Starting phenix.real_space_refine on Wed Mar 12 04:18:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehr_28150/03_2025/8ehr_28150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehr_28150/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ehr_28150/03_2025/8ehr_28150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehr_28150/03_2025/8ehr_28150.map" model { file = "/net/cci-nas-00/data/ceres_data/8ehr_28150/03_2025/8ehr_28150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehr_28150/03_2025/8ehr_28150.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.59, per 1000 atoms: 0.62 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: 1.71 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 1.88 Time building geometry restraints manager: 2.01 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.570 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.030 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- 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= 0.193 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (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 TRP 0.003 0.001 TRP E 84 HIS 0.002 0.001 HIS D 50 PHE 0.005 0.001 PHE G 40 TYR 0.008 0.001 TYR F 33 ARG 0.000 0.000 ARG A 44 *********************** 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 : 0.829 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: 0.1876 time to fit residues: 37.8501 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 : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0010 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN B 48 GLN G 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.098681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.088654 restraints weight = 9057.155| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.23 r_work: 0.2720 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 7455 Z= 0.156 Angle : 0.469 5.187 10199 Z= 0.242 Chirality : 0.045 0.154 1302 Planarity : 0.004 0.032 1295 Dihedral : 4.467 33.153 1057 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 2.08 % Allowed : 7.69 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1008 helix: -5.15 (0.17), residues: 42 sheet: 2.13 (0.26), residues: 350 loop : 0.78 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE D 96 TYR 0.006 0.001 TYR E 33 ARG 0.002 0.000 ARG A 44 *********************** 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 132 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.734 Fit side-chains REVERT: A 53 ASP cc_start: 0.8368 (t0) cc_final: 0.8032 (t70) REVERT: A 56 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8054 (mttt) REVERT: A 95 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8069 (mt-10) REVERT: D 56 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8211 (mtpt) REVERT: E 46 MET cc_start: 0.9245 (tpp) cc_final: 0.8593 (mmt) REVERT: B 56 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7840 (mtmt) REVERT: B 144 THR cc_start: 0.8829 (t) cc_final: 0.8581 (m) REVERT: F 131 THR cc_start: 0.8608 (m) cc_final: 0.8335 (p) REVERT: G 128 THR cc_start: 0.8112 (p) cc_final: 0.7822 (t) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.1861 time to fit residues: 31.4628 Evaluate side-chains 112 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain B residue 91 THR 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 76 VAL 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 84 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 D 19 GLN B 19 GLN G 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.092794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.082723 restraints weight = 9330.181| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 1.24 r_work: 0.2625 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2083 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= 0.350 Angle : 0.600 7.994 10199 Z= 0.302 Chirality : 0.049 0.161 1302 Planarity : 0.004 0.030 1295 Dihedral : 5.279 42.145 1057 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.42 % Allowed : 10.62 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1008 helix: -5.22 (0.17), residues: 42 sheet: 1.80 (0.25), residues: 364 loop : 0.56 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 84 HIS 0.003 0.001 HIS F 50 PHE 0.007 0.001 PHE C 40 TYR 0.010 0.002 TYR E 135 ARG 0.002 0.000 ARG A 44 *********************** 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 134 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.763 Fit side-chains REVERT: A 56 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8150 (mttt) REVERT: C 87 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7174 (mm-40) REVERT: C 109 ASN cc_start: 0.8392 (m110) cc_final: 0.8181 (m-40) REVERT: D 56 LYS cc_start: 0.9019 (mtpp) cc_final: 0.8402 (mtpt) REVERT: E 46 MET cc_start: 0.9310 (tpp) cc_final: 0.8812 (mmt) REVERT: E 95 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: B 144 THR cc_start: 0.8883 (t) cc_final: 0.8540 (m) REVERT: G 87 GLN cc_start: 0.8156 (mt0) cc_final: 0.7721 (mm-40) REVERT: G 128 THR cc_start: 0.8099 (p) cc_final: 0.7856 (t) outliers start: 28 outliers final: 22 residues processed: 126 average time/residue: 0.1645 time to fit residues: 29.0953 Evaluate