Starting phenix.real_space_refine on Fri Aug 22 19:25:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehr_28150/08_2025/8ehr_28150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehr_28150/08_2025/8ehr_28150.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ehr_28150/08_2025/8ehr_28150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehr_28150/08_2025/8ehr_28150.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ehr_28150/08_2025/8ehr_28150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehr_28150/08_2025/8ehr_28150.map" } resolution = 3.2 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 4606 2.51 5 N 1204 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7350 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "C" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "E" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "B" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "F" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "G" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1050 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 138} Time building chain proxies: 1.52, per 1000 atoms: 0.21 Number of scatterers: 7350 At special positions: 0 Unit cell: (85.162, 84.084, 100.254, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1519 8.00 N 1204 7.00 C 4606 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: 0.55 Conformation dependent library (CDL) restraints added in 413.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1904 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 19 sheets defined 4.1% alpha, 52.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 102 removed outlier: 3.782A pdb=" N GLY G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 15 through 19 removed outlier: 5.097A pdb=" N GLN F 67 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL F 138 " --> pdb=" O GLN F 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 28 through 31 removed outlier: 8.122A pdb=" N VAL F 29 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A 6 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU F 31 " --> pdb=" O THR A 6 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR A 8 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL F 138 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN F 67 " --> pdb=" O VAL F 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 77 through 84 current: chain 'F' and resid 94 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.097A pdb=" N GLN A 67 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL A 138 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.882A pdb=" N THR A 39 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER B 10 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A 33 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL A 138 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN A 67 " --> pdb=" O VAL A 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 77 through 84 current: chain 'A' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.098A pdb=" N GLN G 67 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL G 138 " --> pdb=" O GLN G 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 28 through 31 removed outlier: 8.083A pdb=" N VAL G 29 " --> pdb=" O ASN C 4 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR C 6 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LEU G 31 " --> pdb=" O THR C 6 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 8 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL G 138 " --> pdb=" O GLN G 67 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN G 67 " --> pdb=" O VAL G 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 77 through 84 current: chain 'G' and resid 94 through 96 Processing sheet with id=AA7, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AA8, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AA9, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.786A pdb=" N THR C 39 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 94 through 96 Processing sheet with id=AB2, first strand: chain 'D' and resid 15 through 19 removed outlier: 5.098A pdb=" N GLN D 67 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL D 138 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 28 through 31 removed outlier: 4.361A pdb=" N SER E 10 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL D 138 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN D 67 " --> pdb=" O VAL D 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 77 through 84 current: chain 'D' and resid 94 through 96 Processing sheet with