Starting phenix.real_space_refine on Fri Dec 27 13:01:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xyq_10652/12_2024/6xyq_10652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xyq_10652/12_2024/6xyq_10652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xyq_10652/12_2024/6xyq_10652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xyq_10652/12_2024/6xyq_10652.map" model { file = "/net/cci-nas-00/data/ceres_data/6xyq_10652/12_2024/6xyq_10652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xyq_10652/12_2024/6xyq_10652.cif" } resolution = 3.09 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= 0.001 sd= 0.007 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: 3 Type Number sf(0) Gaussians C 3085 2.51 5 N 865 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 4955 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "B" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 442 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Restraints were copied for chains: D, F, H, J, C, E, G, I Time building chain proxies: 2.23, per 1000 atoms: 0.45 Number of scatterers: 4955 At special positions: 0 Unit cell: (106.95, 80.5, 42.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1005 8.00 N 865 7.00 C 3085 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: 1.19 Conformation dependent library (CDL) restraints added in 618.8 milliseconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 20 removed outlier: 6.725A pdb=" N ALA C 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 6.488A pdb=" N VAL G 26 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA I 29 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU G 28 " --> pdb=" O ALA I 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 34 removed outlier: 6.800A pdb=" N THR A 33 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR G 33 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.421A pdb=" N LEU A 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU G 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 45 through 48 removed outlier: 8.182A pdb=" N GLU C 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL E 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N GLU A 46 " --> pdb=" O GLY I 47 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL I 49 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N VAL A 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL I 48 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 49 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS I 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.517A pdb=" N THR C 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLN E 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU C 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR A 59 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLN I 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU A 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.687A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 81 removed outlier: 6.333A pdb=" N ALA C 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLN E 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA A 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLN I 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA A 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N THR I 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS A 80 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 89 through 92 removed outlier: 6.293A pdb=" N ALA A 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N THR E 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ALA A 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA G 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR I 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA G 91 " --> pdb=" O THR I 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.436A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU H 38 " --> pdb=" O TYR J 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 52 removed outlier: 9.005A pdb=" N LYS D 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL F 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS F 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL D 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL F 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY D 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU B 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY F 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL J 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS B 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY J 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 56 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA D 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 52 removed outlier: 9.005A pdb=" N LYS D 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL F 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS F 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL D 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL F 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLY D 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU B 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLY F 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL J 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS B 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY J 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLU H 46 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N VAL J 49 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL H 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY J 51 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N HIS H 50 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA J 53 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL H 52 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 10.008A pdb=" N VAL J 55 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR H 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N GLU J 57 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ALA H 56 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 62 through 66 removed outlier: 6.118A pdb=" N GLN B 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN F 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR B 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN H 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASN J 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.399A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.208A pdb=" N ALA D 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA B 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.687A pdb=" N THR D 81 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 81 " --> pdb=" O VAL J 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 94 through 96 removed outlier: 6.331A pdb=" N VAL B 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL H 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) 103 hydrogen bonds defined for protein. 309 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: 1.26 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 885 1.29 - 1.35: 775 1.35 - 1.41: 173 1.41 - 1.48: 827 1.48 - 1.54: 2315 Bond restraints: 4975 Sorted by residual: bond pdb=" CB VAL E 49 " pdb=" CG2 VAL E 49 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.01e+00 bond pdb=" CB VAL G 49 " pdb=" CG2 VAL G 49 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.00e+00 bond pdb=" CB VAL I 49 " pdb=" CG2 VAL I 49 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.98e+00 bond pdb=" CB VAL C 49 " pdb=" CG2 VAL C 49 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CB VAL A 49 " pdb=" CG2 VAL A 49 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 ... (remaining 4970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 6091 1.14 - 2.27: 534 2.27 - 3.41: 80 3.41 - 4.55: 10 4.55 - 5.68: 5 Bond angle restraints: 6720 Sorted by residual: angle pdb=" C GLN I 24 " pdb=" N GLY I 25 " pdb=" CA GLY I 25 " ideal model delta sigma weight residual 122.18 119.60 2.58 6.90e-01 2.10e+00 1.40e+01 angle pdb=" C GLN G 24 " pdb=" N GLY G 25 " pdb=" CA GLY G 25 " ideal model delta sigma weight residual 122.18 119.60 2.58 6.90e-01 2.10e+00 1.39e+01 angle pdb=" C GLN E 24 " pdb=" N GLY E 25 " pdb=" CA GLY E 25 " ideal model delta sigma weight residual 122.18 119.60 2.58 6.90e-01 2.10e+00 1.39e+01 angle pdb=" C GLN C 24 " pdb=" N GLY C 25 " pdb=" CA GLY C 25 " ideal model delta sigma weight residual 122.18 119.61 2.57 6.90e-01 2.10e+00 1.39e+01 angle pdb=" C GLN A 24 " pdb=" N GLY A 25 " pdb=" CA GLY A 25 " ideal model delta sigma weight residual 122.18 119.63 2.55 6.90e-01 2.10e+00 1.37e+01 ... (remaining 6715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 2590 13.92 - 27.84: 230 27.84 - 41.76: 70 41.76 - 55.67: 5 55.67 - 69.59: 15 Dihedral angle restraints: 2910 sinusoidal: 965 harmonic: 1945 Sorted by residual: dihedral pdb=" CA ALA G 78 " pdb=" C ALA G 78 " pdb=" N GLN G 79 " pdb=" CA GLN G 79 " ideal model delta harmonic sigma weight residual 