Starting phenix.real_space_refine on Fri Dec 27 10:53:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pke_17736/12_2024/8pke_17736.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pke_17736/12_2024/8pke_17736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pke_17736/12_2024/8pke_17736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pke_17736/12_2024/8pke_17736.map" model { file = "/net/cci-nas-00/data/ceres_data/8pke_17736/12_2024/8pke_17736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pke_17736/12_2024/8pke_17736.cif" } resolution = 3.39 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2796 2.51 5 N 708 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4314 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.03, per 1000 atoms: 0.47 Number of scatterers: 4314 At special positions: 0 Unit cell: (78.09, 79.734, 45.21, 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 6 16.00 O 804 8.00 N 708 7.00 C 2796 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: 1.01 Conformation dependent library (CDL) restraints added in 535.8 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.715A pdb=" N MET A 13 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL B 16 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET B 13 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL C 16 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET C 13 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL D 16 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET D 13 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL E 16 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS D 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET E 13 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL F 16 " --> pdb=" O MET E 13 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS E 15 " --> pdb=" O VAL F 16 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.972A pdb=" N ALA A 19 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ALA B 19 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA C 19 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA D 19 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ALA E 19 " --> pdb=" O ILE F 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 removed outlier: 6.409A pdb=" N ALA A 25 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA C 25 " --> pdb=" O ILE D 26 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA D 25 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA E 25 " --> pdb=" O ILE F 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 62 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73 Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 6.886A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER C 77 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR D 78 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER D 77 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR E 78 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N SER E 77 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR F 78 " --> pdb=" O SER E 77 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 99 removed outlier: 6.534A pdb=" N VAL A 93 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR B 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N PHE A 95 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASN B 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA A 97 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL B 93 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR C 96 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE B 95 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASN C 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA B 97 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 93 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR D 96 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE C 95 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASN D 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA C 97 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 93 " --> pdb=" O VAL E 94 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR E 96 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE D 95 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ASN E 98 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA D 97 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL E 93 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR F 96 