Starting phenix.real_space_refine on Fri Aug 22 15:24:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xyq_10652/08_2025/6xyq_10652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xyq_10652/08_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_10652/08_2025/6xyq_10652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xyq_10652/08_2025/6xyq_10652.map" model { file = "/net/cci-nas-00/data/ceres_data/6xyq_10652/08_2025/6xyq_10652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xyq_10652/08_2025/6xyq_10652.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: C, E, G, I, D, F, H, J Time building chain proxies: 0.94, per 1000 atoms: 0.19 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: 0.41 Conformation dependent library (CDL) restraints added in 224.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.27 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: 0.75 Time building geometry restraints manager: 0.55 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: 0.02 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.580 Find NCS groups from input model: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.970 ------------------------------------------------------------------------------- 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= 0.351 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.014 0.003 TYR I 39 PHE 0.004 0.001 PHE B 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00719 ( 4975) covalent geometry : angle 0.70593 ( 6720) hydrogen bonds : bond 0.14892 ( 95) hydrogen bonds : angle 6.79433 ( 309) *********************** 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 : 0.184 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: 0.1124 time to fit residues: 12.5740 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 : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.111226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084542 restraints weight = 5841.430| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.89 r_work: 0.3207 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 4975 Z= 0.255 Angle : 0.516 5.847 6720 Z= 0.288 Chirality : 0.052 0.126 870 Planarity : 0.002 0.008 845 Dihedral : 4.878 17.175 725 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.82 % Allowed : 8.57 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.26 (0.23), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR E 39 PHE 0.003 0.001 PHE F 94 HIS 0.009 0.003 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 4975) covalent geometry : angle 0.51587 ( 6720) hydrogen bonds : bond 0.01944 ( 95) hydrogen bonds : angle 3.88106 ( 309) *********************** 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 88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7748 (mm-30) REVERT: A 60 LYS cc_start: 0.7819 (tttt) cc_final: 0.7333 (ttmt) REVERT: C 60 LYS cc_start: 0.8650 (tttt) cc_final: 0.8250 (ttmt) REVERT: D 88 ILE cc_start: 0.9031 (mp) cc_final: 0.8780 (mt) REVERT: E 35 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7831 (mm-30) REVERT: E 60 LYS cc_start: 0.7993 (tttt) cc_final: 0.7060 (tptp) REVERT: G 58 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8088 (ttmt) REVERT: I 35 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7729 (mm-30) REVERT: I 60 LYS cc_start: 0.8012 (tttt) cc_final: 0.7749 (ttmt) outliers start: 4 outliers final: 3 residues processed: 87 average time/residue: 0.1028 time to fit residues: 10.9520 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 : 0.184 ------------------------------------------------------------------------------- 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 43 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS D 65 ASN F 50 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.094740 restraints weight = 5381.865| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.64 r_work: 0.3208 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1620 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= 0.200 Angle : 0.461 5.701 6720 Z= 0.259 Chirality : 0.050 0.124 870 Planarity : 0.002 0.010 845 Dihedral : 4.654 15.924 725 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.04 % Allowed : 12.04 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.99 (0.24), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR G 39 PHE 0.004 0.001 PHE J 94 HIS 0.012 0.003 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 4975) covalent geometry : angle 0.46052 ( 6720) hydrogen bonds : bond 0.01483 ( 95) hydrogen bonds : angle 3.52869 ( 309) *********************** 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 90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8139 (mp0) cc_final: 0.7697 (mp0) REVERT: A 35 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 60 LYS cc_start: 0.7803 (tttt) cc_final: 0.7336 (ttmt) REVERT: C 60 LYS cc_start: 0.8553 (tttt) cc_final: 0.8171 (ttmt) REVERT: D 88 ILE cc_start: 0.8993 (mp) cc_final: 0.8770 (mt) REVERT: E 35 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7846 (mm-30) REVERT: E 60 LYS cc_start: 0.8016 (tttt) cc_final: 0.7084 (tptp) REVERT: G 58 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7866 (ttmt) REVERT: I 35 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7705 (mm-30) REVERT: I 60 LYS