Starting phenix.real_space_refine on Thu Mar 6 00:45:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pke_17736/03_2025/8pke_17736.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pke_17736/03_2025/8pke_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_17736/03_2025/8pke_17736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pke_17736/03_2025/8pke_17736.map" model { file = "/net/cci-nas-00/data/ceres_data/8pke_17736/03_2025/8pke_17736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pke_17736/03_2025/8pke_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-5624/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: 2.27, per 1000 atoms: 0.53 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: 0.93 Conformation dependent library (CDL) restraints added in 546.9 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: 0.74 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: 1.15 Time building geometry restraints manager: 1.13 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.320 Find NCS groups from input model: 0.090 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- 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 : 0.456 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: 0.2010 time to fit residues: 34.4926 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 : 0.416 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.227087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.176761 restraints weight = 4881.576| |-----------------------------------------------------------------------------| r_work (start): 0.4336 rms_B_bonded: 2.34 r_work: 0.4248 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4135 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2507 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 : 0.663 4.826 6006 Z= 0.377 Chirality : 0.054 0.182 708 Planarity : 0.005 0.039 738 Dihedral : 4.758 16.496 594 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.06 % Allowed : 11.11 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : 0.513 Fit side-chains REVERT: A 35 LYS cc_start: 0.8394 (tttt) cc_final: 0.7938 (tmtt) REVERT: A 63 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7408 (tt0) REVERT: B 23 SER cc_start: 0.9080 (m) cc_final: 0.8854 (t) REVERT: B 26 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8220 (mt) REVERT: B 35 LYS cc_start: 0.8229 (tttp) cc_final: 0.7997 (tttt) REVERT: B 63 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7264 (mt-10) REVERT: C 13 MET cc_start: 0.7353 (ttm) cc_final: 0.6058 (mpp) REVERT: C 63 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7284 (tt0) REVERT: D 13 MET cc_start: 0.7340 (ttm) cc_final: 0.6268 (mpp) REVERT: D 23 SER cc_start: 0.9446 (m) cc_final: 0.8952 (m) REVERT: D 62 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7019 (mp0) REVERT: D 63 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6969 (tt0) REVERT: E 13 MET cc_start: 0.7365 (ttm) cc_final: 0.6322 (mpp) REVERT: E 23 SER cc_start: 0.9028 (m) cc_final: 0.8558 (t) REVERT: E 63 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6944 (tt0) REVERT: F 13 MET cc_start: 0.8141 (ttm) cc_final: 0.7191 (mtm) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.1806 time to fit residues: 25.3917 Evaluate side-chains 110 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.486 ------------------------------------------------------------------------------- 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 26 ILE 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 33 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.208153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.155584 restraints weight = 5119.320| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.18 r_work: 0.4061 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4416 Z= 0.366 Angle : 0.654 4.738 6006 Z= 0.373 Chirality : 0.054 0.151 708 Planarity : 0.004 0.026 738 Dihedral : 5.476 18.994 594 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.27 % Allowed : 10.26 % Favored : 85.47 % 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: -2.54 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 79 HIS 0.005 0.001 