id=AB4, first strand: chain 'D' and resid 33 through 34 removed outlier: 3.713A pdb=" N THR D 39 " --> pdb=" O SER D 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.098A pdb=" N GLN E 67 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL E 138 " --> pdb=" O GLN E 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 39 through 40 removed outlier: 3.738A pdb=" N THR E 39 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F 10 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR E 33 " --> pdb=" O SER F 10 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N VAL E 138 " --> pdb=" O GLN E 67 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN E 67 " --> pdb=" O VAL E 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 77 through 84 current: chain 'E' and resid 94 through 96 Processing sheet with id=AB7, first strand: chain 'B' and resid 15 through 19 removed outlier: 5.097A pdb=" N GLN B 67 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL B 138 " --> pdb=" O GLN B 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.751A pdb=" N THR B 39 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER G 10 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR B 33 " --> pdb=" O SER G 10 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL B 138 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLN B 67 " --> pdb=" O VAL B 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 77 through 84 current: chain 'B' and resid 94 through 96 Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 34 removed outlier: 3.693A pdb=" N THR F 39 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 33 through 34 removed outlier: 3.717A pdb=" N THR G 39 " --> pdb=" O SER G 34 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 705 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: 0.96 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2389 1.34 - 1.45: 691 1.45 - 1.57: 4333 1.57 - 1.68: 0 1.68 - 1.80: 42 Bond restraints: 7455 Sorted by residual: bond pdb=" C SER E 34 " pdb=" O SER E 34 " ideal model delta sigma weight residual 1.244 1.221 0.022 1.10e-02 8.26e+03 4.09e+00 bond pdb=" CA ALA C 32 " pdb=" C ALA C 32 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.18e-02 7.18e+03 3.78e+00 bond pdb=" C SER D 34 " pdb=" O SER D 34 " ideal model delta sigma weight residual 1.240 1.219 0.021 1.14e-02 7.69e+03 3.44e+00 bond pdb=" N TYR E 33 " pdb=" CA TYR E 33 " ideal model delta sigma weight residual 1.456 1.435 0.021 1.23e-02 6.61e+03 2.97e+00 bond pdb=" C SER F 34 " pdb=" O SER F 34 " ideal model delta sigma weight residual 1.240 1.221 0.019 1.14e-02 7.69e+03 2.92e+00 ... (remaining 7450 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 9957 1.50 - 3.00: 212 3.00 - 4.50: 23 4.50 - 6.00: 4 6.00 - 7.50: 3 Bond angle restraints: 10199 Sorted by residual: angle pdb=" C SER A 34 " pdb=" N PRO A 35 " pdb=" CA PRO A 35 " ideal model delta sigma weight residual 119.05 126.55 -7.50 1.11e+00 8.12e-01 4.56e+01 angle pdb=" C SER C 34 " pdb=" N PRO C 35 " pdb=" CA PRO C 35 " ideal model delta sigma weight residual 119.05 125.46 -6.41 1.11e+00 8.12e-01 3.34e+01 angle pdb=" C SER F 34 " pdb=" N PRO F 35 " pdb=" CA PRO F 35 " ideal model delta sigma weight residual 119.05 125.32 -6.27 1.11e+00 8.12e-01 3.19e+01 angle pdb=" C SER G 34 " pdb=" N PRO G 35 " pdb=" CA PRO G 35 " ideal model delta sigma weight residual 119.05 124.85 -5.80 1.11e+00 8.12e-01 2.73e+01 angle pdb=" C SER E 34 " pdb=" N PRO E 35 " pdb=" CA PRO E 35 " ideal model delta sigma weight residual 119.05 124.79 -5.74 1.11e+00 8.12e-01 2.68e+01 ... (remaining 10194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 4211 16.53 - 33.06: 206 33.06 - 49.59: 77 49.59 - 66.12: 14 66.12 - 82.65: 14 Dihedral angle restraints: 4522 sinusoidal: 1575 harmonic: 2947 Sorted by residual: dihedral pdb=" N MET C 46 " pdb=" CA MET C 46 " pdb=" CB MET C 46 " pdb=" CG MET C 46 " ideal model delta sinusoidal sigma weight residual -180.00 -138.60 -41.40 3 1.50e+01 4.44e-03 7.41e+00 dihedral pdb=" N MET E 46 " pdb=" CA MET E 46 " pdb=" CB MET E 46 " pdb=" CG MET E 46 " ideal model delta sinusoidal sigma weight residual -180.00 -138.62 -41.38 3 1.50e+01 4.44e-03 7.40e+00 dihedral pdb=" N MET D 46 " pdb=" CA MET D 46 " pdb=" CB MET D 46 " pdb=" CG MET D 46 " ideal model delta sinusoidal sigma weight residual 180.00 -138.65 -41.35 3 1.50e+01 4.44e-03 7.40e+00 ... (remaining 4519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1035 0.043 - 0.086: 104 0.086 - 0.129: 155 0.129 - 0.172: 4 0.172 - 0.214: 4 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA SER A 37 " pdb=" N