Starting phenix.real_space_refine on Thu Mar 6 04:43:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xyq_10652/03_2025/6xyq_10652.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xyq_10652/03_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_10652/03_2025/6xyq_10652.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xyq_10652/03_2025/6xyq_10652.map" model { file = "/net/cci-nas-00/data/ceres_data/6xyq_10652/03_2025/6xyq_10652.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xyq_10652/03_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-5624/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: 4.67, per 1000 atoms: 0.94 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: 2.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 2.04 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: 2.73 Time building geometry restraints manager: 2.97 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: 0.09 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 117.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 30.670 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.040 ------------------------------------------------------------------------------- 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 : 1.229 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: 0.3247 time to fit residues: 36.4907 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 : 0.529 ------------------------------------------------------------------------------- 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: 3.04 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 : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7754 (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: 0.8044 (mm-30) cc_final: 0.7825 (mm-30) REVERT: E 60 LYS cc_start: 0.7987 (tttt) cc_final: 0.7045 (tptp) REVERT: F 65 ASN cc_start: 0.9157 (t0) cc_final: 0.8933 (t0) REVERT: G 20 GLU cc_start: 0.7868 (mp0) cc_final: 0.7659 (mp0) REVERT: G 58 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7870 (ttmt) REVERT: I 35 GLU cc_start: 0.7998 (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: 0.2201 time to fit residues: 23.9842 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 : 0.550 ------------------------------------------------------------------------------- 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: 6.9990 chunk 8 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 = 0.108259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081989 restraints weight = 5909.062| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.87 r_work: 0.3140 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.049 4975 Z= 0.620 Angle : 0.611 6.738 6720 Z= 0.345 Chirality : 0.055 0.135 870 Planarity : 0.003 0.009 845 Dihedral : 5.127 18.849 725 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.63 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: -4.14 (0.24), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 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 : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8150 (mp0) cc_final: 0.7683 (mp0) REVERT: A 32 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7836 (mtpp) REVERT: A 35 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 60 LYS cc_start: 0.7773 (tttt) cc_final: 0.7302 (ttmt) REVERT: C 60 LYS cc_start: 0.8660 (tttt) cc_final: 0.8240 (ttmt) REVERT: D 88 ILE cc_start: 0.9014 (mp) cc_final: 0.8756 (mt) REVERT: E 35 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7758 (mm-30) REVERT: E 60 LYS cc_start: 0.8009 (tttt) cc_final: 0.7060 (tptp) REVERT: F 65 ASN cc_start: 0.9295 (t0) cc_final: 0.9059 (t0) REVERT: G 50 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8279 (t-170) REVERT: G 58 LYS cc_start: 0.8293 (mtpt) cc_final: 0.7941 (ttmt) REVERT: I 35 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7718 (mm-30) REVERT: I 60 LYS cc_start: 0.8008 (tttt) cc_final: 0.7747 (ttmt) outliers start: 12 outliers final: 10 residues processed: 92 average time/residue: 0.2260 time to fit residues: 25.1966 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 : 0.525 ------------------------------------------------------------------------------- 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: 2.