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N PHE E 95 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASN F 98 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ALA E 97 " --> pdb=" O ASN F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 106 through 110 removed outlier: 9.074A pdb=" N THR A 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ALA B 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA A 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N THR B 106 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ALA C 109 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA B 108 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N THR C 106 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ALA D 109 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA C 108 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 9.074A pdb=" N THR D 106 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ALA E 109 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA D 108 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N THR E 106 " --> pdb=" O ILE F 107 " (cutoff:3.500A) removed outlier: 9.384A pdb=" N ALA F 109 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA E 108 " --> pdb=" O ALA F 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115 Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122 75 hydrogen bonds defined for protein. 225 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: 1.16 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 777 1.32 - 1.45: 1125 1.45 - 1.57: 2502 1.57 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 4416 Sorted by residual: bond pdb=" N SER F 85 " pdb=" CA SER F 85 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.10e-03 1.21e+04 1.41e+01 bond pdb=" N SER E 85 " pdb=" CA SER E 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.36e+01 bond pdb=" N SER C 85 " pdb=" CA SER C 85 " ideal model delta sigma weight residual 1.457 1.489 -0.033 9.10e-03 1.21e+04 1.30e+01 bond pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta sigma weight residual 1.457 1.489 -0.033 9.10e-03 1.21e+04 1.30e+01 bond pdb=" N SER B 85 " pdb=" CA SER B 85 " ideal model delta sigma weight residual 1.457 1.489 -0.032 9.10e-03 1.21e+04 1.26e+01 ... (remaining 4411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 3411 1.29 - 2.59: 1737 2.59 - 3.88: 694 3.88 - 5.17: 123 5.17 - 6.46: 41 Bond angle restraints: 6006 Sorted by residual: angle pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" N PRO A 86 " ideal model delta sigma weight residual 118.16 122.33 -4.17 7.00e-01 2.04e+00 3.55e+01 angle pdb=" CA SER F 85 " pdb=" C SER F 85 " pdb=" N PRO F 86 " ideal model delta sigma weight residual 118.16 122.32 -4.16 7.00e-01 2.04e+00 3.53e+01 angle pdb=" CA SER B 85 " pdb=" C SER B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.16 122.29 -4.13 7.00e-01 2.04e+00 3.49e+01 angle pdb=" CA SER D 85 " pdb=" C SER D 85 " pdb=" N PRO D 86 " ideal model delta sigma weight residual 118.16 122.28 -4.12 7.00e-01 2.04e+00 3.47e+01 angle pdb=" CA SER E 85 " pdb=" C SER E 85 " pdb=" N PRO E 86 " ideal model delta sigma weight residual 118.16 122.26 -4.10 7.00e-01 2.04e+00 3.44e+01 ... (remaining 6001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.54: 2223 10.54 - 21.07: 279 21.07 - 31.61: 48 31.61 - 42.14: 42 42.14 - 52.67: 12 Dihedral angle restraints: 2604 sinusoidal: 990 harmonic: 1614 Sorted by residual: dihedral pdb=" C TYR E 78 " pdb=" N TYR E 78 " pdb=" CA TYR E 78 " pdb=" CB TYR E 78 " ideal model delta harmonic sigma weight residual -122.60 -131.08 8.48 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" C TYR A 78 " pdb=" N TYR A 78 " pdb=" CA TYR A 78 " pdb=" CB TYR A 78 " ideal model delta harmonic sigma weight residual -122.60 -131.07 8.47 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" C TYR F 78 " pdb=" N TYR F 78 " pdb=" CA TYR F 78 " pdb=" CB TYR F 78 " ideal model delta harmonic sigma weight residual -122.60 -131.06 8.46 0 2.50e+00 1.60e-01 1.15e+01 ... (remaining 2601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 166 0.058 - 0.116: 256 0.116 - 0.174: 172 0.174 - 0.232: 65 0.232 - 0.290: 49 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA ILE D 20 " pdb=" N ILE D 20 " pdb=" C ILE D 20 " pdb=" CB ILE D 20 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ILE B 20 " pdb=" N ILE B 20 " pdb=" C ILE B 20 " pdb=" CB ILE B 20 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA ILE C 20 " pdb=" N ILE C 20 " pdb=" C ILE C 20 " pdb=" CB ILE C 20 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 705 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 118 " 0.011 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C THR C 118 " -0.040 2.00e-02 2.50e+03 pdb=" O THR C 118 " 0.015 2.00e-02 2.50e+03 pdb=" N THR C 119 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 118 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C THR E 118 " -0.040 2.00e-02 2.50e+03 pdb=" O THR E 118 " 0.015 2.00e-02 2.50e+03 pdb=" N THR E 119 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 118 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.27e+00 pdb=" C THR A 118 " -0.040 2.00e-02 2.50e+03 pdb=" O THR A 118 " 0.015 2.00e-02 2.50e+03 pdb=" N THR A 119 " 0.014 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 10 2.37 - 3.00: 2431 3.00 - 3.63: 6016 3.63 - 4.27: 10325 4.27 - 4.90: 18821 Nonbonded interactions: 37603 Sorted by model distance: nonbonded pdb=" CB PHE D 64 " pdb=" CZ PHE E 64 " model vdw 1.732 3.740 nonbonded pdb=" CB PHE E 64 " pdb=" CZ PHE F 64 " model vdw 1.733 3.740 nonbonded pdb=" CB PHE C 64 " pdb=" CZ PHE D 64 " model vdw 1.733 3.740 nonbonded pdb=" CB PHE B 64 " pdb=" CZ PHE C 64 " model vdw 1.733 3.740 nonbonded pdb=" CB PHE A 64 " pdb=" CZ PHE B 64 " model vdw 1.733 3.740 ... (remaining 37598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 0.910 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: 0.030 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.013 0.041 4416 Z= 0.863 Angle : 1.748 6.463 6006 Z= 1.298 Chirality : 0.128 0.290 708 Planarity : 0.005 0.023 738 Dihedral : 11.503 52.674 1560 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 0.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % 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: -3.31 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 79 HIS 0.005 0.001 HIS C 31 PHE 0.017 0.004 PHE A 87 TYR 0.010 0.002 TYR D 105 ARG 0.002 0.001 ARG F 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7787 (mtpp) REVERT: A 63 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7213 (mt-10) REVERT: A 76 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8365 (mttt) REVERT: B 23 SER cc_start: 0.9317 (m) cc_final: 0.8796 (t) REVERT: B 63 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7140 (mt-10) REVERT: B 115 SER cc_start: 0.8982 (t) cc_final: 0.8760 (t) REVERT: C 13 MET cc_start: 0.7403 (ttm) cc_final: 0.6275 (mpp) REVERT: C 15 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7281 (mtpp) REVERT: C 23 SER cc_start: 0.9364 (m) cc_final: 0.8841 (t) REVERT: C 34 ARG cc_start: 0.6808 (ttt-90) cc_final: 0.6531 (ttt180) REVERT: C 63 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7425 (mt-10) REVERT: D 13 MET cc_start: 0.7412 (ttm) cc_final: 0.6538 (mpp) REVERT: D 23 SER cc_start: 0.9435 (m) cc_final: 0.9177 (m) REVERT: D 63 GLU cc_start: 0.7565 (mt-10) cc_final: 0.6791 (mt-10) REVERT: D 100 SER cc_start: 0.7727 (m) cc_final: 0.7495 (p) REVERT: E 13 MET cc_start: 0.7382 (ttm) cc_final: 0.6535 (mpp) REVERT: E 23 SER cc_start: 0.9418 (m) cc_final: 0.8883 (t) REVERT: E 34 ARG cc_start: 0.6757 (ttt-90) cc_final: 0.6437 (ttt90) REVERT: E 63 GLU cc_start: 0.7592 (mt-10) cc_final: 0.6755 (mt-10) REVERT: F 13 MET cc_start: 0.7987 (ttm) cc_final: 0.7212 (mtm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2127 time to fit residues: 36.2387 Evaluate side-chains 121 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4416 Z= 0.251 Angle : 0.662 4.839 6006 Z= 0.377 Chirality : 0.054 0.183 708 Planarity : 0.005 0.039 738 Dihedral : 4.758 16.504 594 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.06 % Allowed : 11.32 % Favored : 84.62 % 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: -2.73 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 79 HIS 0.001 0.000 HIS A 88 PHE 0.037 0.004 PHE D 64 TYR 0.031 0.003 TYR B 114 ARG 0.004 0.000 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.472 Fit side-chains REVERT: A 35 LYS cc_start: 0.8190 (tttt) cc_final: 0.7798 (tmtt) REVERT: A 63 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7515 (tt0) REVERT: B 35 LYS cc_start: 0.8008 (tttp) cc_final: 0.7792 (tttt) REVERT: B 63 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7344 (mt-10) REVERT: C 13 MET cc_start: 0.7358 (ttm) cc_final: 0.6184 (mpp) REVERT: C 63 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7354 (tt0) REVERT: D 