180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ALA I 78 " pdb=" C ALA I 78 " pdb=" N GLN I 79 " pdb=" CA GLN I 79 " ideal model delta harmonic sigma weight residual -180.00 -163.54 -16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ALA C 78 " pdb=" C ALA C 78 " pdb=" N GLN C 79 " pdb=" CA GLN C 79 " ideal model delta harmonic sigma weight residual -180.00 -163.56 -16.44 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 2907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 556 0.043 - 0.086: 177 0.086 - 0.129: 132 0.129 - 0.172: 0 0.172 - 0.215: 5 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB VAL E 49 " pdb=" CA VAL E 49 " pdb=" CG1 VAL E 49 " pdb=" CG2 VAL E 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL I 49 " pdb=" CA VAL I 49 " pdb=" CG1 VAL I 49 " pdb=" CG2 VAL I 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB VAL A 49 " pdb=" CA VAL A 49 " pdb=" CG1 VAL A 49 " pdb=" CG2 VAL A 49 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 867 not shown) Planarity restraints: 845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 39 " 0.010 2.00e-02 2.50e+03 6.47e-03 8.37e-01 pdb=" CG TYR I 39 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR I 39 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR I 39 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR I 39 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR I 39 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR I 39 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 39 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 39 " 0.010 2.00e-02 2.50e+03 6.42e-03 8.25e-01 pdb=" CG TYR A 39 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 39 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 39 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 39 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 39 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 39 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 39 " 0.010 2.00e-02 2.50e+03 6.33e-03 8.01e-01 pdb=" CG TYR G 39 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR G 39 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR G 39 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR G 39 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR G 39 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G 39 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 39 " 0.001 2.00e-02 2.50e+03 ... (remaining 842 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 146 2.68 - 3.24: 4539 3.24 - 3.79: 7372 3.79 - 4.35: 10126 4.35 - 4.90: 18913 Nonbonded interactions: 41096 Sorted by model distance: nonbonded pdb=" NZ LYS H 60 " pdb=" OE1 GLU I 28 " model vdw 2.130 3.120 nonbonded pdb=" OE1 GLU C 28 " pdb=" NZ LYS F 60 " model vdw 2.176 3.120 nonbonded pdb=" O GLY H 84 " pdb=" OG SER H 87 " model vdw 2.226 3.040 nonbonded pdb=" O GLY D 84 " pdb=" OG SER D 87 " model vdw 2.227 3.040 nonbonded pdb=" O GLY F 84 " pdb=" OG SER F 87 " model vdw 2.227 3.040 ... (remaining 41091 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } 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: 0.730 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.540 Find NCS groups from input model: 0.170 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.007 0.047 4975 Z= 0.490 Angle : 0.706 5.682 6720 Z= 0.457 Chirality : 0.053 0.215 870 Planarity : 0.002 0.008 845 Dihedral : 12.970 69.593 1690 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: -4.52 (0.22), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.17), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.004 0.001 PHE B 94 TYR 0.014 0.003 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8330 (mp0) cc_final: 0.8027 (mp0) REVERT: A 35 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 60 LYS cc_start: 0.8065 (tttt) cc_final: 0.7601 (ttmt) REVERT: C 23 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7530 (mtpt) REVERT: C 60 LYS cc_start: 0.8724 (tttt) cc_final: 0.8405 (ttmt) REVERT: D 88 ILE cc_start: 0.9004 (mp) cc_final: 0.8785 (mt) REVERT: E 23 LYS cc_start: 0.7817 (ttmt) cc_final: 0.7481 (mtpt) REVERT: E 43 LYS cc_start: 0.8300 (mttt) cc_final: 0.7811 (mttp) REVERT: E 60 LYS cc_start: 0.8058 (tttt) cc_final: 0.7171 (tptp) REVERT: F 62 GLN cc_start: 0.8710 (mt0) cc_final: 0.8450 (mt0) REVERT: G 20 GLU cc_start: 0.7856 (mp0) cc_final: 0.7115 (mp0) REVERT: G 60 LYS cc_start: 0.8121 (tttt) cc_final: 0.7262 (tmtt) REVERT: H 60 LYS cc_start: 0.9024 (mppt) cc_final: 0.8739 (mptt) REVERT: H 88 ILE cc_start: 0.9060 (mp) cc_final: 0.8857 (mt) REVERT: I 35 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7454 (mm-30) REVERT: I 60 LYS cc_start: 0.8132 (tttt) cc_final: 0.7361 (tmtt) REVERT: J 46 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7946 (mt-10) REVERT: J 65 ASN cc_start: 0.8897 (t0) cc_final: 0.8592 (t0) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2341 time to fit residues: 26.2719 Evaluate side-chains 82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 65 ASN B 99 GLN C 50 HIS G 50 HIS H 50 HIS I 50 HIS J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4975 Z= 0.438 Angle : 0.540 5.957 6720 Z= 0.302 Chirality : 0.052 0.129 870 Planarity : 0.002 0.007 845 Dihedral : 4.972 17.768 725 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.02 % Allowed : 9.59 % Favored : 89.39 % 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: -4.27 (0.23), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.25 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS J 50 PHE 0.003 0.001 PHE F 94 TYR 0.017 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 60 LYS cc_start: 0.7927 (tttt) cc_final: 0.7451 (ttmt) REVERT: C 60 LYS cc_start: 0.8649 (tttt) cc_final: 0.8291 (ttmt) REVERT: D 88 ILE cc_start: 0.9029 (mp) cc_final: 0.8791 (mt) REVERT: E 60 LYS cc_start: 0.8094 (tttt) cc_final: 0.7224 (tptp) REVERT: F 62 GLN cc_start: 0.8734 (mt0) cc_final: 0.8522 (mt0) REVERT: F 65 ASN cc_start: 0.9038 (t0) cc_final: 0.8786 (t0) REVERT: G 58 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8046 (ttmt) REVERT: I 35 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7538 (mm-30) REVERT: I 60 LYS cc_start: 0.8202 (tttt) cc_final: 0.7963 (ttmt) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.2424 time to fit residues: 26.8682 Evaluate side-chains 84 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 63 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS B 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS D 65 ASN G 50 HIS H 50 HIS I 50 HIS J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4975 Z= 0.144 Angle : 0.412 5.062 6720 Z= 0.230 Chirality : 0.050 0.122 870 Planarity : 0.001 0.009 845 Dihedral : 4.405 14.428 725 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.22 % Allowed : 11.84 % Favored : 86.94 % 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: -3.95 (0.24), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS J 50 PHE 0.004 0.001 PHE J 94 TYR 0.008 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7634 (mm-30) REVERT: A 60 LYS cc_start: 0.7916 (tttt) cc_final: 0.7443 (ttmt) REVERT: C 57 GLU cc_start: 0.7883 (tt0) cc_final: 0.7558 (pm20) REVERT: C 60 LYS cc_start: 0.8527 (tttt) cc_final: 0.8193 (ttmt) REVERT: D 88 ILE cc_start: 0.9037 (mp) cc_final: 0.8818 (mt) REVERT: E 60 LYS cc_start: 0.8080 (tttt) cc_final: 0.7238 (tptp) REVERT: I 35 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7539 (mm-30) REVERT: I 60 LYS cc_start: 0.8203 (tttt) cc_final: 0.7950 (ttmt) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.2075 time to fit residues: 20.6277 Evaluate side-chains 81 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN F 50 HIS G 50 HIS H 50 HIS I 50 HIS J 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 4975 Z= 0.502 Angle : 0.538 6.123 6720 Z= 0.304 Chirality : 0.052 0.132 870 Planarity : 0.002 0.008 845 Dihedral : 4.820 16.925 725 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.86 % Allowed : 12.65 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.25), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS H 50 PHE 0.002 0.001 PHE J 94 TYR 0.019 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8221 (mp0) cc_final: 0.7803 (mp0) REVERT: A 35 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7604 (mm-30) REVERT: A 60 LYS cc_start: 0.7954 (tttt) cc_final: 0.7493 (ttmt) REVERT: C 60 LYS cc_start: 0.8546 (tttt) cc_final: 0.8186 (ttmt) REVERT: D 88 ILE cc_start: 0.9019 (mp) cc_final: 0.8786 (mt) REVERT: E 60 LYS cc_start: 0.8112 (tttt) cc_final: 0.7240 (tptp) REVERT: G 58 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8072 (ttmt) REVERT: I 35 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7555 (mm-30) REVERT: I 60 LYS cc_start: 0.8199 (tttt) cc_final: 0.7957 (ttmt) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 0.2092 time to fit residues: 23.4972 Evaluate side-chains 93 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 99 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 57 optimal weight: 0.0870 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS G 50 HIS H 50 HIS I 50 HIS J 