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.121620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096616 restraints weight = 5459.014| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.67 r_work: 0.3230 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4975 Z= 0.182 Angle : 0.433 6.019 6720 Z= 0.241 Chirality : 0.050 0.123 870 Planarity : 0.001 0.008 845 Dihedral : 4.532 15.688 725 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.06 % Allowed : 15.10 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (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 HIS 0.010 0.003 HIS H 50 PHE 0.005 0.001 PHE B 94 TYR 0.009 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 : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8160 (mp0) cc_final: 0.7693 (mp0) REVERT: A 35 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 60 LYS cc_start: 0.7769 (tttt) cc_final: 0.7319 (ttmt) REVERT: C 57 GLU cc_start: 0.8231 (tt0) cc_final: 0.7454 (pm20) REVERT: C 60 LYS cc_start: 0.8570 (tttt) cc_final: 0.8183 (ttmt) REVERT: D 88 ILE cc_start: 0.8990 (mp) cc_final: 0.8782 (mt) REVERT: D 99 GLN cc_start: 0.6188 (tm-30) cc_final: 0.5799 (pm20) REVERT: E 35 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7777 (mm-30) REVERT: E 60 LYS cc_start: 0.8009 (tttt) cc_final: 0.7078 (tptp) REVERT: I 35 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7688 (mm-30) REVERT: I 60 LYS cc_start: 0.8046 (tttt) cc_final: 0.7810 (ttmt) outliers start: 15 outliers final: 7 residues processed: 89 average time/residue: 0.2676 time to fit residues: 29.5768 Evaluate side-chains 83 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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: 9.9990 chunk 9 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN G 50 HIS H 50 HIS I 50 HIS J 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.118077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.092748 restraints weight = 5530.683| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.67 r_work: 0.3174 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1855 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= 0.357 Angle : 0.480 6.062 6720 Z= 0.270 Chirality : 0.050 0.127 870 Planarity : 0.002 0.012 845 Dihedral : 4.618 16.313 725 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.04 % Allowed : 15.92 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (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 HIS 0.011 0.003 HIS J 50 PHE 0.003 0.001 PHE F 94 TYR 0.016 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 88 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8215 (mp0) cc_final: 0.7722 (mp0) REVERT: A 35 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7786 (mm-30) REVERT: A 60 LYS cc_start: 0.7787 (tttt) cc_final: 0.7336 (ttmt) REVERT: C 57 GLU cc_start: 0.8205 (tt0) cc_final: 0.7450 (pm20) REVERT: C 60 LYS cc_start: 0.8511 (tttt) cc_final: 0.8160 (ttmt) REVERT: D 88 ILE cc_start: 0.8953 (mp) cc_final: 0.8745 (mt) REVERT: E 35 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7775 (mm-30) REVERT: E 60 LYS cc_start: 0.8027 (tttt) cc_final: 0.7076 (tptp) REVERT: G 58 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7962 (ttmt) REVERT: I 35 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7715 (mm-30) REVERT: I 60 LYS cc_start: 0.8028 (tttt) cc_final: 0.7787 (ttmt) outliers start: 10 outliers final: 8 residues processed: 83 average time/residue: 0.2072 time to fit residues: 21.1689 Evaluate side-chains 84 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 F residue 72 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 61 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 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** D 65 ASN G 50 HIS I 50 HIS J 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.108905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082545 restraints weight = 5902.079| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.91 r_work: 0.3168 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 4975 Z= 0.478 Angle : 0.539 6.203 6720 Z= 0.303 Chirality : 0.051 0.131 870 Planarity : 0.002 0.010 845 Dihedral : 4.783 16.648 725 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.65 % Allowed : 15.31 % 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: -3.77 (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 HIS 0.011 0.003 HIS J 50 PHE 0.003 0.001 PHE F 94 TYR 0.018 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 99 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8185 (mp0) cc_final: 0.7688 (mp0) REVERT: A 23 LYS cc_start: 0.7554 (ttmt) cc_final: 0.7213 (mtpt) REVERT: A 35 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 60 LYS cc_start: 0.7773 (tttt) cc_final: 0.7309 (ttmt) REVERT: C 57 GLU cc_start: 0.8247 (tt0) cc_final: 0.7444 (pm20) REVERT: C 60 LYS cc_start: 0.8435 (tttt) cc_final: 0.8111 (ttmt) REVERT: D 88 ILE cc_start: 0.8996 (mp) cc_final: 0.8733 (mt) REVERT: E 60 LYS cc_start: 0.7994 (tttt) cc_final: 0.7043 (tptp) REVERT: G 58 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7876 (ttmt) REVERT: I 35 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7227 (mm-30) REVERT: I 60 LYS cc_start: 0.7974 (tttt) cc_final: 0.7710 (ttmt) outliers start: 13 outliers final: 11 residues processed: 93 average time/residue: 0.2518 time to fit residues: 28.4995 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 : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J 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: 0.9980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 16 optimal weight: 0.2980 chunk 46 