13 MET cc_start: 0.7320 (ttm) cc_final: 0.6399 (mpp) REVERT: D 23 SER cc_start: 0.9512 (m) cc_final: 0.8983 (m) REVERT: D 62 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7097 (mp0) REVERT: D 63 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7040 (tt0) REVERT: E 13 MET cc_start: 0.7379 (ttm) cc_final: 0.6464 (mpp) REVERT: E 23 SER cc_start: 0.9110 (m) cc_final: 0.8767 (t) REVERT: E 63 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7002 (tt0) REVERT: F 13 MET cc_start: 0.7957 (ttm) cc_final: 0.7147 (mtm) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.1554 time to fit residues: 21.7340 Evaluate side-chains 108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4416 Z= 0.311 Angle : 0.623 4.864 6006 Z= 0.353 Chirality : 0.053 0.148 708 Planarity : 0.004 0.026 738 Dihedral : 5.359 18.441 594 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.06 % Allowed : 11.54 % Favored : 84.40 % 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: -2.52 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.004 0.001 HIS A 31 PHE 0.016 0.003 PHE D 64 TYR 0.025 0.003 TYR B 114 ARG 0.004 0.001 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.490 Fit side-chains REVERT: A 35 LYS cc_start: 0.8135 (tttt) cc_final: 0.7843 (tmtt) REVERT: A 63 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7463 (tt0) REVERT: A 116 TYR cc_start: 0.8803 (m-80) cc_final: 0.8557 (m-10) REVERT: B 76 LYS cc_start: 0.8468 (mttt) cc_final: 0.8117 (mtmm) REVERT: B 117 SER cc_start: 0.9061 (p) cc_final: 0.8790 (m) REVERT: C 13 MET cc_start: 0.7461 (ttm) cc_final: 0.6213 (mpp) REVERT: D 13 MET cc_start: 0.7414 (ttm) cc_final: 0.6414 (mpp) REVERT: D 23 SER cc_start: 0.9355 (m) cc_final: 0.9114 (m) REVERT: E 13 MET cc_start: 0.7473 (ttm) cc_final: 0.6413 (mpp) REVERT: E 93 VAL cc_start: 0.9315 (t) cc_final: 0.9008 (p) REVERT: F 13 MET cc_start: 0.8165 (ttm) cc_final: 0.7138 (mtm) REVERT: F 35 LYS cc_start: 0.8666 (tttt) cc_final: 0.8321 (mttt) REVERT: F 63 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7111 (tt0) REVERT: F 92 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7604 (tm-30) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 0.1253 time to fit residues: 18.1386 Evaluate side-chains 109 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 52 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4416 Z= 0.177 Angle : 0.533 4.058 6006 Z= 0.301 Chirality : 0.051 0.141 708 Planarity : 0.004 0.025 738 Dihedral : 5.053 17.062 594 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 15.17 % Favored : 82.69 % 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: -2.31 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 79 HIS 0.001 0.000 HIS D 90 PHE 0.025 0.002 PHE F 64 TYR 0.023 0.002 TYR B 114 ARG 0.002 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8078 (tttt) cc_final: 0.7829 (tmtt) REVERT: A 63 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7541 (mt-10) REVERT: A 116 TYR cc_start: 0.8801 (m-80) cc_final: 0.8563 (m-10) REVERT: A 117 SER cc_start: 0.9057 (p) cc_final: 0.8758 (m) REVERT: C 13 MET cc_start: 0.7459 (ttm) cc_final: 0.6223 (mpp) REVERT: C 78 TYR cc_start: 0.8958 (m-80) cc_final: 0.8745 (m-80) REVERT: D 13 MET cc_start: 0.7450 (ttm) cc_final: 0.6447 (mpp) REVERT: D 23 SER cc_start: 0.9336 (m) cc_final: 0.9135 (m) REVERT: E 13 MET cc_start: 0.7478 (ttm) cc_final: 0.6415 (mpp) REVERT: F 13 MET cc_start: 0.8121 (ttm) cc_final: 0.7181 (mtm) outliers start: 10 outliers final: 9 residues processed: 101 average time/residue: 0.1349 time to fit residues: 18.2059 Evaluate side-chains 102 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 77 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4416 Z= 0.344 Angle : 0.619 4.233 6006 Z= 0.353 Chirality : 0.052 0.152 708 Planarity : 0.004 0.025 738 Dihedral : 5.391 18.802 594 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.99 % Allowed : 13.25 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.24 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.004 0.001 HIS A 31 PHE 0.023 0.003 PHE F 64 TYR 0.026 0.002 TYR B 114 ARG 0.003 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.477 Fit side-chains REVERT: A 13 MET cc_start: 0.7384 (ttp) cc_final: 0.6980 (ttt) REVERT: A 35 LYS cc_start: 0.8093 (tttt) cc_final: 0.7777 (tmtt) REVERT: A 63 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7580 (mt-10) REVERT: B 76 LYS cc_start: 0.8358 (mttt) cc_final: 0.8091 (mtmm) REVERT: B 117 SER cc_start: 