side-chains 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 128 THR 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 E residue 83 SER Chi-restraints excluded: chain E residue 95 GLU 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 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.091783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.081640 restraints weight = 9448.649| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 1.30 r_work: 0.2630 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7455 Z= 0.257 Angle : 0.529 6.614 10199 Z= 0.267 Chirality : 0.046 0.154 1302 Planarity : 0.003 0.030 1295 Dihedral : 5.149 44.656 1057 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.17 % Allowed : 12.70 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1008 helix: -5.12 (0.21), residues: 42 sheet: 1.77 (0.25), residues: 364 loop : 0.52 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE C 40 TYR 0.009 0.001 TYR A 33 ARG 0.001 0.000 ARG A 44 *********************** 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 130 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.790 Fit side-chains REVERT: A 56 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8166 (mttt) REVERT: C 21 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8306 (p0) REVERT: D 56 LYS cc_start: 0.8977 (mtpp) cc_final: 0.8359 (mtpt) REVERT: E 46 MET cc_start: 0.9333 (tpp) cc_final: 0.8830 (mmt) REVERT: E 95 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: B 144 THR cc_start: 0.8945 (t) cc_final: 0.8636 (m) REVERT: G 87 GLN cc_start: 0.8176 (mt0) cc_final: 0.7826 (mm-40) REVERT: G 128 THR cc_start: 0.8008 (p) cc_final: 0.7787 (t) outliers start: 26 outliers final: 23 residues processed: 122 average time/residue: 0.1603 time to fit residues: 27.8384 Evaluate side-chains 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 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 95 GLU 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 128 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 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 50 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 61 optimal weight: 0.0970 chunk 52 optimal weight: 0.0070 chunk 21 optimal weight: 8.9990 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.090580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.080513 restraints weight = 9431.307| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 1.30 r_work: 0.2616 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2436 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= 0.312 Angle : 0.566 7.411 10199 Z= 0.284 Chirality : 0.048 0.156 1302 Planarity : 0.004 0.030 1295 Dihedral : 5.357 47.204 1057 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.54 % Allowed : 14.04 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.24), residues: 1008 helix: -5.08 (0.25), residues: 42 sheet: 1.71 (0.25), residues: 364 loop : 0.38 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.006 0.001 PHE C 40 TYR 0.010 0.002 TYR A 33 ARG 0.001 0.000 ARG A 44 *********************** 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 131 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.833 Fit side-chains REVERT: A 56 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8160 (mttt) REVERT: A 87 GLN cc_start: 0.8302 (mt0) cc_final: 0.7974 (mm110) REVERT: C 21 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8255 (p0) REVERT: C 87 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7068 (mm-40) REVERT: D 53 ASP cc_start: 0.8260 (t70) cc_final: 0.8011 (p0) REVERT: D 56 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8343 (mtpt) REVERT: E 95 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: B 53 ASP cc_start: 0.8308 (t0) cc_final: 0.8024 (t0) REVERT: B 87 GLN cc_start: 0.8383 (mt0) cc_final: 0.8043 (mm-40) REVERT: B 144 THR cc_start: 0.8974 (t) cc_final: 0.8644 (m) REVERT: G 87 GLN cc_start: 0.8218 (mt0) cc_final: 0.7839 (mm-40) REVERT: G 128 THR cc_start: 0.8115 (p) cc_final: 0.7840 (t) outliers start: 29 outliers final: 22 residues processed: 122 average time/residue: 0.1660 time to fit residues: 28.4019 Evaluate side-chains 127 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 95 GLU 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 G residue 21 ASP Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.089677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.079674 restraints weight = 9416.584| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 1.28 r_work: 0.2598 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2484 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7455 Z= 0.362 Angle : 0.597 7.540 10199 Z= 0.299 Chirality : 0.049 0.158 1302 Planarity : 0.004 0.031 1295 Dihedral : 5.608 50.590 1057 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 4.03 % Allowed : 14.41 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1008 helix: -5.08 (0.27), residues: 42 sheet: 1.25 (0.25), residues: 406 loop : 0.43 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 84 HIS 0.003 0.001 HIS F 50 PHE 0.006 0.001 PHE C 40 TYR 0.012 0.002 TYR A 33 ARG 0.001 0.000 ARG A 44 *********************** 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 