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4975 Z= 0.223 Angle : 0.433 5.691 6720 Z= 0.243 Chirality : 0.050 0.123 870 Planarity : 0.001 0.011 845 Dihedral : 4.471 15.341 725 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.45 % Allowed : 14.29 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.67 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS H 50 PHE 0.004 0.001 PHE J 94 TYR 0.011 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8190 (mp0) cc_final: 0.7782 (mp0) REVERT: A 35 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 60 LYS cc_start: 0.7920 (tttt) cc_final: 0.7449 (ttmt) REVERT: C 57 GLU cc_start: 0.7784 (tt0) cc_final: 0.7391 (pm20) REVERT: C 60 LYS cc_start: 0.8479 (tttt) cc_final: 0.8166 (ttmt) REVERT: D 88 ILE cc_start: 0.9084 (mp) cc_final: 0.8819 (mt) REVERT: E 60 LYS cc_start: 0.8089 (tttt) cc_final: 0.7201 (tptp) REVERT: I 35 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7573 (mm-30) REVERT: I 60 LYS cc_start: 0.8188 (tttt) cc_final: 0.7948 (ttmt) outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.2465 time to fit residues: 24.3002 Evaluate side-chains 82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain I residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.2980 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 22 optimal weight: 0.0000 chunk 35 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS I 50 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4975 Z= 0.243 Angle : 0.430 5.349 6720 Z= 0.241 Chirality : 0.049 0.123 870 Planarity : 0.001 0.007 845 Dihedral : 4.364 14.727 725 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.24 % Allowed : 14.49 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.54 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 50 PHE 0.004 0.001 PHE J 94 TYR 0.012 0.002 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8208 (mp0) cc_final: 0.7812 (mp0) REVERT: A 35 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7593 (mm-30) REVERT: A 60 LYS cc_start: 0.7866 (tttt) cc_final: 0.7407 (ttmt) REVERT: C 57 GLU cc_start: 0.7821 (tt0) cc_final: 0.7483 (pm20) REVERT: C 60 LYS cc_start: 0.8488 (tttt) cc_final: 0.8110 (ttmt) REVERT: D 88 ILE cc_start: 0.9089 (mp) cc_final: 0.8821 (mt) REVERT: E 60 LYS cc_start: 0.8089 (tttt) cc_final: 0.7205 (tptp) REVERT: I 35 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7564 (mm-30) REVERT: I 60 LYS cc_start: 0.8184 (tttt) cc_final: 0.7929 (ttmt) outliers start: 11 outliers final: 9 residues processed: 78 average time/residue: 0.2230 time to fit residues: 21.4636 Evaluate side-chains 82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain I residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS I 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 4975 Z= 0.389 Angle : 0.489 5.791 6720 Z= 0.275 Chirality : 0.050 0.128 870 Planarity : 0.002 0.008 845 Dihedral : 4.582 15.859 725 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.24 % Allowed : 15.31 % Favored : 82.45 % 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: -3.55 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 50 PHE 0.003 0.001 PHE J 94 TYR 0.018 0.003 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8158 (mp0) cc_final: 0.7746 (mp0) REVERT: A 35 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 60 LYS cc_start: 0.7953 (tttt) cc_final: 0.7493 (ttmt) REVERT: C 57 GLU cc_start: 0.7760 (tt0) cc_final: 0.7389 (pm20) REVERT: C 60 LYS cc_start: 0.8450 (tttt) cc_final: 0.8208 (ttmt) REVERT: D 88 ILE cc_start: 0.9052 (mp) cc_final: 0.8795 (mt) REVERT: E 60 LYS cc_start: 0.8094 (tttt) cc_final: 0.7205 (tptp) REVERT: F 62 GLN cc_start: 0.8946 (mt0) cc_final: 0.8431 (mt0) REVERT: G 58 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8084 (ttmt) REVERT: I 35 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7044 (mm-30) REVERT: I 60 LYS cc_start: 0.8165 (tttt) cc_final: 0.7909 (ttmt) outliers start: 11 outliers final: 10 residues processed: 85 average time/residue: 0.2121 time to fit residues: 22.3961 Evaluate side-chains 87 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain I residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS G 50 HIS I 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4975 Z= 0.316 Angle : 0.460 5.432 6720 Z= 0.258 Chirality : 0.050 0.126 870 Planarity : 0.002 0.006 845 Dihedral : 4.482 15.375 725 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.45 % Allowed : 15.31 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 50 PHE 0.004 0.001 PHE J 94 TYR 0.014 0.003 