SER A 37 " pdb=" C SER A 37 " pdb=" CB SER A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA SER F 37 " pdb=" N SER F 37 " pdb=" C SER F 37 " pdb=" CB SER F 37 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA SER E 37 " pdb=" N SER E 37 " pdb=" C SER E 37 " pdb=" CB SER E 37 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.25e-01 ... (remaining 1299 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 31 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.68e+00 pdb=" C LEU D 31 " -0.051 2.00e-02 2.50e+03 pdb=" O LEU D 31 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA D 32 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 31 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LEU C 31 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU C 31 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA C 32 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 31 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C LEU A 31 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU A 31 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 32 " 0.014 2.00e-02 2.50e+03 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 2657 2.88 - 3.38: 6088 3.38 - 3.89: 11512 3.89 - 4.39: 12825 4.39 - 4.90: 23520 Nonbonded interactions: 56602 Sorted by model distance: nonbonded pdb=" OD2 ASP C 21 " pdb=" ND2 ASN C 23 " model vdw 2.374 3.120 nonbonded pdb=" OD2 ASP A 21 " pdb=" ND2 ASN A 23 " model vdw 2.374 3.120 nonbonded pdb=" OD2 ASP E 21 " pdb=" ND2 ASN E 23 " model vdw 2.375 3.120 nonbonded pdb=" OD2 ASP G 21 " pdb=" ND2 ASN G 23 " model vdw 2.375 3.120 nonbonded pdb=" OD2 ASP D 21 " pdb=" ND2 ASN D 23 " model vdw 2.375 3.120 ... (remaining 56597 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 'D' selection = chain 'E' selection = chain 'B' selection = chain 'F' selection = chain 'G' } 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7455 Z= 0.179 Angle : 0.550 7.499 10199 Z= 0.352 Chirality : 0.045 0.214 1302 Planarity : 0.004 0.038 1295 Dihedral : 13.081 82.654 2618 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.25), residues: 1008 helix: None (None), residues: 0 sheet: 1.91 (0.25), residues: 385 loop : 0.86 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 44 TYR 0.008 0.001 TYR F 33 PHE 0.005 0.001 PHE G 40 TRP 0.003 0.001 TRP E 84 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7455) covalent geometry : angle 0.55048 (10199) hydrogen bonds : bond 0.24232 ( 222) hydrogen bonds : angle 7.37861 ( 705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.168 Fit side-chains REVERT: A 46 MET cc_start: 0.8745 (tpp) cc_final: 0.8212 (mmt) REVERT: A 53 ASP cc_start: 0.8173 (t0) cc_final: 0.7839 (t70) REVERT: A 56 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8174 (mttt) REVERT: A 72 LEU cc_start: 0.8296 (mt) cc_final: 0.8086 (mt) REVERT: C 48 GLN cc_start: 0.8850 (mt0) cc_final: 0.8552 (mt0) REVERT: D 53 ASP cc_start: 0.7824 (t0) cc_final: 0.7294 (t70) REVERT: D 56 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8096 (mttt) REVERT: D 90 SER cc_start: 0.8545 (t) cc_final: 0.8294 (p) REVERT: B 56 LYS cc_start: 0.8241 (mtpp) cc_final: 0.8028 (mtpt) REVERT: B 81 SER cc_start: 0.8514 (p) cc_final: 0.7864 (t) REVERT: B 144 THR cc_start: 0.8628 (t) cc_final: 0.8349 (m) REVERT: F 131 THR cc_start: 0.8458 (m) cc_final: 0.8194 (p) REVERT: G 128 THR cc_start: 0.7968 (p) cc_final: 0.7637 (t) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0851 time to fit residues: 17.1430 Evaluate side-chains 108 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN D 19 GLN B 19 GLN B 48 GLN G 19 GLN G 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.093842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.083694 restraints weight = 9286.686| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 1.26 r_work: 0.2642 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7455 Z= 0.196 Angle : 0.587 7.506 10199 Z= 0.299 Chirality : 0.048 0.168 1302 Planarity : 0.004 0.032 1295 Dihedral : 5.172 40.911 1057 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 2.08 % Allowed : 9.16 % Favored : 88.77 % 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 aren not related in a simple way. whole: 1.15 (0.25), residues: 1008 helix: -5.32 (0.14), residues: 42 sheet: 1.82 (0.25), residues: 364 loop : 0.65 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.010 0.002 TYR A 33 PHE 0.006 0.001 PHE D 96 TRP 0.009 0.002 TRP E 84 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 7455) covalent geometry : angle 0.58701 (10199) hydrogen bonds : bond 0.03826 ( 222) hydrogen bonds : angle 