141 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.764 Fit side-chains REVERT: A 56 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8153 (mttt) REVERT: A 87 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7998 (mm110) REVERT: C 21 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8254 (p0) REVERT: C 87 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7092 (mm-40) REVERT: D 56 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8416 (mtpt) REVERT: E 95 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: B 53 ASP cc_start: 0.8378 (t0) cc_final: 0.8117 (t0) REVERT: B 56 LYS cc_start: 0.8241 (mtpp) cc_final: 0.7735 (mtpt) REVERT: B 87 GLN cc_start: 0.8436 (mt0) cc_final: 0.8153 (mm-40) REVERT: B 144 THR cc_start: 0.8996 (t) cc_final: 0.8656 (m) REVERT: G 87 GLN cc_start: 0.8199 (mt0) cc_final: 0.7859 (mm-40) REVERT: G 128 THR cc_start: 0.8006 (p) cc_final: 0.7678 (t) outliers start: 33 outliers final: 26 residues processed: 130 average time/residue: 0.1710 time to fit residues: 30.9200 Evaluate side-chains 135 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 95 GLU Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 THR 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 49 VAL Chi-restraints excluded: chain G residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- 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 D 134 ASN G 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.095438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.085660 restraints weight = 9212.555| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.26 r_work: 0.2695 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7455 Z= 0.115 Angle : 0.430 4.055 10199 Z= 0.219 Chirality : 0.044 0.146 1302 Planarity : 0.003 0.030 1295 Dihedral : 4.635 47.012 1057 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.08 % Allowed : 17.34 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1008 helix: -4.73 (0.33), residues: 42 sheet: 1.96 (0.25), residues: 364 loop : 0.46 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 84 HIS 0.001 0.001 HIS C 50 PHE 0.004 0.001 PHE G 40 TYR 0.005 0.001 TYR A 33 ARG 0.001 0.000 ARG A 44 *********************** 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 121 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.830 Fit side-chains REVERT: A 56 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8096 (mttt) REVERT: A 87 GLN cc_start: 0.8236 (mt0) cc_final: 0.7939 (mm110) REVERT: A 95 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7974 (mm-30) REVERT: C 87 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7093 (mm-40) REVERT: C 120 SER cc_start: 0.8612 (t) cc_final: 0.8231 (p) REVERT: D 56 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8351 (mttt) REVERT: E 46 MET cc_start: 0.9257 (tpp) cc_final: 0.8665 (mmt) REVERT: E 95 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: B 87 GLN cc_start: 0.8402 (mt0) cc_final: 0.8162 (mm-40) REVERT: F 16 ASP cc_start: 0.8038 (p0) cc_final: 0.7806 (t70) REVERT: G 87 GLN cc_start: 0.8250 (mt0) cc_final: 0.7868 (mm-40) REVERT: G 128 THR cc_start: 0.8063 (p) cc_final: 0.7807 (t) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.1696 time to fit residues: 28.0845 Evaluate side-chains 113 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 E residue 95 GLU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 90 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.2844 r_free = 0.2844 target = 0.092077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.081911 restraints weight = 9459.722| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 1.32 r_work: 0.2631 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7455 Z= 0.229 Angle : 0.505 5.689 10199 Z= 0.255 Chirality : 0.046 0.150 1302 Planarity : 0.003 0.030 1295 Dihedral : 4.945 45.779 1057 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1008 helix: -4.61 (0.35), residues: 42 sheet: 1.94 (0.25), residues: 364 loop : 0.41 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE C 40 TYR 0.008 0.001 TYR A 33 ARG 0.001 0.000 ARG A 44 *********************** 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 121 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.820 Fit side-chains REVERT: A 56 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8088 (mttt) REVERT: A 87 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7986 (mm110) REVERT: C 87 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7118 (mm-40) REVERT: D 56 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8398 (mtpt) REVERT: E 95 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: B 56 LYS cc_start: 0.8212 (mtpp) cc_final: 0.7695 (mtpt) REVERT: B 87 GLN cc_start: 0.8424 (mt0) cc_final: 0.8168 (mm-40) REVERT: G 87 GLN cc_start: 0.8216 (mt0) cc_final: 0.7903 (mm-40) REVERT: G 128 THR cc_start: 0.8060 (p) cc_final: 0.7788 (t) outliers start: 21 outliers final: 17 residues processed: 114 average time/residue: 0.1729 time to fit residues: 27.6480 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 : 0.789 ------------------------------------------------------------------------------- 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 C residue 