cc_start: 0.8042 (tttt) cc_final: 0.7801 (ttmt) outliers start: 10 outliers final: 4 residues processed: 85 average time/residue: 0.1036 time to fit residues: 10.7783 Evaluate side-chains 84 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 66 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN D 65 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS H 50 HIS I 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.107383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.081021 restraints weight = 5916.935| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.90 r_work: 0.3150 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4975 Z= 0.270 Angle : 0.502 6.068 6720 Z= 0.283 Chirality : 0.051 0.128 870 Planarity : 0.002 0.010 845 Dihedral : 4.746 16.903 725 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.06 % Allowed : 12.65 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.87 (0.25), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR G 39 PHE 0.003 0.001 PHE J 94 HIS 0.008 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 4975) covalent geometry : angle 0.50204 ( 6720) hydrogen bonds : bond 0.01474 ( 95) hydrogen bonds : angle 3.52639 ( 309) *********************** 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: 15 poor density : 82 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8203 (mp0) cc_final: 0.7725 (mp0) REVERT: A 35 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 60 LYS cc_start: 0.7724 (tttt) cc_final: 0.7272 (ttmt) REVERT: C 57 GLU cc_start: 0.8192 (tt0) cc_final: 0.7429 (pm20) REVERT: C 60 LYS cc_start: 0.8554 (tttt) cc_final: 0.8152 (ttmt) REVERT: D 88 ILE cc_start: 0.8942 (mp) cc_final: 0.8717 (mt) REVERT: E 35 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7805 (mm-30) REVERT: E 60 LYS cc_start: 0.7975 (tttt) cc_final: 0.7031 (tptp) REVERT: G 50 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8309 (t-170) REVERT: G 58 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7905 (ttmt) REVERT: I 35 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7716 (mm-30) REVERT: I 60 LYS cc_start: 0.7988 (tttt) cc_final: 0.7759 (ttmt) outliers start: 15 outliers final: 9 residues processed: 90 average time/residue: 0.0993 time to fit residues: 10.9861 Evaluate side-chains 91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 G residue 50 HIS Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 G 50 HIS H 50 HIS I 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 = 0.3729 r_free = 0.3729 target = 0.117973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092848 restraints weight = 5592.598| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.67 r_work: 0.3176 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4975 Z= 0.280 Angle : 0.512 6.100 6720 Z= 0.289 Chirality : 0.051 0.128 870 Planarity : 0.002 0.011 845 Dihedral : 4.738 16.931 725 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.65 % Allowed : 13.88 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.82 (0.25), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR G 39 PHE 0.003 0.001 PHE J 94 HIS 0.013 0.003 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00613 ( 4975) covalent geometry : angle 0.51248 ( 6720) hydrogen bonds : bond 0.01460 ( 95) hydrogen bonds : angle 3.51913 ( 309) *********************** 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 94 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8210 (mp0) cc_final: 0.7722 (mp0) REVERT: A 35 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 60 LYS cc_start: 0.7743 (tttt) cc_final: 0.7303 (ttmt) REVERT: B 62 GLN cc_start: 0.9080 (mt0) cc_final: 0.8762 (mt0) REVERT: C 57 GLU cc_start: 0.8189 (tt0) cc_final: 0.7428 (pm20) REVERT: C 60 LYS cc_start: 0.8494 (tttt) cc_final: 0.8145 (ttmt) REVERT: D 88 ILE cc_start: 0.8930 (mp) cc_final: 0.8699 (mt) REVERT: E 35 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7773 (mm-30) REVERT: E 60 LYS cc_start: 0.7988 (tttt) cc_final: 0.7046 (tptp) REVERT: G 58 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7955 (ttmt) REVERT: I 35 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7166 (mm-30) REVERT: I 60 LYS cc_start: 0.7997 (tttt) cc_final: 0.7768 (ttmt) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.1002 time to fit residues: 10.6849 Evaluate side-chains 88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN C 50 HIS D 65 ASN G 50 HIS H 50 HIS I 50 HIS ** J 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.117525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.092148 restraints weight = 5684.757| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.69 r_work: 0.3171 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4975 Z= 0.279 Angle : 0.515 6.310 6720 Z= 0.289 Chirality : 0.051 0.129 870 Planarity : 0.002 0.008 845 Dihedral : 4.744 16.857 725 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.65 % Allowed : 14.