5.30081 ( 705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.236 Fit side-chains REVERT: A 46 MET cc_start: 0.8868 (tpp) cc_final: 0.8386 (mmt) REVERT: A 53 ASP cc_start: 0.8533 (t0) cc_final: 0.8332 (t70) REVERT: A 56 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8165 (mttt) REVERT: C 109 ASN cc_start: 0.8363 (m110) cc_final: 0.8160 (m-40) REVERT: D 56 LYS cc_start: 0.8933 (mtpp) cc_final: 0.8342 (mtpt) REVERT: D 90 SER cc_start: 0.8649 (t) cc_final: 0.8318 (p) REVERT: E 46 MET cc_start: 0.9283 (tpp) cc_final: 0.8718 (mmt) REVERT: B 144 THR cc_start: 0.8883 (t) cc_final: 0.8573 (m) REVERT: G 128 THR cc_start: 0.8104 (p) cc_final: 0.7844 (t) outliers start: 17 outliers final: 12 residues processed: 124 average time/residue: 0.0711 time to fit residues: 12.3861 Evaluate side-chains 115 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 90 optimal weight: 7.9990 chunk 37 optimal weight: 0.0270 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN G 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.096310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.086808 restraints weight = 9137.306| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 1.15 r_work: 0.2688 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7455 Z= 0.112 Angle : 0.476 5.642 10199 Z= 0.243 Chirality : 0.045 0.154 1302 Planarity : 0.003 0.029 1295 Dihedral : 4.766 40.317 1057 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.69 % Allowed : 10.74 % Favored : 86.57 % 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 aren not related in a simple way. whole: 1.23 (0.25), residues: 1008 helix: -5.21 (0.16), residues: 42 sheet: 1.93 (0.25), residues: 364 loop : 0.66 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 44 TYR 0.006 0.001 TYR A 33 PHE 0.004 0.001 PHE C 40 TRP 0.004 0.001 TRP F 84 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7455) covalent geometry : angle 0.47622 (10199) hydrogen bonds : bond 0.03114 ( 222) hydrogen bonds : angle 4.82912 ( 705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.273 Fit side-chains REVERT: A 56 LYS cc_start: 0.8716 (mtpp) cc_final: 0.8180 (mttt) REVERT: C 87 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7086 (mm-40) REVERT: D 56 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8376 (mtpt) REVERT: D 90 SER cc_start: 0.8540 (t) cc_final: 0.8262 (p) REVERT: E 46 MET cc_start: 0.9300 (tpp) cc_final: 0.8732 (mmt) REVERT: B 115 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8281 (mp10) REVERT: B 144 THR cc_start: 0.8884 (t) cc_final: 0.8539 (m) REVERT: G 87 GLN cc_start: 0.8114 (mt0) cc_final: 0.7716 (mm-40) REVERT: G 128 THR cc_start: 0.8109 (p) cc_final: 0.7868 (t) outliers start: 22 outliers final: 14 residues processed: 121 average time/residue: 0.0690 time to fit residues: 11.8538 Evaluate side-chains 114 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 0.0980 chunk 83 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN C 19 GLN C 67 GLN G 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.089584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.079368 restraints weight = 9697.504| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 1.31 r_work: 0.2591 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 7455 Z= 0.262 Angle : 0.646 8.968 10199 Z= 0.323 Chirality : 0.051 0.163 1302 Planarity : 0.004 0.030 1295 Dihedral : 5.611 48.749 1057 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.42 % Allowed : 13.31 % Favored : 83.27 % 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 aren not related in a simple way. whole: 0.81 (0.24), residues: 1008 helix: -5.25 (0.16), residues: 42 sheet: 1.64 (0.25), residues: 364 loop : 0.35 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.013 0.002 TYR A 33 PHE 0.007 0.001 PHE C 40 TRP 0.010 0.002 TRP E 84 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00655 ( 7455) covalent geometry : angle 0.64594 (10199) hydrogen bonds : bond 0.03864 ( 222) hydrogen bonds : angle 5.25543 ( 705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.256 Fit side-chains REVERT: A 56 LYS cc_start: 0.8683 (mtpp) cc_final: 0.8150 (mttt) REVERT: A 87 GLN cc_start: 0.8281 (mt0) cc_final: 0.7992 (mm110) REVERT: C 21 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8250 (p0) REVERT: C 87 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7191 (mm-40) REVERT: D 56 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8400 (mtpt) REVERT: D 90 SER cc_start: 0.8602 (t) cc_final: 0.8269 (p) REVERT: G 87 GLN cc_start: 0.8226 (mt0) cc_final: 0.7845 (mm-40) REVERT: G 128 THR cc_start: 0.8011 (p) cc_final: 