Starting phenix.real_space_refine on Wed Feb 12 04:39:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ehr_28150/02_2025/8ehr_28150.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ehr_28150/02_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_28150/02_2025/8ehr_28150.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ehr_28150/02_2025/8ehr_28150.map" model { file = "/net/cci-nas-00/data/ceres_data/8ehr_28150/02_2025/8ehr_28150.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ehr_28150/02_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-5592/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: 4.48, per 1000 atoms: 0.61 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 1.2 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: 1.31 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: 2.18 Time building geometry restraints manager: 2.03 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: 0.07 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: 0.520 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.110 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.200 ------------------------------------------------------------------------------- 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 : 0.740 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: 0.1991 time to fit residues: 40.0236 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 : 0.822 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.088624 restraints weight = 9057.155| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 1.24 r_work: 0.2719 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 : 0.739 Fit side-chains REVERT: A 53 ASP cc_start: 0.8367 (t0) cc_final: 0.8032 (t70) REVERT: A 56 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8052 (mttt) REVERT: A 95 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8069 (mt-10) REVERT: D 56 LYS cc_start: 0.8919 (mtpp) cc_final: 0.8208 (mtpt) REVERT: E 46 MET cc_start: 0.9245 (tpp) cc_final: 0.8596 (mmt) REVERT: B 56 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7838 (mtmt) REVERT: B 144 THR cc_start: 0.8830 (t) cc_final: 0.8581 (m) REVERT: F 131 THR cc_start: 0.8608 (m) cc_final: 0.8334 (p) REVERT: G 128 THR cc_start: 0.8111 (p) cc_final: 0.7823 (t) outliers start: 17 outliers final: 13 residues processed: 123 average time/residue: 0.1883 time to fit residues: 31.6951 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 : 0.820 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.2837 r_free = 0.2837 target = 0.091574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.081583 restraints weight = 9395.259| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 1.21 r_work: 0.2616 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 7455 Z= 0.445 Angle : 0.660 8.767 10199 Z= 0.331 Chirality : 0.051 0.165 1302 Planarity : 0.004 0.031 1295 Dihedral : 5.561 45.796 1057 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.79 % Allowed : 10.38 % Favored : 85.84 % 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: 0.92 (0.24), residues: 1008 helix: -5.29 (0.15), residues: 42 sheet: 1.68 (0.25), residues: 364 loop : 0.46 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 84 HIS 0.003 0.001 HIS F 50 PHE 0.008 0.001 PHE C 40 TYR 0.012 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 137 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.824 Fit side-chains REVERT: A 56 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8134 (mttt) REVERT: C 87 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7229 (mm-40) REVERT: C 109 ASN cc_start: 0.8414 (m110) cc_final: 0.8198 (m-40) REVERT: D 56 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8380 (mtpt) REVERT: E 46 MET cc_start: 0.9309 (tpp) cc_final: 0.8832 (mmt) REVERT: B 53 ASP cc_start: 0.8302 (t0) cc_final: 0.8005 (t0) REVERT: B 144 THR cc_start: 0.8913 (t) cc_final: 0.8554 (m) REVERT: G 87 GLN cc_start: 0.8204 (mt0) cc_final: 0.7788 (mm-40) REVERT: G 128 THR cc_start: 0.8001 (p) cc_final: 0.7763 (t) outliers start: 31 outliers final: 24 residues processed: 129 average time/residue: 0.1591 time to fit residues: 28.9391 Evaluate side-chains 123 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.857 ------------------------------------------------------------------------------- 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 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 8 THR 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 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 G 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.093466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.083351 restraints weight = 9378.818| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.29 r_work: 0.2659 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2244 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= 0.173 Angle : 0.473 5.401 10199 Z= 0.242 Chirality : 0.045 0.151 1302 Planarity : 0.003 0.029 1295 Dihedral : 4.928 44.473 1057 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.44 % Allowed : 12.70 % Favored : 