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.78 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR G 39 PHE 0.004 0.001 PHE J 94 HIS 0.011 0.003 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00612 ( 4975) covalent geometry : angle 0.51450 ( 6720) hydrogen bonds : bond 0.01405 ( 95) hydrogen bonds : angle 3.51137 ( 309) *********************** 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 98 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8241 (mp0) cc_final: 0.7772 (mp0) REVERT: A 23 LYS cc_start: 0.7624 (ttmt) cc_final: 0.7280 (mtpt) REVERT: A 35 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 60 LYS cc_start: 0.7781 (tttt) cc_final: 0.7337 (ttmt) REVERT: C 57 GLU cc_start: 0.8193 (tt0) cc_final: 0.7431 (pm20) REVERT: C 60 LYS cc_start: 0.8504 (tttt) cc_final: 0.8144 (ttmt) REVERT: D 88 ILE cc_start: 0.8977 (mp) cc_final: 0.8725 (mt) REVERT: E 35 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7795 (mm-30) REVERT: E 60 LYS cc_start: 0.8023 (tttt) cc_final: 0.7059 (tptp) REVERT: G 58 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8001 (ttmt) REVERT: I 35 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7179 (mm-30) REVERT: I 60 LYS cc_start: 0.8007 (tttt) cc_final: 0.7781 (ttmt) outliers start: 13 outliers final: 11 residues processed: 92 average time/residue: 0.1063 time to fit residues: 11.8650 Evaluate side-chains 95 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 50 HIS 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 H residue 50 HIS Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 F 50 HIS G 50 HIS H 50 HIS I 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 = 0.3724 r_free = 0.3724 target = 0.117352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.091970 restraints weight = 5569.968| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.68 r_work: 0.3165 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4975 Z= 0.289 Angle : 0.520 6.333 6720 Z= 0.292 Chirality : 0.051 0.129 870 Planarity : 0.002 0.013 845 Dihedral : 4.743 16.922 725 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.06 % Allowed : 14.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR G 39 PHE 0.004 0.001 PHE J 94 HIS 0.015 0.003 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00634 ( 4975) covalent geometry : angle 0.52033 ( 6720) hydrogen bonds : bond 0.01396 ( 95) hydrogen bonds : angle 3.54093 ( 309) *********************** 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 100 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8245 (mp0) cc_final: 0.7769 (mp0) REVERT: A 23 LYS cc_start: 0.7590 (ttmt) cc_final: 0.7247 (mtpt) REVERT: A 35 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 60 LYS cc_start: 0.7765 (tttt) cc_final: 0.7323 (ttmt) REVERT: C 57 GLU cc_start: 0.8217 (tt0) cc_final: 0.7427 (pm20) REVERT: C 60 LYS cc_start: 0.8451 (tttt) cc_final: 0.8120 (ttmt) REVERT: D 88 ILE cc_start: 0.8971 (mp) cc_final: 0.8718 (mt) REVERT: E 60 LYS cc_start: 0.7995 (tttt) cc_final: 0.7027 (tptp) REVERT: G 58 LYS cc_start: 0.8341 (mtpt) cc_final: 0.7969 (ttmt) REVERT: I 35 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7214 (mm-30) REVERT: I 60 LYS cc_start: 0.7994 (tttt) cc_final: 0.7765 (ttmt) outliers start: 15 outliers final: 11 residues processed: 93 average time/residue: 0.1009 time to fit residues: 11.4976 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 : 0.196 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain J residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 23 optimal weight: 0.0270 chunk 7 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- 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** C 50 HIS E 50 HIS G 50 HIS H 50 HIS I 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 = 0.3756 r_free = 0.3756 target = 0.119732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094590 restraints weight = 5495.659| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.62 r_work: 0.3222 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 0.028 4975 Z= 0.169 Angle : 0.455 5.952 6720 Z= 0.255 Chirality : 0.050 0.127 870 Planarity : 0.001 0.009 845 Dihedral : 4.488 15.537 725 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.24 % Allowed : 15.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR C 39 PHE 0.005 0.001 PHE J 94 HIS 0.012 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4975) covalent geometry : angle 0.45487 ( 6720) hydrogen bonds : bond 0.01201 ( 95) hydrogen bonds : angle 3.39335 ( 309) *********************** 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 85 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8260 (mp0) cc_final: 0.7789 (mp0) REVERT: A 23 LYS cc_start: 0.7618 (ttmt) cc_final: 0.7258 (mtpt) REVERT: A 35 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 60 LYS cc_start: 0.7811 (tttt) cc_final: 0.7366 (ttmt) REVERT: C 57 GLU cc_start: 0.8292 (tt0) cc_final: 0.7707 (pm20) REVERT: C 60 LYS cc_start: 0.8495 (tttt) cc_final: 0.8166 (ttmt) REVERT: D 88 ILE cc_start: 0.9073 (mp) cc_final: 0.8812 (mt) REVERT: E 60 LYS cc_start: 0.8049 (tttt) cc_final: 0.7104 (tptp) REVERT: I 35 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7206 (mm-30) REVERT: I 60 LYS cc_start: 0.8044 (tttt) cc_final: 0.7808 (ttmt) outliers start: 11 outliers final: 9 residues processed: 80 average time/residue: 0.1067 time to fit residues: 10.3099 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 : 0.181 ------------------------------------------------------------------------------- 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 H residue 50 HIS Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 35 