HIS A 31 PHE 0.016 0.003 PHE C 64 TYR 0.025 0.003 TYR B 114 ARG 0.003 0.001 ARG A 103 *********************** 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 125 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.478 Fit side-chains REVERT: A 35 LYS cc_start: 0.8347 (tttt) cc_final: 0.8027 (tmtt) REVERT: A 63 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7633 (mt-10) REVERT: A 76 LYS cc_start: 0.8805 (ptpp) cc_final: 0.8555 (mttp) REVERT: B 23 SER cc_start: 0.9356 (m) cc_final: 0.9154 (m) REVERT: B 76 LYS cc_start: 0.8587 (mttt) cc_final: 0.8202 (mtmm) REVERT: B 117 SER cc_start: 0.9185 (p) cc_final: 0.8804 (m) REVERT: C 13 MET cc_start: 0.7592 (ttm) cc_final: 0.6311 (mpp) REVERT: D 13 MET cc_start: 0.7652 (ttm) cc_final: 0.6569 (mpp) REVERT: D 23 SER cc_start: 0.9351 (m) cc_final: 0.8921 (m) REVERT: E 13 MET cc_start: 0.7733 (ttm) cc_final: 0.6564 (mpp) REVERT: E 23 SER cc_start: 0.9407 (m) cc_final: 0.8684 (t) REVERT: E 93 VAL cc_start: 0.9234 (t) cc_final: 0.8875 (p) REVERT: F 13 MET cc_start: 0.8347 (ttm) cc_final: 0.7315 (mtm) REVERT: F 35 LYS cc_start: 0.8665 (tttt) cc_final: 0.8429 (mtpt) REVERT: F 63 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7260 (tt0) REVERT: F 92 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7195 (tm-30) outliers start: 20 outliers final: 12 residues processed: 110 average time/residue: 0.1180 time to fit residues: 17.5834 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 : 0.466 ------------------------------------------------------------------------------- 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 43 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 13 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: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.216604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.159962 restraints weight = 5000.950| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.21 r_work: 0.4096 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4416 Z= 0.220 Angle : 0.557 4.099 6006 Z= 0.317 Chirality : 0.051 0.143 708 Planarity : 0.004 0.028 738 Dihedral : 5.210 19.177 594 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 14.10 % 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: -2.34 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (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 0.021 0.002 PHE F 64 TYR 0.024 0.002 TYR B 114 ARG 0.001 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 104 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.519 Fit side-chains REVERT: A 35 LYS cc_start: 0.8382 (tttt) cc_final: 0.8051 (tmtt) REVERT: A 63 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 76 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8396 (mttp) REVERT: A 117 SER cc_start: 0.9077 (p) cc_final: 0.8791 (m) REVERT: B 78 TYR cc_start: 0.9018 (m-80) cc_final: 0.8660 (m-80) REVERT: C 13 MET cc_start: 0.7663 (ttm) cc_final: 0.6331 (mpp) REVERT: D 13 MET cc_start: 0.7696 (ttm) cc_final: 0.6604 (mpp) REVERT: D 23 SER cc_start: 0.9457 (m) cc_final: 0.8972 (m) REVERT: E 13 MET cc_start: 0.7755 (ttm) cc_final: 0.6563 (mpp) REVERT: E 23 SER cc_start: 0.9336 (m) cc_final: 0.8566 (t) REVERT: E 93 VAL cc_start: 0.9242 (t) cc_final: 0.8825 (p) REVERT: F 13 MET cc_start: 0.8397 (ttm) cc_final: 0.7331 (mtm) REVERT: F 92 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7122 (tm-30) outliers start: 10 outliers final: 9 residues processed: 99 average time/residue: 0.1354 time to fit residues: 17.8867 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 : 0.548 ------------------------------------------------------------------------------- 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 28 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 77 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.194560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.138561 restraints weight = 5100.676| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.73 r_work: 0.3935 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4416 Z= 0.303 Angle : 0.598 4.104 6006 Z= 0.340 Chirality : 0.052 0.150 708 Planarity : 0.004 0.029 738 Dihedral : 5.379 17.796 594 