84.86 % 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: 1.09 (0.25), residues: 1008 helix: -5.12 (0.20), residues: 42 sheet: 1.84 (0.25), residues: 364 loop : 0.54 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 84 HIS 0.001 0.001 HIS F 50 PHE 0.004 0.001 PHE C 40 TYR 0.006 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 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.923 Fit side-chains REVERT: A 56 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8117 (mttt) REVERT: C 21 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8309 (p0) REVERT: D 56 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8345 (mtpt) REVERT: E 46 MET cc_start: 0.9307 (tpp) cc_final: 0.8773 (mmt) REVERT: E 95 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: B 144 THR cc_start: 0.8955 (t) cc_final: 0.8654 (m) REVERT: G 87 GLN cc_start: 0.8114 (mt0) cc_final: 0.7767 (mm-40) REVERT: G 128 THR cc_start: 0.7976 (p) cc_final: 0.7767 (t) outliers start: 20 outliers final: 16 residues processed: 118 average time/residue: 0.1631 time to fit residues: 27.1253 Evaluate side-chains 119 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 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 B residue 143 MET Chi-restraints excluded: chain F residue 21 ASP Chi-restraints excluded: chain F 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: 10.0000 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 45 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 chunk 61 optimal weight: 10.0000 chunk 52 optimal weight: 0.0970 chunk 21 optimal weight: 10.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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 = 0.2867 r_free = 0.2867 target = 0.093398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.083448 restraints weight = 9315.861| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 1.27 r_work: 0.2664 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2328 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= 0.174 Angle : 0.473 5.818 10199 Z= 0.240 Chirality : 0.045 0.149 1302 Planarity : 0.003 0.028 1295 Dihedral : 4.775 43.324 1057 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 3.17 % Allowed : 14.04 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.25), residues: 1008 helix: -4.90 (0.26), residues: 42 sheet: 1.92 (0.25), residues: 364 loop : 0.55 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 84 HIS 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE C 40 TYR 0.005 0.001 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 129 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.811 Fit side-chains REVERT: A 46 MET cc_start: 0.9082 (mmp) cc_final: 0.8783 (mmt) REVERT: A 56 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8126 (mttt) REVERT: A 87 GLN cc_start: 0.8248 (mt0) cc_final: 0.7942 (mm110) REVERT: C 21 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8294 (p0) REVERT: D 56 LYS cc_start: 0.8887 (mtpp) cc_final: 0.8384 (mttt) REVERT: E 95 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: B 87 GLN cc_start: 0.8296 (mt0) cc_final: 0.7933 (mm-40) REVERT: B 144 THR cc_start: 0.8966 (t) cc_final: 0.8622 (m) REVERT: G 87 GLN cc_start: 0.8180 (mt0) cc_final: 0.7788 (mm-40) REVERT: G 128 THR cc_start: 0.8050 (p) cc_final: 0.7838 (t) outliers start: 26 outliers final: 22 residues processed: 120 average time/residue: 0.1674 time to fit residues: 28.3179 Evaluate side-chains 124 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 D residue 2 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 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 56 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 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 = 0.2785 r_free = 0.2785 target = 0.087952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.077944 restraints weight = 9523.722| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 1.29 r_work: 0.2567 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 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 : 0.009 0.057 7455 Z= 0.570 Angle : 0.728 9.522 10199 Z= 0.363 Chirality : 0.054 0.168 1302 Planarity : 0.004 0.032 1295 Dihedral : 6.052 53.492 1057 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 4.15 % Allowed : 14.41 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.24), residues: 1008 helix: -5.16 (0.22), residues: 42 sheet: 1.15 (0.24), residues: 413 loop : 0.30 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP E 84 HIS 0.004 0.001 HIS F 50 PHE 0.009 0.002 PHE C 40 TYR 0.015 0.003 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 140 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.808 Fit side-chains REVERT: A 56 LYS cc_start: 0.8640 (mtpp) cc_final: 0.8111 (mttt) REVERT: A 87 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8023 (mm110) REVERT: C 21 ASP cc_start: 0.8641 (OUTLIER) cc_final: 0.8167 (p0) REVERT: C 87 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7147 (mm-40) REVERT: C 120 SER cc_start: 0.8718 (t) cc_final: 0.8383 (p) REVERT: D 56 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8401 (mtpt) REVERT: E 46 MET cc_start: 0.9313 (tpp) cc_final: 0.8732 (mmt) REVERT: B 53 ASP cc_start: 0.8368 (t0) cc_final: 0.8163 (t0) REVERT: B 56 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7753 (mtpt) REVERT: G 16 ASP cc_start: 0.8540 (p0) cc_final: 0.8273 (p0) REVERT: G 87 GLN cc_start: 0.8231 (mt0) cc_final: 0.7989 (mm-40) REVERT: G 128 THR cc_start: 0.8053 (p) cc_final: 0.7724 (t) outliers start: 34 outliers final: 25 residues processed: 128 average time/residue: 0.1649 time to fit residues: 29.5479 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 : 0.851 ------------------------------------------------------------------------------- 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 2 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN D 134 ASN 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 = 0.2873 r_free = 0.2873 target = 0.093882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.083839 restraints weight = 9246.806| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 1.29 r_work: 0.2666 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2573 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= 0.129 Angle : 0.443 4.169 10199 Z= 0.228 Chirality : 0.044 0.146 1302 Planarity : 0.003 0.031 1295 Dihedral : 4.975 51.297 1057 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.20 % Allowed : 17.09 % Favored : 80.71 % 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: 1.01 (0.25), residues: 1008 helix: -4.85 (0.29), residues: 42 sheet: 1.83 (0.25), residues: 364 loop : 0.43 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 84 HIS 0.001 0.000 HIS A 50 PHE 0.004 0.001 PHE G 40 TYR 0.005 0.001 TYR A 33 ARG 0.001 0.000 ARG D 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 122 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.791 Fit side-chains REVERT: A 56 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8095 (mttt) REVERT: A 87 GLN cc_start: 0.8227 (mt0) cc_final: 0.7915 (mm110) REVERT: C 87 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7044 (mm-40) REVERT: C 120 SER cc_start: 0.8608 (t) cc_final: 0.8222 (p) REVERT: D 56 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8373 (mtpt) REVERT: E 46 MET cc_start: 0.9271 (tpp) cc_final: 0.8578 (mmt) REVERT: B 53 ASP cc_start: 0.8391 (t0) cc_final: 0.8042 (t0) REVERT: B 87 GLN cc_start: 0.8396 (mt0) cc_final: 0.8144 (mm-40) REVERT: B 144 THR cc_start: 0.8977 (t) cc_final: 0.8612 (m) REVERT: G 87 GLN cc_start: 0.8227 (mt0) cc_final: 0.7822 (mm-40) REVERT: G 128 THR cc_start: 0.8007 (p) cc_final: 0.7764 (t) outliers start: 18 outliers final: 14 residues processed: 118 average time/residue: 0.1655 time to fit residues: 27.5163 Evaluate side-chains 117 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 90 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 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 G 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.089641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.079617 restraints weight = 9538.411| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 1.30 r_work: 0.2595 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7455 Z= 0.362 Angle : 0.592 7.245 10199 Z= 0.297 Chirality : 0.048 0.157 1302 Planarity : 0.004 0.031 1295 Dihedral : 5.556 53.571 1057 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.17 % Allowed : 16.85 % 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 (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: 0.75 (0.25), residues: 1008 helix: -4.96 (0.27), residues: 42 sheet: 1.29 (0.25), residues: 406 loop : 0.44 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 84 HIS 0.002 0.001 HIS F 50 PHE 0.006 0.001 PHE C 40 TYR 0.012 0.002 TYR A 33 ARG 0.002 0.000 ARG G 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 129 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.800 Fit side-chains REVERT: A 56 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8109 (mttt) REVERT: A 87 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7994 (mm110) REVERT: C 21 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8272 (p0) REVERT: C 87 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7127 (mm-40) REVERT: D 56 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8428 (mtpt) REVERT: E 46 MET cc_start: 0.9296 (tpp) cc_final: 0.8651 (mmt) REVERT: E 95 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: B 53 ASP cc_start: 0.8423 (t0) cc_final: 0.8171 (t0) REVERT: B 56 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7726 (mtpt) REVERT: B 87 GLN cc_start: 0.8440 (mt0) cc_final: 0.8183 (mm-40) REVERT: G 87 GLN cc_start: 0.8229 (mt0) cc_final: 0.7899 (mm-40) REVERT: G 128 THR cc_start: 0.7986 (p) cc_final: 0.7664 (t) outliers start: 26 outliers final: 18 residues processed: 120 average time/residue: 0.1807 time to fit residues: 30.0229 Evaluate side-chains 123 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.089181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.079125 restraints weight = 9654.725| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 