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 20 optimal weight: 0.3980 chunk 18 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 H 50 HIS I 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 = 0.3791 r_free = 0.3791 target = 0.122245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.097080 restraints weight = 5386.482| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.65 r_work: 0.3262 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4975 Z= 0.121 Angle : 0.427 5.630 6720 Z= 0.239 Chirality : 0.049 0.137 870 Planarity : 0.001 0.009 845 Dihedral : 4.293 14.296 725 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.45 % Allowed : 15.92 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR C 39 PHE 0.005 0.001 PHE B 94 HIS 0.011 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4975) covalent geometry : angle 0.42651 ( 6720) hydrogen bonds : bond 0.01105 ( 95) hydrogen bonds : angle 3.32844 ( 309) *********************** 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 82 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8201 (mp0) cc_final: 0.7712 (mp0) REVERT: A 35 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 60 LYS cc_start: 0.7719 (tttt) cc_final: 0.7260 (ttmt) REVERT: C 35 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7486 (mm-30) REVERT: C 57 GLU cc_start: 0.8252 (tt0) cc_final: 0.7737 (pm20) REVERT: C 60 LYS cc_start: 0.8436 (tttt) cc_final: 0.8156 (ttmt) REVERT: D 88 ILE cc_start: 0.9061 (mp) cc_final: 0.8812 (mt) REVERT: E 35 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7640 (mm-30) REVERT: E 60 LYS cc_start: 0.8014 (tttt) cc_final: 0.6989 (tptp) REVERT: H 62 GLN cc_start: 0.9042 (mt0) cc_final: 0.8775 (mt0) REVERT: I 35 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7730 (mm-30) REVERT: I 60 LYS cc_start: 0.8025 (tttt) cc_final: 0.7785 (ttmt) outliers start: 12 outliers final: 9 residues processed: 76 average time/residue: 0.0872 time to fit residues: 8.3674 Evaluate side-chains 77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 45 optimal weight: 0.0570 chunk 58 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 0.0970 chunk 43 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 overall best weight: 5.4302 ------------------------------------------------------------------------------- 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 H 50 HIS I 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.117358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092075 restraints weight = 5607.178| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.69 r_work: 0.3175 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 4975 Z= 0.301 Angle : 0.530 5.888 6720 Z= 0.298 Chirality : 0.051 0.129 870 Planarity : 0.002 0.008 845 Dihedral : 4.648 15.835 725 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.04 % Allowed : 16.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.26), 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 TYR 0.018 0.003 TYR A 39 PHE 0.003 0.001 PHE F 94 HIS 0.008 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 4975) covalent geometry : angle 0.53001 ( 6720) hydrogen bonds : bond 0.01343 ( 95) hydrogen bonds : angle 3.50056 ( 309) ********************** 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 91 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8269 (mp0) cc_final: 0.7770 (mp0) REVERT: A 23 LYS cc_start: 0.7664 (ttmt) cc_final: 0.7277 (mtpt) REVERT: A 35 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 60 LYS cc_start: 0.7793 (tttt) cc_final: 0.7340 (ttmt) REVERT: C 57 GLU cc_start: 0.8186 (tt0) cc_final: 0.7419 (pm20) REVERT: C 60 LYS cc_start: 0.8446 (tttt) cc_final: 0.8210 (ttmt) REVERT: D 88 ILE cc_start: 0.8986 (mp) cc_final: 0.8733 (mt) REVERT: E 60 LYS cc_start: 0.7980 (tttt) cc_final: 0.7011 (tptp) REVERT: G 58 LYS cc_start: 0.8423 (mtpt) cc_final: 0.8034 (ttmt) REVERT: I 35 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7207 (mm-30) REVERT: I 60 LYS cc_start: 0.7999 (tttt) cc_final: 0.7750 (ttmt) outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 0.1161 time to fit residues: 12.0138 Evaluate side-chains 88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR 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 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 61 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 H 50 HIS I 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.119104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.093948 restraints weight = 5584.799| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.68 r_work: 0.3210 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4975 Z= 0.209 Angle : 0.480 5.937 6720 Z= 0.268 Chirality : 0.050 0.126 870 Planarity : 0.002 0.010 845 Dihedral : 4.512 15.312 725 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.04 % Allowed : 16.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.013 0.002 TYR G 39 PHE 0.005 0.001 PHE J 94 HIS 0.012 0.003 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 4975) covalent geometry : angle 0.47981 ( 6720) hydrogen bonds : bond 0.01227 ( 95) hydrogen bonds : angle 3.40861 ( 309) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1588.88 seconds wall clock time: 28 minutes 1.77 seconds (1681.77 seconds total)