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.78 % Allowed : 14.10 % 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: -2.30 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.004 0.001 HIS A 31 PHE 0.023 0.003 PHE F 64 TYR 0.025 0.002 TYR B 114 ARG 0.002 0.001 ARG B 21 *********************** 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 100 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.472 Fit side-chains REVERT: A 13 MET cc_start: 0.7380 (ttp) cc_final: 0.6950 (ttt) REVERT: A 35 LYS cc_start: 0.8282 (tttt) cc_final: 0.7915 (tmtt) REVERT: A 63 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7483 (mt-10) REVERT: A 117 SER cc_start: 0.9032 (p) cc_final: 0.8789 (m) REVERT: B 76 LYS cc_start: 0.8408 (mttt) cc_final: 0.8079 (mtmm) REVERT: B 78 TYR cc_start: 0.8746 (m-80) cc_final: 0.8492 (m-80) REVERT: B 117 SER cc_start: 0.9298 (p) cc_final: 0.8649 (m) REVERT: C 13 MET cc_start: 0.7402 (ttm) cc_final: 0.6063 (mpp) REVERT: D 13 MET cc_start: 0.7537 (ttm) cc_final: 0.6361 (mpp) REVERT: D 23 SER cc_start: 0.9276 (m) cc_final: 0.8792 (m) REVERT: E 13 MET cc_start: 0.7575 (ttm) cc_final: 0.6292 (mpp) REVERT: E 23 SER cc_start: 0.9222 (m) cc_final: 0.8453 (t) REVERT: E 93 VAL cc_start: 0.9163 (t) cc_final: 0.8718 (p) REVERT: F 13 MET cc_start: 0.8361 (ttm) cc_final: 0.7168 (mpp) REVERT: F 92 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7114 (tm-30) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1200 time to fit residues: 15.7687 Evaluate side-chains 96 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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 28 VAL 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 46 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 16 optimal weight: 0.0980 chunk 10 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 overall best weight: 1.6782 ------------------------------------------------------------------------------- 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** F 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.197375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.140913 restraints weight = 5020.753| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 2.69 r_work: 0.3964 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4416 Z= 0.262 Angle : 0.569 4.044 6006 Z= 0.323 Chirality : 0.051 0.146 708 Planarity : 0.004 0.028 738 Dihedral : 5.309 19.436 594 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.35 % Allowed : 14.96 % 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: -2.34 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP F 79 HIS 0.003 0.001 HIS A 31 PHE 0.020 0.002 PHE E 64 TYR 0.025 0.002 TYR B 114 ARG 0.001 0.000 ARG E 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 103 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.436 Fit side-chains REVERT: A 13 MET cc_start: 0.7440 (ttp) cc_final: 0.7031 (ttt) REVERT: A 35 LYS cc_start: 0.8408 (tttt) cc_final: 0.8045 (tmtt) REVERT: A 63 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7662 (mt-10) REVERT: B 117 SER cc_start: 0.9265 (p) cc_final: 0.8625 (m) REVERT: C 13 MET cc_start: 0.7496 (ttm) cc_final: 0.6209 (mpp) REVERT: D 13 MET cc_start: 0.7599 (ttm) cc_final: 0.6463 (mpp) REVERT: D 23 SER cc_start: 0.9352 (m) cc_final: 0.8868 (m) REVERT: E 13 MET cc_start: 0.7675 (ttm) cc_final: 0.6429 (mpp) REVERT: E 23 SER cc_start: 0.9259 (m) cc_final: 0.8520 (t) REVERT: E 93 VAL cc_start: 0.9224 (t) cc_final: 0.8778 (p) REVERT: F 13 MET cc_start: 0.8377 (ttm) cc_final: 0.7272 (mpp) REVERT: F 92 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7168 (tm-30) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 0.1189 time to fit residues: 15.6805 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 : 0.438 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.147568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.115171 restraints weight = 5115.806| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 2.62 r_work: 0.3942 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3826 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4416 Z= 0.324 Angle : 0.611 4.220 6006 Z= 0.345 Chirality : 