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8151 (mp0) cc_final: 0.7733 (mp0) REVERT: A 35 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 60 LYS cc_start: 0.7952 (tttt) cc_final: 0.7492 (ttmt) REVERT: C 35 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7362 (mm-30) REVERT: C 57 GLU cc_start: 0.7846 (tt0) cc_final: 0.7515 (pm20) REVERT: C 60 LYS cc_start: 0.8448 (tttt) cc_final: 0.8199 (ttmt) REVERT: D 88 ILE cc_start: 0.9116 (mp) cc_final: 0.8842 (mt) REVERT: E 60 LYS cc_start: 0.8092 (tttt) cc_final: 0.7208 (tptp) REVERT: I 35 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7056 (mm-30) REVERT: I 60 LYS cc_start: 0.8162 (tttt) cc_final: 0.7909 (ttmt) outliers start: 12 outliers final: 12 residues processed: 81 average time/residue: 0.2602 time to fit residues: 25.8356 Evaluate side-chains 85 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 50 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 HIS G 50 HIS I 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4975 Z= 0.356 Angle : 0.482 5.491 6720 Z= 0.271 Chirality : 0.050 0.126 870 Planarity : 0.002 0.009 845 Dihedral : 4.506 15.472 725 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.86 % Allowed : 15.10 % Favored : 82.04 % 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: -3.51 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS I 50 PHE 0.004 0.001 PHE J 94 TYR 0.016 0.003 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8161 (mp0) cc_final: 0.7756 (mp0) REVERT: A 35 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7607 (mm-30) REVERT: A 60 LYS cc_start: 0.7953 (tttt) cc_final: 0.7493 (ttmt) REVERT: C 57 GLU cc_start: 0.7844 (tt0) cc_final: 0.7513 (pm20) REVERT: C 60 LYS cc_start: 0.8453 (tttt) cc_final: 0.8200 (ttmt) REVERT: D 88 ILE cc_start: 0.9105 (mp) cc_final: 0.8833 (mt) REVERT: E 60 LYS cc_start: 0.8098 (tttt) cc_final: 0.7214 (tptp) REVERT: G 58 LYS cc_start: 0.8455 (mtpt) cc_final: 0.8097 (ttmt) REVERT: I 35 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7051 (mm-30) REVERT: I 60 LYS cc_start: 0.8160 (tttt) cc_final: 0.7904 (ttmt) REVERT: J 62 GLN cc_start: 0.8722 (mt0) cc_final: 0.8493 (mt0) outliers start: 14 outliers final: 11 residues processed: 84 average time/residue: 0.2190 time to fit residues: 22.6248 Evaluate side-chains 85 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain I residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS I 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 4975 Z= 0.118 Angle : 0.398 6.194 6720 Z= 0.223 Chirality : 0.049 0.123 870 Planarity : 0.001 0.006 845 Dihedral : 4.081 13.204 725 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.04 % Allowed : 15.92 % Favored : 82.04 % 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: -3.36 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS I 50 PHE 0.005 0.001 PHE J 94 TYR 0.006 0.001 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8193 (mp0) cc_final: 0.7803 (mp0) REVERT: A 35 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 60 LYS cc_start: 0.7870 (tttt) cc_final: 0.7395 (ttmt) REVERT: C 60 LYS cc_start: 0.8425 (tttt) cc_final: 0.8112 (ttmt) REVERT: D 88 ILE cc_start: 0.9087 (mp) cc_final: 0.8833 (mt) REVERT: E 60 LYS cc_start: 0.8098 (tttt) cc_final: 0.7215 (tptp) REVERT: H 62 GLN cc_start: 0.8785 (mt0) cc_final: 0.8479 (mt0) REVERT: I 35 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7582 (mm-30) REVERT: I 60 LYS cc_start: 0.8187 (tttt) cc_final: 0.7914 (ttmt) outliers start: 10 outliers final: 4 residues processed: 74 average time/residue: 0.1867 time to fit residues: 17.6009 Evaluate side-chains 70 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain I residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS B 62 GLN G 50 HIS I 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.131557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.107685 restraints weight = 5115.179| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.45 r_work: 0.3279 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 4975 Z= 0.451 Angle : 0.534 5.583 6720 Z= 0.297 Chirality : 0.051 0.129 870 Planarity : 0.002 0.007 845 Dihedral : 4.547 15.512 725 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.63 % Allowed : 16.53 % 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: -3.42 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS I 50 PHE 0.003 0.001 PHE J 94 TYR 0.018 0.003 TYR G 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1450.80 seconds wall clock time: 27 minutes 7.00 seconds (1627.00 seconds total)