Starting phenix.real_space_refine on Tue Feb 11 08:51:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xyq_10652/02_2025/6xyq_10652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xyq_10652/02_2025/6xyq_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_10652/02_2025/6xyq_10652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xyq_10652/02_2025/6xyq_10652.map" model { file = "/net/cci-nas-00/data/ceres_data/6xyq_10652/02_2025/6xyq_10652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xyq_10652/02_2025/6xyq_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-5592/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: 2.08, per 1000 atoms: 0.42 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: 1.05 Conformation dependent library (CDL) restraints added in 691.3 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: 0.94 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: 1.51 Time building geometry restraints manager: 1.24 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.670 Find NCS groups from input model: 0.110 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- 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 : 0.540 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: 0.2422 time to fit residues: 27.0154 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 : 0.496 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.110484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083832 restraints weight = 5777.566| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.86 r_work: 0.3192 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 60 LYS cc_start: 0.7786 (tttt) cc_final: 0.7301 (ttmt) REVERT: C 60 LYS cc_start: 0.8649 (tttt) cc_final: 0.8250 (ttmt) REVERT: D 88 ILE cc_start: 0.8997 (mp) cc_final: 0.8743 (mt) REVERT: E 35 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7825 (mm-30) REVERT: E 60 LYS cc_start: 0.7987 (tttt) cc_final: 0.7046 (tptp) REVERT: F 65 ASN cc_start: 0.9158 (t0) cc_final: 0.8933 (t0) REVERT: G 20 GLU cc_start: 0.7868 (mp0) cc_final: 0.7660 (mp0) REVERT: G 58 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7871 (ttmt) REVERT: I 35 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7725 (mm-30) REVERT: I 60 LYS cc_start: 0.8012 (tttt) cc_final: 0.7752 (ttmt) outliers start: 5 outliers final: 3 residues processed: 89 average time/residue: 0.2260 time to fit residues: 24.5616 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 : 0.731 ------------------------------------------------------------------------------- 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 32 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 B 99 GLN C 50 HIS D 65 ASN F 50 HIS F 62 GLN G 50 HIS H 50 HIS H 62 GLN I 50 HIS J 50 HIS J 62 GLN J 99 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.108144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081875 restraints weight = 5912.055| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.87 r_work: 0.3139 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 4975 Z= 0.603 Angle : 0.604 6.806 6720 Z= 0.340 Chirality : 0.054 0.135 870 Planarity : 0.002 0.009 845 Dihedral : 5.117 18.768 725 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.45 % Allowed : 12.86 % Favored : 84.69 % 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: -4.13 (0.24), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS J 50 PHE 0.003 0.001 PHE A 94 TYR 0.021 0.004 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 99 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8155 (mp0) cc_final: 0.7690 (mp0) REVERT: A 32 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7836 (mtpp) REVERT: A 35 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 60 LYS cc_start: 0.7777 (tttt) cc_final: 0.7307 (ttmt) REVERT: C 60 LYS cc_start: 0.8659 (tttt) cc_final: 0.8242 (ttmt) REVERT: D 88 ILE cc_start: 0.9015 (mp) cc_final: 0.8758 (mt) REVERT: E 35 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7756 (mm-30) REVERT: E 60 LYS cc_start: 0.8010 (tttt) cc_final: 0.7064 (tptp) REVERT: F 65 ASN cc_start: 0.9297 (t0) cc_final: 0.9063 (t0) REVERT: G 50 HIS cc_start: 0.8523 (OUTLIER) cc_final: 0.8284 (t-170) REVERT: G 58 LYS cc_start: 0.8296 (mtpt) cc_final: 0.7937 (ttmt) REVERT: I 35 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7717 (mm-30) REVERT: I 60 LYS cc_start: 0.8012 (tttt) cc_final: 0.7752 (ttmt) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.2292 time to fit residues: 25.6474 Evaluate side-chains 96 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 99 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 E 24 GLN F 50 HIS G 50 HIS H 50 HIS ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.119684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.094603 restraints weight = 5520.748| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.67 r_work: 0.3197 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4975 Z= 0.257 Angle : 0.459 6.230 6720 Z= 0.256 Chirality : 0.050 0.125 870 Planarity : 0.002 0.009 845 Dihedral : 4.652 16.305 725 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.06 % Allowed : 14.90 % 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: -3.91 (0.25), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS H 50 PHE 0.004 0.001 PHE J 94 TYR 0.011 0.002 TYR C 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 95 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8166 (mp0) cc_final: 0.7692 (mp0) REVERT: A 35 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7793 (mm-30) REVERT: A 60 LYS cc_start: 0.7760 (tttt) cc_final: 0.7312 (ttmt) REVERT: C 57 GLU cc_start: 0.8234 (tt0) cc_final: 0.7436 (pm20) REVERT: C 60 LYS cc_start: 0.8565 (tttt) cc_final: 0.8175 (ttmt) REVERT: D 88 ILE cc_start: 0.8987 (mp) cc_final: 0.8785 (mt) REVERT: E 35 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7795 (mm-30) REVERT: E 60 LYS cc_start: 0.8010 (tttt) cc_final: 0.7095 (tptp) REVERT: I 35 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7686 (mm-30) REVERT: I 60 LYS cc_start: 0.8031 (tttt) cc_final: 0.7801 (ttmt) outliers start: 15 outliers final: 7 residues processed: 89 average time/residue: 0.2119 time to fit residues: 23.1883 Evaluate side-chains 85 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.108544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.082488 restraints weight = 5961.854| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.89 r_work: 0.3147 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 4975 Z= 0.431 Angle : 0.514 6.445 6720 Z= 0.289 Chirality : 0.051 0.129 870 Planarity : 0.002 0.011 845 Dihedral : 4.766 16.866 725 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.45 % Allowed : 16.33 % Favored : 81.22 % 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: -3.84 (0.25), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS J 50 PHE 0.003 0.001 PHE J 94 TYR 0.017 0.003 TYR G 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 97 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8201 (mp0) cc_final: 0.7697 (mp0) REVERT: A 23 LYS cc_start: 0.7624 (ttmt) cc_final: 0.7284 (mtpt) REVERT: A 35 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7807 (mm-30) REVERT: A 60 LYS cc_start: 0.7751 (tttt) cc_final: 0.7308 (ttmt) REVERT: B 62 GLN cc_start: 0.9041 (mt0) cc_final: 0.8789 (mt0) REVERT: C 57 GLU cc_start: 0.8218 (tt0) cc_final: 0.7424 (pm20) REVERT: C 60 LYS cc_start: 0.8502 (tttt) cc_final: 0.8140 (ttmt) REVERT: D 88 ILE cc_start: 0.8947 (mp) cc_final: 0.8727 (mt) REVERT: E 60 LYS cc_start: 0.8001 (tttt) cc_final: 0.7051 (tptp) REVERT: G 58 LYS cc_start: 0.8330 (mtpt) cc_final: 0.7957 (ttmt) REVERT: I 35 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7714 (mm-30) REVERT: I 60 LYS cc_start: 0.7996 (tttt) cc_final: 0.7765 (ttmt) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.2230 time to fit residues: 24.9130 Evaluate side-chains 94 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 61 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 8 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 C 50 HIS G 50 HIS I 50 HIS J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083849 restraints weight = 5859.459| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.92 r_work: 0.3188 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4975 Z= 0.359 Angle : 0.496 6.228 6720 Z= 0.277 Chirality : 0.050 0.127 870 Planarity : 0.002 0.012 845 Dihedral : 4.673 16.464 725 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.45 % Allowed : 16.12 % Favored : 81.43 % 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: -3.74 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS J 50 PHE 0.004 0.001 PHE J 94 TYR 0.015 0.003 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 94 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8154 (mp0) cc_final: 0.7639 (mp0) REVERT: A 23 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7260 (mtpt) REVERT: A 35 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7767 (mm-30) REVERT: A 60 LYS cc_start: 0.7752 (tttt) cc_final: 0.7290 (ttmt) REVERT: C 57 GLU cc_start: 0.8227 (tt0) cc_final: 0.7399 (pm20) REVERT: C 60 LYS cc_start: 0.8473 (tttt) cc_final: 0.8109 (ttmt) REVERT: D 88 ILE cc_start: 0.9025 (mp) cc_final: 0.8755 (mt) REVERT: E 60 LYS cc_start: 0.7964 (tttt) cc_final: 0.6995 (tptp) REVERT: G 58 LYS cc_start: 0.8285 (mtpt) cc_final: 0.7913 (ttmt) REVERT: I 35 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7202 (mm-30) REVERT: I 60 LYS cc_start: 0.7962 (tttt) cc_final: 0.7705 (ttmt) outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.2193 time to fit residues: 23.6230 Evaluate side-chains 90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 16 optimal weight: 0.4980 chunk 46 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS E 50 HIS G 50 HIS ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.118769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.093569 restraints weight = 5419.254| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.66 r_work: 0.3192 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4975 Z= 0.307 Angle : 0.477 5.960 6720 Z= 0.266 Chirality : 0.050 0.125 870 Planarity : 0.002 0.009 845 Dihedral : 4.569 16.081 725 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.24 % Allowed : 16.33 % Favored : 81.43 % 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: -3.65 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS J 50 PHE 0.004 0.001 PHE F 94 TYR 0.014 0.002 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 : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8193 (mp0) cc_final: 0.7692 (mp0) REVERT: A 23 LYS cc_start: 0.7500 (ttmt) cc_final: 0.7141 (mtpt) REVERT: A 35 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 60 LYS cc_start: 0.7699 (tttt) cc_final: 0.7257 (ttmt) REVERT: C 57 GLU cc_start: 0.8186 (tt0) cc_final: 0.7377 (pm20) REVERT: C 60 LYS cc_start: 0.8451 (tttt) cc_final: 0.8120 (ttmt) REVERT: D 88 ILE cc_start: 0.8987 (mp) cc_final: 0.8722 (mt) REVERT: E 60 LYS cc_start: 0.7956 (tttt) cc_final: 0.6989 (tptp) REVERT: G 58 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7972 (ttmt) REVERT: I 35 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7152 (mm-30) REVERT: I 60 LYS cc_start: 0.7943 (tttt) cc_final: 0.7710 (ttmt) outliers start: 11 outliers final: 10 residues processed: 84 average time/residue: 0.2415 time to fit residues: 24.7957 Evaluate side-chains 89 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 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 J residue 50 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 HIS ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.110609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084658 restraints weight = 5831.685| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.88 r_work: 0.3210 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4975 Z= 0.300 Angle : 0.476 5.865 6720 Z= 0.266 Chirality : 0.050 0.126 870 Planarity : 0.002 0.010 845 Dihedral : 4.514 15.654 725 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.24 % Allowed : 16.73 % Favored : 81.02 % 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: -3.59 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS J 50 PHE 0.004 0.001 PHE J 94 TYR 0.013 0.002 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 87 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8157 (mp0) cc_final: 0.7648 (mp0) REVERT: A 23 LYS cc_start: 0.7529 (ttmt) cc_final: 0.7198 (mtpt) REVERT: A 35 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 60 LYS cc_start: 0.7750 (tttt) cc_final: 0.7285 (ttmt) REVERT: C 57 GLU cc_start: 0.8324 (tt0) cc_final: 0.7506 (pm20) REVERT: C 60 LYS cc_start: 0.8438 (tttt) cc_final: 0.8151 (ttmt) REVERT: D 88 ILE cc_start: 0.9061 (mp) cc_final: 0.8784 (mt) REVERT: E 60 LYS cc_start: 0.7954 (tttt) cc_final: 0.6995 (tptp) REVERT: I 35 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7192 (mm-30) REVERT: I 60 LYS cc_start: 0.7954 (tttt) cc_final: 0.7687 (ttmt) outliers start: 11 outliers final: 10 residues processed: 82 average time/residue: 0.2332 time to fit residues: 23.7847 Evaluate side-chains 86 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 