8 THR Chi-restraints excluded: chain C residue 49 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 95 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN D 50 HIS E 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.088412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.077934 restraints weight = 9692.960| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 1.39 r_work: 0.2568 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2452 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 7455 Z= 0.497 Angle : 0.680 9.003 10199 Z= 0.339 Chirality : 0.052 0.163 1302 Planarity : 0.004 0.032 1295 Dihedral : 5.930 56.184 1057 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.66 % Allowed : 17.34 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.24), residues: 1008 helix: -5.00 (0.29), residues: 42 sheet: 1.23 (0.25), residues: 413 loop : 0.28 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP E 84 HIS 0.003 0.001 HIS F 50 PHE 0.008 0.002 PHE C 40 TYR 0.012 0.002 TYR A 33 ARG 0.001 0.000 ARG A 44 *********************** 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 132 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.771 Fit side-chains REVERT: A 56 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8089 (mttt) REVERT: A 87 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8016 (mm110) REVERT: C 21 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8299 (p0) REVERT: C 87 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7185 (mm-40) REVERT: C 120 SER cc_start: 0.8692 (t) cc_final: 0.8342 (p) REVERT: D 56 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8436 (mtpt) REVERT: B 87 GLN cc_start: 0.8451 (mt0) cc_final: 0.8172 (mm-40) REVERT: G 87 GLN cc_start: 0.8206 (mt0) cc_final: 0.7849 (mm-40) REVERT: G 128 THR cc_start: 0.8029 (p) cc_final: 0.7680 (t) outliers start: 30 outliers final: 25 residues processed: 122 average time/residue: 0.1638 time to fit residues: 28.0803 Evaluate side-chains 129 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 95 GLU 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 B residue 144 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 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 GLN E 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 = 0.2881 r_free = 0.2881 target = 0.094428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.084321 restraints weight = 9408.942| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 1.31 r_work: 0.2674 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7455 Z= 0.121 Angle : 0.443 4.363 10199 Z= 0.228 Chirality : 0.044 0.146 1302 Planarity : 0.003 0.033 1295 Dihedral : 4.869 51.089 1057 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.44 % Allowed : 18.68 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1008 helix: -4.55 (0.37), residues: 42 sheet: 1.94 (0.26), residues: 364 loop : 0.39 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 84 HIS 0.003 0.001 HIS A 50 PHE 0.005 0.001 PHE G 40 TYR 0.005 0.001 TYR G 33 ARG 0.001 0.000 ARG G 44 ********************** 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 118 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.861 Fit side-chains REVERT: A 56 LYS cc_start: 0.8626 (mtpp) cc_final: 0.8108 (mttt) REVERT: A 87 GLN cc_start: 0.8282 (mt0) cc_final: 0.7966 (mm110) REVERT: C 87 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.7064 (mm-40) REVERT: C 120 SER cc_start: 0.8607 (t) cc_final: 0.8228 (p) REVERT: D 49 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8716 (m) REVERT: D 56 LYS cc_start: 0.8991 (mtpp) cc_final: 0.8386 (mtpt) REVERT: E 46 MET cc_start: 0.9262 (tpp) cc_final: 0.8685 (mmt) REVERT: E 95 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: B 87 GLN cc_start: 0.8410 (mt0) cc_final: 0.8194 (mm-40) REVERT: G 87 GLN cc_start: 0.8248 (mt0) cc_final: 0.7947 (mm-40) REVERT: G 128 THR cc_start: 0.8018 (p) cc_final: 0.7700 (t) outliers start: 20 outliers final: 15 residues processed: 111 average time/residue: 0.1736 time to fit residues: 26.9686 Evaluate side-chains 114 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 95 GLU 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 F residue 83 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 26 optimal weight: 0.0570 chunk 84 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.095096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.085013 restraints weight = 9287.521| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 1.30 r_work: 0.2686 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7455 Z= 0.127 Angle : 0.443 4.733 10199 Z= 0.226 Chirality : 0.044 0.144 1302 Planarity : 0.003 0.031 1295 Dihedral : 4.580 50.330 1057 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 2.32 % Allowed : 18.68 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1008 helix: -4.11 (0.45), residues: 42 sheet: 2.12 (0.26), residues: 364 loop : 0.47 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 84 HIS 0.003 0.001 HIS F 50 PHE 0.004 0.001 PHE G 40 TYR 0.005 0.001 TYR A 33 ARG 0.001 0.000 ARG A 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3616.24 seconds wall clock time: 64 minutes 25.41 seconds (3865.41 seconds total)