0.7767 (t) outliers start: 28 outliers final: 22 residues processed: 123 average time/residue: 0.0603 time to fit residues: 10.6016 Evaluate side-chains 126 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 72 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 89 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 86 optimal weight: 0.1980 chunk 54 optimal weight: 0.0570 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN D 19 GLN D 134 ASN B 19 GLN G 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.096569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.086485 restraints weight = 9335.086| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.30 r_work: 0.2707 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7455 Z= 0.071 Angle : 0.424 3.546 10199 Z= 0.217 Chirality : 0.044 0.146 1302 Planarity : 0.003 0.029 1295 Dihedral : 4.499 44.242 1057 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.32 % Allowed : 15.87 % Favored : 81.81 % 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 aren not related in a simple way. whole: 1.21 (0.25), residues: 1008 helix: -4.89 (0.26), residues: 42 sheet: 2.00 (0.25), residues: 364 loop : 0.56 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 44 TYR 0.004 0.001 TYR G 33 PHE 0.005 0.001 PHE B 40 TRP 0.002 0.000 TRP C 84 HIS 0.001 0.000 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00159 ( 7455) covalent geometry : angle 0.42383 (10199) hydrogen bonds : bond 0.02349 ( 222) hydrogen bonds : angle 4.40689 ( 705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.217 Fit side-chains REVERT: A 56 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8141 (mttt) REVERT: A 87 GLN cc_start: 0.8227 (mt0) cc_final: 0.7902 (mm110) REVERT: D 56 LYS cc_start: 0.8993 (mtpp) cc_final: 0.8328 (mtpt) REVERT: E 46 MET cc_start: 0.9109 (mmm) cc_final: 0.8439 (mmt) REVERT: B 87 GLN cc_start: 0.8396 (mt0) cc_final: 0.8088 (mm-40) REVERT: B 115 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8344 (mp10) REVERT: G 87 GLN cc_start: 0.8154 (mt0) cc_final: 0.7677 (mm-40) outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 0.0663 time to fit residues: 11.7426 Evaluate side-chains 111 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN D 19 GLN B 19 GLN G 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.091205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.080909 restraints weight = 9447.775| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 1.32 r_work: 0.2613 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7455 Z= 0.185 Angle : 0.558 7.351 10199 Z= 0.279 Chirality : 0.047 0.153 1302 Planarity : 0.003 0.028 1295 Dihedral : 5.114 46.445 1057 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.42 % Allowed : 15.75 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.24), residues: 1008 helix: -4.92 (0.28), residues: 42 sheet: 1.83 (0.25), residues: 364 loop : 0.42 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.009 0.002 TYR A 33 PHE 0.006 0.001 PHE C 40 TRP 0.008 0.001 TRP E 84 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 7455) covalent geometry : angle 0.55839 (10199) hydrogen bonds : bond 0.03274 ( 222) hydrogen bonds : angle 4.81034 ( 705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.301 Fit side-chains REVERT: A 56 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8098 (mttt) REVERT: A 87 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7990 (mm110) REVERT: C 21 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8232 (p0) REVERT: C 87 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.7114 (mm-40) REVERT: D 56 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8358 (mtpt) REVERT: E 46 MET cc_start: 0.9198 (mmm) cc_final: 0.8627 (mmt) REVERT: B 87 GLN cc_start: 0.8441 (mt0) cc_final: 0.8143 (mm-40) REVERT: G 87 GLN cc_start: 0.8217 (mt0) cc_final: 0.7872 (mm-40) outliers start: 28 outliers final: 20 residues processed: 121 average time/residue: 0.0714 time to fit residues: 12.2774 Evaluate side-chains 126 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 0.3980 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN C 67 GLN G 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.095518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.085345 restraints weight = 9383.126| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.31 r_work: 0.2689 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7455 Z= 0.079 Angle : 0.433 4.113 10199 Z= 0.220 Chirality : 0.044 0.145 1302 Planarity : 0.003 0.032 1295 Dihedral : 4.448 42.526 1057 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.44 % Allowed : 17.34 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.25), residues: 1008 helix: -4.51 (0.36), residues: 42 sheet: 2.09 (0.25), residues: 364 loop : 0.56 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 44 TYR 0.005 0.001 TYR A 33 PHE 0.003 0.001 PHE G 40 TRP 0.003 0.000 TRP E 84 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00182 ( 7455) covalent geometry : angle 0.43329 (10199) hydrogen bonds : bond 0.02396 ( 222) hydrogen bonds : angle 4.33139 ( 705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.275 Fit side-chains REVERT: A 56 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8118 (mttt) REVERT: A 87 GLN cc_start: 0.8289 (mt0) cc_final: 0.7967 (mm110) REVERT: C 21 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8219 (p0) REVERT: D 52 ASN cc_start: 0.7568 (t0) cc_final: 0.7290 (p0) REVERT: D 56 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8341 (mtpt) REVERT: E 46 MET cc_start: 0.9130 (mmm) cc_final: 0.8548 (mmt) REVERT: B 21 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7853 (p0) REVERT: B 87 GLN cc_start: 0.8437 (mt0) cc_final: 0.8174 (mm-40) REVERT: B 115 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8337 (mp10) REVERT: G 87 GLN cc_start: 0.8172 (mt0) cc_final: 0.7845 (mm-40) outliers start: 20 outliers final: 17 residues processed: 111 average time/residue: 0.0682 time to fit residues: 10.8394 Evaluate side-chains 116 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 ASN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 60 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 67 GLN D 50 HIS E 19 GLN G 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.088782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.078291 restraints weight = 9765.881| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 1.37 r_work: 0.2569 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 7455 Z= 0.313 Angle : 0.702 9.628 10199 Z= 0.349 Chirality : 0.053 0.164 1302 Planarity : 0.004 0.034 1295 Dihedral : 5.778 50.635 1057 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.79 % Allowed : 16.24 % Favored : 79.98 % 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 aren not related in a simple way. whole: 0.64 (0.24), residues: 1008 helix: -4.99 (0.27), residues: 42 sheet: 1.23 (0.25), residues: 406 loop : 0.35 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 44 TYR 0.012 0.002 TYR A 33 PHE 0.008 0.002 PHE C 40 TRP 0.011 0.002 TRP E 84 HIS 0.004 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00780 ( 7455) covalent geometry : angle 0.70248 (10199) hydrogen bonds : bond 0.03923 ( 222) hydrogen bonds : angle 5.20897 ( 705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.246 Fit side-chains REVERT: A 56 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8086 (mttt) REVERT: A 87 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8018 (mm110) REVERT: C 21 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8233 (p0) REVERT: C 87 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7198 (mm-40) REVERT: D 56 LYS cc_start: 0.9093 (mtpp) cc_final: 0.8393 (mtpt) REVERT: E 46 MET cc_start: 0.9203 (mmm) cc_final: 0.8772 (mmt) REVERT: B 87 GLN cc_start: 0.8479 (mt0) cc_final: 0.8190 (mm-40) REVERT: G 16 ASP cc_start: 0.8522 (p0) cc_final: 0.8265 (p0) REVERT: G 87 GLN cc_start: 0.8234 (mt0) cc_final: 0.7876 (mm-40) outliers start: 31 outliers final: 26 residues processed: 125 average time/residue: 0.0657 time to fit residues: 11.6582 Evaluate side-chains 131 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 0.0050 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN D 19 GLN E 19 GLN G 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.094854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.084719 restraints weight = 9291.505| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.30 r_work: 0.2678 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7455 Z= 0.079 Angle : 0.442 5.068 10199 Z= 0.226 Chirality : 0.044 0.143 1302 Planarity : 0.003 0.032 1295 Dihedral : 4.700 47.300 1057 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.56 % Allowed : 17.58 % Favored : 79.85 % 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 aren not related in a simple way. whole: 1.13 (0.25), residues: 1008 helix: -4.52 (0.37), residues: 42 sheet: 1.96 (0.26), residues: 364 loop : 0.45 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 44 TYR 0.005 0.001 TYR G 33 PHE 0.004 0.001 PHE G 40 TRP 0.002 0.000 TRP F 84 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00179 ( 7455) covalent geometry : angle 0.44217 (10199) hydrogen bonds : bond 0.02363 ( 222) hydrogen bonds : angle 4.40053 ( 705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.191 Fit side-chains REVERT: A 46 MET cc_start: 0.9041 (mmp) cc_final: 0.8742 (mmt) REVERT: A 56 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8118 (mttt) REVERT: A 87 GLN cc_start: 0.8287 (mt0) cc_final: 0.7971 (mm110) REVERT: C 21 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8284 (p0) REVERT: D 49 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8710 (m) REVERT: D 52 ASN cc_start: 0.7549 (t0) cc_final: 0.7263 (p0) REVERT: D 53 ASP cc_start: 0.8284 (t0) cc_final: 0.7859 (t0) REVERT: D 56 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8344 (mtpt) REVERT: E 46 MET cc_start: 0.9123 (mmm) cc_final: 0.8613 (mmt) REVERT: E 91 THR cc_start: 0.8395 (m) cc_final: 0.8029 (p) REVERT: B 21 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7903 (p0) REVERT: B 87 GLN cc_start: 0.8464 (mt0) cc_final: 0.8240 (mm-40) REVERT: G 87 GLN cc_start: 0.8203 (mt0) cc_final: 0.7886 (mm-40) outliers start: 21 outliers final: 18 residues processed: 112 average time/residue: 0.0574 time to fit residues: 9.1928 Evaluate side-chains 119 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 56 LYS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 95 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 94 optimal weight: 0.0010 chunk 68 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 82 optimal weight: 0.2980 overall best weight: 2.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN D 19 GLN G 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.091829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.081486 restraints weight = 9488.379| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 1.33 r_work: 0.2626 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7455 Z= 0.163 Angle : 0.530 6.520 10199 Z= 0.267 Chirality : 0.047 0.152 1302 Planarity : 0.004 0.031 1295 Dihedral : 5.070 48.154 1057 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.81 % Allowed : 17.22 % Favored : 79.98 % 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 aren not related in a simple way. whole: 1.02 (0.24), residues: 1008 helix: -4.44 (0.39), residues: 42 sheet: 1.86 (0.25), residues: 364 loop : 0.37 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 44 TYR 0.008 0.001 TYR A 33 PHE 0.005 0.001 PHE C 40 TRP 0.006 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7455) covalent geometry : angle 0.53019 (10199) hydrogen bonds : bond 0.03010 ( 222) hydrogen bonds : angle 4.64930 ( 705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.204 Fit side-chains REVERT: A 56 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8129 (mttt) REVERT: A 87 GLN cc_start: 0.8319 (mt0) cc_final: 0.7986 (mm110) REVERT: C 21 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8244 (p0) REVERT: D 56 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8439 (mtpt) REVERT: D 77 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8143 (mm-40) REVERT: E 46 MET cc_start: 0.9156 (mmm) cc_final: 0.8726 (mmt) REVERT: B 21 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7967 (p0) REVERT: B 87 GLN cc_start: 0.8490 (mt0) cc_final: 0.8255 (mm-40) REVERT: G 87 GLN cc_start: 0.8231 (mt0) cc_final: 0.7899 (mm-40) outliers start: 23 outliers final: 21 residues processed: 119 average time/residue: 0.0629 time to fit residues: 10.6605 Evaluate side-chains 126 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN C 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.092680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.082436 restraints weight = 9428.667| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 1.32 r_work: 0.2639 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7455 Z= 0.129 Angle : 0.494 5.690 10199 Z= 0.250 Chirality : 0.045 0.149 1302 Planarity : 0.004 0.032 1295 Dihedral : 4.953 47.953 1057 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.05 % Allowed : 17.09 % Favored : 79.85 % 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 aren not related in a simple way. whole: 1.10 (0.25), residues: 1008 helix: -4.23 (0.43), residues: 42 sheet: 1.91 (0.26), residues: 364 loop : 0.43 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 44 TYR 0.007 0.001 TYR A 33 PHE 0.004 0.001 PHE C 40 TRP 0.004 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7455) covalent geometry : angle 0.49399 (10199) hydrogen bonds : bond 0.02783 ( 222) hydrogen bonds : angle 4.54310 ( 705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1414.29 seconds wall clock time: 25 minutes 0.58 seconds (1500.58 seconds total)