0.9173 (p) cc_final: 0.8677 (m) REVERT: C 13 MET cc_start: 0.7479 (ttm) cc_final: 0.6237 (mpp) REVERT: D 13 MET cc_start: 0.7490 (ttm) cc_final: 0.6372 (mpp) REVERT: D 23 SER cc_start: 0.9340 (m) cc_final: 0.9103 (m) REVERT: E 13 MET cc_start: 0.7531 (ttm) cc_final: 0.6399 (mpp) REVERT: E 93 VAL cc_start: 0.9351 (t) cc_final: 0.8989 (p) REVERT: F 13 MET cc_start: 0.8225 (ttm) cc_final: 0.7170 (mpp) REVERT: F 92 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7584 (tm-30) outliers start: 14 outliers final: 9 residues processed: 103 average time/residue: 0.1285 time to fit residues: 17.9849 Evaluate side-chains 96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 0.0050 chunk 5 optimal weight: 10.0000 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS F 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4416 Z= 0.195 Angle : 0.543 4.108 6006 Z= 0.306 Chirality : 0.051 0.150 708 Planarity : 0.004 0.028 738 Dihedral : 5.213 19.133 594 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.71 % Allowed : 15.17 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.24 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 79 HIS 0.001 0.000 HIS A 31 PHE 0.023 0.002 PHE E 64 TYR 0.027 0.002 TYR E 114 ARG 0.001 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.394 Fit side-chains REVERT: A 13 MET cc_start: 0.7403 (ttp) cc_final: 0.7042 (ttt) REVERT: A 35 LYS cc_start: 0.8101 (tttt) cc_final: 0.7791 (tmtt) REVERT: A 63 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7623 (mt-10) REVERT: B 76 LYS cc_start: 0.8330 (mttt) cc_final: 0.8078 (mtmm) REVERT: B 117 SER cc_start: 0.9092 (p) cc_final: 0.8597 (m) REVERT: C 13 MET cc_start: 0.7444 (ttm) cc_final: 0.6202 (mpp) REVERT: D 13 MET cc_start: 0.7489 (ttm) cc_final: 0.6415 (mpp) REVERT: D 23 SER cc_start: 0.9318 (m) cc_final: 0.8937 (m) REVERT: E 13 MET cc_start: 0.7547 (ttm) cc_final: 0.6393 (mpp) REVERT: E 23 SER cc_start: 0.9271 (m) cc_final: 0.8844 (t) REVERT: E 92 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7414 (tm-30) REVERT: E 93 VAL cc_start: 0.9348 (t) cc_final: 0.9003 (p) REVERT: F 13 MET cc_start: 0.8221 (ttm) cc_final: 0.7173 (mpp) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.1360 time to fit residues: 16.6958 Evaluate side-chains 95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4416 Z= 0.421 Angle : 0.668 4.403 6006 Z= 0.381 Chirality : 0.053 0.166 708 Planarity : 0.004 0.030 738 Dihedral : 5.577 19.924 594 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.35 % Allowed : 14.32 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.40 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.004 0.001 HIS B 31 PHE 0.022 0.003 PHE E 64 TYR 0.036 0.003 TYR C 78 ARG 0.003 0.001 ARG C 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.489 Fit side-chains REVERT: A 13 MET cc_start: 0.7412 (ttp) cc_final: 0.6990 (ttt) REVERT: A 35 LYS cc_start: 0.8122 (tttt) cc_final: 0.7801 (tmtt) REVERT: A 63 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7798 (mt-10) REVERT: B 117 SER cc_start: 0.9206 (p) cc_final: 0.8761 (m) REVERT: C 13 MET cc_start: 0.7470 (ttm) cc_final: 0.6253 (mpp) REVERT: D 13 MET cc_start: 0.7503 (ttm) cc_final: 0.6412 (mpp) REVERT: D 23 SER cc_start: 0.9325 (m) cc_final: 0.8931 (m) REVERT: E 13 MET cc_start: 0.7568 (ttm) cc_final: 0.6388 (mpp) REVERT: E 23 SER cc_start: 0.9313 (m) cc_final: 0.8852 (t) REVERT: E 93 VAL cc_start: 0.9379 (t) cc_final: 0.9076 (p) REVERT: F 13 MET cc_start: 0.8311 (ttm) cc_final: 0.7169 (mpt) outliers start: 11 outliers final: 8 residues processed: 92 average time/residue: 0.1367 time to fit residues: 16.6208 Evaluate side-chains 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4416 Z= 0.238 Angle : 0.572 4.005 6006 Z= 0.323 Chirality : 0.051 0.153 708 Planarity : 0.004 0.033 738 Dihedral : 5.334 19.390 594 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.92 % Allowed : 15.38 % Favored : 82.69 % 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: -2.38 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 79 HIS 0.001 0.001 HIS E 31 PHE 0.027 0.002 PHE E 64 TYR 0.025 0.002 TYR C 78 ARG 0.002 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.494 Fit side-chains REVERT: A 13 MET cc_start: 0.7445 (ttp) cc_final: 0.7054 (ttt) REVERT: A 35 LYS cc_start: 0.8044 (tttt) cc_final: 0.7740 (tmtt) REVERT: A 63 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 76 LYS cc_start: 0.8314 (mttt) cc_final: 0.8043 (mtmm) REVERT: B 117 SER