60 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: G 50 HIS ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.110089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083788 restraints weight = 5779.594| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.96 r_work: 0.3202 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4975 Z= 0.358 Angle : 0.493 5.928 6720 Z= 0.276 Chirality : 0.050 0.126 870 Planarity : 0.002 0.009 845 Dihedral : 4.558 15.965 725 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.45 % Allowed : 16.53 % Favored : 81.02 % 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: -3.57 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS J 50 PHE 0.004 0.001 PHE F 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 88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8135 (mp0) cc_final: 0.7613 (mp0) REVERT: A 23 LYS cc_start: 0.7499 (ttmt) cc_final: 0.7158 (mtpt) REVERT: A 35 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 60 LYS cc_start: 0.7714 (tttt) cc_final: 0.7258 (ttmt) REVERT: C 57 GLU cc_start: 0.8309 (tt0) cc_final: 0.7480 (pm20) REVERT: C 60 LYS cc_start: 0.8421 (tttt) cc_final: 0.8183 (ttmt) REVERT: D 88 ILE cc_start: 0.9048 (mp) cc_final: 0.8772 (mt) REVERT: E 60 LYS cc_start: 0.7930 (tttt) cc_final: 0.6966 (tptp) REVERT: G 58 LYS cc_start: 0.8310 (mtpt) cc_final: 0.7929 (ttmt) REVERT: I 35 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7166 (mm-30) REVERT: I 60 LYS cc_start: 0.7920 (tttt) cc_final: 0.7652 (ttmt) outliers start: 12 outliers final: 11 residues processed: 83 average time/residue: 0.2241 time to fit residues: 23.0754 Evaluate side-chains 87 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 38 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 50 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 45 optimal weight: 0.0970 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.123282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.098268 restraints weight = 5360.489| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.64 r_work: 0.3276 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2236 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= 0.155 Angle : 0.429 6.091 6720 Z= 0.239 Chirality : 0.049 0.129 870 Planarity : 0.001 0.007 845 Dihedral : 4.218 13.919 725 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.24 % Allowed : 16.73 % Favored : 81.02 % 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: -3.44 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS J 50 PHE 0.006 0.001 PHE B 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 79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8221 (mp0) cc_final: 0.7731 (mp0) REVERT: A 35 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 60 LYS cc_start: 0.7684 (tttt) cc_final: 0.7239 (ttmt) REVERT: C 57 GLU cc_start: 0.8228 (tt0) cc_final: 0.7713 (pm20) REVERT: C 60 LYS cc_start: 0.8429 (tttt) cc_final: 0.8099 (ttmt) REVERT: D 88 ILE cc_start: 0.9065 (mp) cc_final: 0.8819 (mt) REVERT: D 99 GLN cc_start: 0.6311 (tm-30) cc_final: 0.6099 (pm20) REVERT: E 60 LYS cc_start: 0.7984 (tttt) cc_final: 0.7044 (tptp) REVERT: H 62 GLN cc_start: 0.9058 (mt0) cc_final: 0.8748 (mt0) REVERT: I 35 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7734 (mm-30) REVERT: I 60 LYS cc_start: 0.8024 (tttt) cc_final: 0.7766 (ttmt) outliers start: 11 outliers final: 7 residues processed: 75 average time/residue: 0.1938 time to fit residues: 18.3780 Evaluate side-chains 72 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 50 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** F 50 HIS G 50 HIS I 50 HIS J 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.108885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.082192 restraints weight = 5893.881| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.99 r_work: 0.3180 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4975 Z= 0.480 Angle : 0.552 6.129 6720 Z= 0.309 Chirality : 0.052 0.130 870 Planarity : 0.002 0.010 845 Dihedral : 4.636 15.831 725 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.84 % Allowed : 17.14 % Favored : 81.02 % 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 0.012 0.002 HIS J 50 PHE 0.003 0.001 PHE F 94 TYR 0.020 0.003 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.15 seconds wall clock time: 63 minutes 0.64 seconds (3780.64 seconds total)