0.052 0.149 708 Planarity : 0.004 0.029 738 Dihedral : 5.415 19.459 594 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.14 % Allowed : 16.03 % Favored : 81.84 % 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: -2.39 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 79 HIS 0.004 0.001 HIS A 31 PHE 0.023 0.003 PHE E 64 TYR 0.023 0.002 TYR C 78 ARG 0.002 0.000 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: 10 poor density : 86 time to evaluate : 0.434 Fit side-chains REVERT: A 13 MET cc_start: 0.7543 (ttp) cc_final: 0.7104 (ttt) REVERT: A 35 LYS cc_start: 0.8300 (tttt) cc_final: 0.7960 (tmtt) REVERT: A 63 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7760 (mt-10) REVERT: B 117 SER cc_start: 0.9306 (p) cc_final: 0.8685 (m) REVERT: C 13 MET cc_start: 0.7581 (ttm) cc_final: 0.6252 (mpp) REVERT: D 13 MET cc_start: 0.7647 (ttm) cc_final: 0.6442 (mpp) REVERT: D 23 SER cc_start: 0.9343 (m) cc_final: 0.8821 (m) REVERT: E 13 MET cc_start: 0.7750 (ttm) cc_final: 0.6450 (mpp) REVERT: E 23 SER cc_start: 0.9266 (m) cc_final: 0.8524 (t) REVERT: E 93 VAL cc_start: 0.9250 (t) cc_final: 0.8792 (p) REVERT: F 13 MET cc_start: 0.8520 (ttm) cc_final: 0.7236 (mpt) REVERT: F 92 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7209 (tm-30) outliers start: 10 outliers final: 9 residues processed: 93 average time/residue: 0.1114 time to fit residues: 14.1578 Evaluate side-chains 91 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 19 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.147325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.115306 restraints weight = 5059.246| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.60 r_work: 0.3979 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3867 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4969 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= 0.312 Angle : 0.602 5.605 6006 Z= 0.340 Chirality : 0.052 0.157 708 Planarity : 0.004 0.032 738 Dihedral : 5.416 20.025 594 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.14 % Allowed : 16.45 % Favored : 81.41 % 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: -2.43 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 79 HIS 0.003 0.001 HIS A 31 PHE 0.024 0.002 PHE E 64 TYR 0.030 0.003 TYR C 78 ARG 0.002 0.000 ARG C 103 *********************** 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 93 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.481 Fit side-chains REVERT: A 13 MET cc_start: 0.7584 (ttp) cc_final: 0.7149 (ttt) REVERT: A 35 LYS cc_start: 0.8363 (tttt) cc_final: 0.7985 (tmtt) REVERT: A 63 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7796 (mt-10) REVERT: B 117 SER cc_start: 0.9306 (p) cc_final: 0.8737 (m) REVERT: C 13 MET cc_start: 0.7578 (ttm) cc_final: 0.6222 (mpp) REVERT: C 34 ARG cc_start: 0.7130 (ttt-90) cc_final: 0.6857 (tpp80) REVERT: D 13 MET cc_start: 0.7566 (ttm) cc_final: 0.6283 (mpp) REVERT: D 23 SER cc_start: 0.9351 (m) cc_final: 0.8828 (m) REVERT: E 13 MET cc_start: 0.7774 (ttm) cc_final: 0.6448 (mpp) REVERT: E 23 SER cc_start: 0.9258 (m) cc_final: 0.8511 (t) REVERT: F 13 MET cc_start: 0.8486 (ttm) cc_final: 0.7228 (mpt) REVERT: F 92 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7134 (tm-30) outliers start: 10 outliers final: 9 residues processed: 91 average time/residue: 0.1482 time to fit residues: 17.6663 Evaluate side-chains 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 52 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 overall best weight: 1.0920 ------------------------------------------------------------------------------- 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** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS E 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.200874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.151146 restraints weight = 5142.906| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 2.28 r_work: 0.4085 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4416 Z= 0.221 Angle : 0.566 4.757 6006 Z= 0.318 Chirality : 0.051 0.150 708 Planarity : 0.004 0.032 738 Dihedral : 5.227 19.559 594 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.50 % Allowed : 16.67 % Favored : 81.84 % 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: -2.46 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (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 0.025 0.002 PHE E 64 TYR 0.028 0.002 TYR C 78 ARG 0.001 0.000 ARG B 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: 7 poor density : 85 time to evaluate : 0.551 Fit side-chains REVERT: A 35 LYS cc_start: 0.8306 (tttt) cc_final: 0.7958 (tmtt) REVERT: A 63 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 117 SER cc_start: 0.9187 (p) cc_final: 0.8704 (m) REVERT: C 13 MET cc_start: 0.7663 (ttm) cc_final: 0.6355 (mpp) REVERT: C 34 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6898 (tpp80) REVERT: D 13 MET cc_start: 0.7700 (ttm) cc_final: 0.6482 (mpp) REVERT: D 23 SER cc_start: 0.9330 (m) cc_final: 0.8823 (m) REVERT: E 13 MET cc_start: 0.7968 (ttm) cc_final: 0.6667 (mpp) REVERT: E 23 SER cc_start: 0.9293 (m) cc_final: 0.8575 (t) REVERT: F 13 MET cc_start: 0.8516 (ttm) cc_final: 0.7352 (mpt) REVERT: F 92 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7264 (tm-30) outliers start: 7 outliers final: 7 residues processed: 90 average time/residue: 0.1778 time to fit residues: 20.9147 Evaluate side-chains 89 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.203307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.149911 restraints weight = 4909.813| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.27 r_work: 0.4071 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3956 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4416 Z= 0.245 Angle : 0.577 5.731 6006 Z= 0.324 Chirality : 0.051 0.151 708 Planarity : 0.004 0.031 738 Dihedral : 5.188 19.237 594 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.71 % Allowed : 16.24 % Favored : 82.05 % 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: -2.46 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 79 HIS 0.002 0.001 HIS A 31 PHE 0.024 0.002 PHE E 64 TYR 0.035 0.003 TYR C 78 ARG 0.001 0.000 ARG C 21 ********************** 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 88 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.396 Fit side-chains REVERT: A 35 LYS cc_start: 0.8335 (tttt) cc_final: 0.7980 (tmtt) REVERT: A 63 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7782 (mt-10) REVERT: B 92 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 117 SER cc_start: 0.9181 (p) cc_final: 0.8686 (m) REVERT: C 13 MET cc_start: 0.7648 (ttm) cc_final: 0.6298 (mpp) REVERT: C 34 ARG cc_start: 0.7211 (ttt-90) cc_final: 0.6918 (tpp80) REVERT: D 13 MET cc_start: 0.7658 (ttm) cc_final: 0.6461 (mpp) REVERT: D 23 SER cc_start: 0.9336 (m) cc_final: 0.8833 (m) REVERT: E 13 MET cc_start: 0.7967 (ttm) cc_final: 0.6651 (mpp) REVERT: E 23 SER cc_start: 0.9288 (m) cc_final: 0.8572 (t) REVERT: F 13 MET cc_start: 0.8511 (ttm) cc_final: 0.7354 (mpt) REVERT: F 92 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7261 (tm-30) outliers start: 8 outliers final: 5 residues processed: 86 average time/residue: 0.2299 time to fit residues: 26.9571 Evaluate side-chains 86 residues out of total 468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain C residue 23 SER Chi-restraints excluded: chain C residue 28 VAL 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 2 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.205110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.150113 restraints weight = 4962.130| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.28 r_work: 0.4076 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4416 Z= 0.257 Angle : 0.582 5.596 6006 Z= 0.327 Chirality : 0.051 0.145 708 Planarity : 0.004 0.031 738 Dihedral : 5.185 19.405 594 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.07 % Allowed : 16.67 % Favored : 82.26 % 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: -2.46 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.002 0.001 HIS A 31 PHE 0.024 0.002 PHE E 64 TYR 0.033 0.003 TYR C 78 ARG 0.002 0.000 ARG C 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2557.73 seconds wall clock time: 46 minutes 40.04 seconds (2800.04 seconds total)