1.32 r_work: 0.2589 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.006 0.038 7455 Z= 0.373 Angle : 0.602 7.479 10199 Z= 0.302 Chirality : 0.049 0.156 1302 Planarity : 0.004 0.033 1295 Dihedral : 5.759 57.555 1057 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.05 % Allowed : 17.46 % Favored : 79.49 % 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 (0.25), residues: 1008 helix: -5.01 (0.27), residues: 42 sheet: 1.20 (0.25), residues: 406 loop : 0.32 (0.23), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 G 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 125 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.784 Fit side-chains REVERT: A 56 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8118 (mttt) REVERT: A 87 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8000 (mm110) REVERT: C 21 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8320 (p0) REVERT: C 87 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7108 (mm-40) REVERT: D 56 LYS cc_start: 0.9102 (mtpp) cc_final: 0.8463 (mtpt) REVERT: E 46 MET cc_start: 0.9298 (tpp) cc_final: 0.8672 (mmt) REVERT: E 95 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: B 53 ASP cc_start: 0.8435 (t0) cc_final: 0.8153 (t0) REVERT: B 87 GLN cc_start: 0.8441 (mt0) cc_final: 0.8198 (mm-40) REVERT: G 87 GLN cc_start: 0.8234 (mt0) cc_final: 0.7907 (mm-40) REVERT: G 128 THR cc_start: 0.8124 (p) cc_final: 0.7771 (t) outliers start: 25 outliers final: 21 residues processed: 116 average time/residue: 0.1739 time to fit residues: 28.4882 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 : 0.960 ------------------------------------------------------------------------------- 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 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 95 GLU Chi-restraints excluded: chain B residue 31 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 0.0670 chunk 62 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN 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 = 0.2888 r_free = 0.2888 target = 0.094990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.085067 restraints weight = 9386.859| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.28 r_work: 0.2686 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2711 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= 0.117 Angle : 0.436 4.263 10199 Z= 0.223 Chirality : 0.044 0.144 1302 Planarity : 0.003 0.034 1295 Dihedral : 4.777 53.517 1057 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.20 % Allowed : 18.56 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.25), residues: 1008 helix: -4.44 (0.39), residues: 42 sheet: 1.94 (0.26), residues: 364 loop : 0.36 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 84 HIS 0.002 0.001 HIS F 50 PHE 0.005 0.001 PHE F 40 TYR 0.004 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 115 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.646 Fit side-chains REVERT: A 56 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8101 (mttt) REVERT: A 87 GLN cc_start: 0.8263 (mt0) cc_final: 0.7955 (mm110) REVERT: A 95 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7965 (mm-30) REVERT: C 21 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8292 (p0) REVERT: C 87 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7097 (mm-40) REVERT: C 120 SER cc_start: 0.8609 (t) cc_final: 0.8245 (p) REVERT: D 56 LYS cc_start: 0.8993 (mtpp) cc_final: 0.8365 (mtpt) REVERT: E 46 MET cc_start: 0.9268 (tpp) cc_final: 0.8596 (mmt) REVERT: B 53 ASP cc_start: 0.8407 (t0) cc_final: 0.8058 (t0) REVERT: B 87 GLN cc_start: 0.8408 (mt0) cc_final: 0.8206 (mm-40) REVERT: G 87 GLN cc_start: 0.8277 (mt0) cc_final: 0.7955 (mm-40) REVERT: G 128 THR cc_start: 0.8038 (p) cc_final: 0.7736 (t) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.1755 time to fit residues: 27.0997 Evaluate side-chains 111 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 52 ASN 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 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 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.2859 r_free = 0.2859 target = 0.093132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.083107 restraints weight = 9347.639| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 1.29 r_work: 0.2655 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.003 0.023 7455 Z= 0.187 Angle : 0.479 5.022 10199 Z= 0.243 Chirality : 0.045 0.148 1302 Planarity : 0.003 0.031 1295 Dihedral : 4.925 54.493 1057 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.69 % Allowed : 17.95 % Favored : 79.37 % 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: 1.11 (0.25), residues: 1008 helix: -4.08 (0.48), residues: 42 sheet: 1.98 (0.26), residues: 364 loop : 0.37 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 84 HIS 0.002 0.001 HIS A 50 PHE 0.004 0.001 PHE G 40 TYR 0.008 0.001 TYR A 33 ARG 0.001 0.000 ARG C 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3325.40 seconds wall clock time: 59 minutes 58.43 seconds (3598.43 seconds total)