8683 Evaluate side-chains 14 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 12 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.145817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131430 restraints weight = 1547.929| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.34 r_work: 0.3734 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1401 Z= 0.115 Angle : 0.476 4.681 1896 Z= 0.273 Chirality : 0.055 0.193 249 Planarity : 0.002 0.013 237 Dihedral : 4.650 19.181 198 Min Nonbonded Distance : 2.685 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.36 % Allowed : 10.20 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR E 39 PHE 0.005 0.001 PHE A 94 HIS 0.010 0.005 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 1401) covalent geometry : angle 0.47624 ( 1896) hydrogen bonds : bond 0.01172 ( 26) hydrogen bonds : angle 4.21886 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.052 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 14 average time/residue: 0.0406 time to fit residues: 0.7003 Evaluate side-chains 15 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.129199 restraints weight = 1553.929| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.41 r_work: 0.3705 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1401 Z= 0.131 Angle : 0.495 5.112 1896 Z= 0.284 Chirality : 0.056 0.199 249 Planarity : 0.002 0.012 237 Dihedral : 4.814 19.686 198 Min Nonbonded Distance : 2.682 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.36 % Allowed : 9.52 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR E 39 PHE 0.004 0.001 PHE E 94 HIS 0.010 0.005 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 1401) covalent geometry : angle 0.49504 ( 1896) hydrogen bonds : bond 0.01299 ( 26) hydrogen bonds : angle 4.20354 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.034 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0422 time to fit residues: 0.7413 Evaluate side-chains 15 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.144072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.129279 restraints weight = 1606.140| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.44 r_work: 0.3702 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1401 Z= 0.132 Angle : 0.497 5.049 1896 Z= 0.284 Chirality : 0.056 0.200 249 Planarity : 0.002 0.012 237 Dihedral : 4.819 19.695 198 Min Nonbonded Distance : 2.681 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.36 % Allowed : 9.52 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR E 39 PHE 0.005 0.001 PHE A 94 HIS 0.010 0.005 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 1401) covalent geometry : angle 0.49654 ( 1896) hydrogen bonds : bond 0.01315 ( 26) hydrogen bonds : angle 4.15373 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 384 Ramachandran restraints generated. 192 Oldfield, 0 Emsley, 192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.054 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.0664 time to fit residues: 1.1559 Evaluate side-chains 15 residues out of total 147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN C 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.142519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.127993 restraints weight = 1606.333| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.35 r_work: 0.3692 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1401 Z= 0.152 Angle : 0.525 4.972 1896 Z= 0.300 Chirality : 0.056 0.208 249 Planarity : 0.002 0.013 237 Dihedral : 4.963 19.741 198 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.36 % Allowed : 9.52 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.50), residues: 192 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.38), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR E 39 PHE 0.004 0.002 PHE E 94 HIS 0.011 0.006 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 1401) covalent geometry : angle 0.52457 ( 1896) hydrogen bonds : bond 0.01350 ( 26) hydrogen bonds : angle 4.16675 ( 78) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 616.93 seconds wall clock time: 11 minutes 17.65 seconds (677.65 seconds total)