cc_start: 0.9105 (p) cc_final: 0.8686 (m) REVERT: C 13 MET cc_start: 0.7426 (ttm) cc_final: 0.6216 (mpp) REVERT: D 13 MET cc_start: 0.7459 (ttm) cc_final: 0.6400 (mpp) REVERT: D 23 SER cc_start: 0.9303 (m) cc_final: 0.8910 (m) REVERT: D 34 ARG cc_start: 0.6945 (ttt-90) cc_final: 0.6342 (ttt180) REVERT: E 13 MET cc_start: 0.7588 (ttm) cc_final: 0.6381 (mpp) REVERT: E 23 SER cc_start: 0.9266 (m) cc_final: 0.8813 (t) REVERT: F 13 MET cc_start: 0.8259 (ttm) cc_final: 0.7160 (mpt) outliers start: 9 outliers final: 8 residues processed: 92 average time/residue: 0.1357 time to fit residues: 16.4695 Evaluate side-chains 90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 49 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4416 Z= 0.235 Angle : 0.572 4.828 6006 Z= 0.321 Chirality : 0.051 0.147 708 Planarity : 0.004 0.031 738 Dihedral : 5.197 19.066 594 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.92 % Allowed : 15.60 % Favored : 82.48 % 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: -2.39 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 79 HIS 0.002 0.000 HIS B 31 PHE 0.023 0.002 PHE E 64 TYR 0.026 0.002 TYR C 78 ARG 0.002 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.484 Fit side-chains REVERT: A 13 MET cc_start: 0.7488 (ttp) cc_final: 0.7092 (ttt) REVERT: A 35 LYS cc_start: 0.8059 (tttt) cc_final: 0.7749 (tmtt) REVERT: A 63 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7784 (mt-10) REVERT: B 117 SER cc_start: 0.9051 (p) cc_final: 0.8653 (m) REVERT: C 13 MET cc_start: 0.7446 (ttm) cc_final: 0.6219 (mpp) REVERT: D 13 MET cc_start: 0.7439 (ttm) cc_final: 0.6371 (mpp) REVERT: D 23 SER cc_start: 0.9351 (m) cc_final: 0.8943 (m) REVERT: D 34 ARG cc_start: 0.6928 (ttt-90) cc_final: 0.6317 (ttt180) REVERT: E 13 MET cc_start: 0.7592 (ttm) cc_final: 0.6395 (mpp) REVERT: E 23 SER cc_start: 0.9268 (m) cc_final: 0.8810 (t) REVERT: F 13 MET cc_start: 0.8257 (ttm) cc_final: 0.7163 (mpt) outliers start: 9 outliers final: 8 residues processed: 88 average time/residue: 0.1374 time to fit residues: 15.9080 Evaluate side-chains 90 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4416 Z= 0.387 Angle : 0.649 5.168 6006 Z= 0.368 Chirality : 0.053 0.161 708 Planarity : 0.004 0.033 738 Dihedral : 5.460 19.988 594 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.71 % Allowed : 14.96 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.53 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.004 0.001 HIS A 90 PHE 0.020 0.002 PHE E 64 TYR 0.037 0.003 TYR C 78 ARG 0.002 0.001 ARG C 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.497 Fit side-chains REVERT: A 13 MET cc_start: 0.7500 (ttp) cc_final: 0.7070 (ttt) REVERT: A 35 LYS cc_start: 0.8086 (tttt) cc_final: 0.7743 (tmtt) REVERT: A 63 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7879 (mt-10) REVERT: B 117 SER cc_start: 0.9132 (p) cc_final: 0.8791 (m) REVERT: C 13 MET cc_start: 0.7449 (ttm) cc_final: 0.6267 (mpp) REVERT: D 13 MET cc_start: 0.7481 (ttm) cc_final: 0.6315 (mpp) REVERT: D 23 SER cc_start: 0.9357 (m) cc_final: 0.8974 (m) REVERT: D 34 ARG cc_start: 0.6955 (ttt-90) cc_final: 0.6350 (ttt180) REVERT: E 13 MET cc_start: 0.7647 (ttm) cc_final: 0.6370 (mpp) REVERT: E 23 SER cc_start: 0.9301 (m) cc_final: 0.8875 (t) REVERT: F 13 MET cc_start: 0.8314 (ttm) cc_final: 0.7149 (mpt) REVERT: F 92 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7727 (tm-30) outliers start: 8 outliers final: 8 residues processed: 84 average time/residue: 0.1544 time to fit residues: 16.8278 Evaluate side-chains 84 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 0.0070 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.152028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.119294 restraints weight = 4939.235| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.68 r_work: 0.4014 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4416 Z= 0.201 Angle : 0.565 4.810 6006 Z= 0.316 Chirality : 0.051 0.148 708 Planarity : 0.004 0.031 738 Dihedral : 5.177 19.310 594 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.71 % Allowed : 15.38 % Favored : 82.91 % 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: -2.44 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 79 HIS 0.002 0.000 HIS A 31 PHE 0.020 0.002 PHE E 64 TYR 0.026 0.002 TYR C 78 ARG 0.002 0.000 ARG D 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.52 seconds wall clock time: 25 minutes 35.32 seconds (1535.32 seconds total)