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS F 50 HIS G 50 HIS I 50 HIS J 50 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.123549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.098553 restraints weight = 5277.761| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.64 r_work: 0.3292 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4975 Z= 0.130 Angle : 0.422 5.361 6720 Z= 0.234 Chirality : 0.050 0.157 870 Planarity : 0.001 0.009 845 Dihedral : 4.216 14.088 725 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.04 % Allowed : 16.73 % 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: -3.53 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.20), 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 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 81 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8194 (mp0) cc_final: 0.7703 (mp0) REVERT: A 35 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7732 (mm-30) REVERT: A 60 LYS cc_start: 0.7691 (tttt) cc_final: 0.7243 (ttmt) REVERT: C 57 GLU cc_start: 0.8217 (tt0) cc_final: 0.7713 (pm20) REVERT: C 60 LYS cc_start: 0.8510 (tttt) cc_final: 0.8140 (ttmt) REVERT: D 88 ILE cc_start: 0.9095 (mp) cc_final: 0.8847 (mt) REVERT: E 35 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7689 (mm-30) REVERT: E 60 LYS cc_start: 0.8026 (tttt) cc_final: 0.7096 (tptp) REVERT: H 62 GLN cc_start: 0.9004 (mt0) cc_final: 0.8709 (mt0) REVERT: I 35 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7733 (mm-30) REVERT: I 60 LYS cc_start: 0.8048 (tttt) cc_final: 0.7799 (ttmt) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.2233 time to fit residues: 22.0026 Evaluate side-chains 76 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 68 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS J 50 HIS J 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.109778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.083160 restraints weight = 5864.121| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.00 r_work: 0.3178 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2041 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= 0.437 Angle : 0.527 5.805 6720 Z= 0.294 Chirality : 0.051 0.128 870 Planarity : 0.002 0.010 845 Dihedral : 4.599 16.166 725 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 16.94 % 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: -3.56 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS J 50 PHE 0.003 0.001 PHE F 94 TYR 0.016 0.003 TYR A 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 93 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8119 (mp0) cc_final: 0.7590 (mp0) REVERT: A 35 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7703 (mm-30) REVERT: A 60 LYS cc_start: 0.7718 (tttt) cc_final: 0.7258 (ttmt) REVERT: C 35 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7558 (mm-30) REVERT: C 57 GLU cc_start: 0.8303 (tt0) cc_final: 0.7467 (pm20) REVERT: C 60 LYS cc_start: 0.8419 (tttt) cc_final: 0.8131 (ttmt) REVERT: D 88 ILE cc_start: 0.9001 (mp) cc_final: 0.8729 (mt) REVERT: E 60 LYS cc_start: 0.7887 (tttt) cc_final: 0.6935 (tptp) REVERT: F 97 LYS cc_start: 0.7932 (mttt) cc_final: 0.7417 (mtpp) REVERT: G 58 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7810 (ttmt) REVERT: I 35 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7165 (mm-30) REVERT: I 60 LYS cc_start: 0.7902 (tttt) cc_final: 0.7630 (ttmt) outliers start: 10 outliers final: 8 residues processed: 88 average time/residue: 0.2315 time to fit residues: 25.0256 Evaluate side-chains 90 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain J 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: 3.9990 chunk 34 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 0.0970 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.122428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097296 restraints weight = 5294.123| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.64 r_work: 0.3263 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4975 Z= 0.170 Angle : 0.438 5.823 6720 Z= 0.242 Chirality : 0.050 0.146 870 Planarity : 0.001 0.009 845 Dihedral : 4.236 14.397 725 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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 : -2.62 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS J 50 PHE 0.005 0.001 PHE B 94 TYR 0.008 0.002 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 78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8197 (mp0) cc_final: 0.7707 (mp0) REVERT: A 35 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 60 LYS cc_start: 0.7709 (tttt) cc_final: 0.7257 (ttmt) REVERT: B 99 GLN cc_start: 0.6752 (mm-40) cc_final: 0.6277 (mm110) REVERT: C 35 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7491 (mm-30) REVERT: C 57 GLU cc_start: 0.8313 (tt0) cc_final: 0.7779 (pm20) REVERT: C 60 LYS cc_start: 0.8474 (tttt) cc_final: 0.8135 (ttmt) REVERT: D 88 ILE cc_start: 0.9067 (mp) cc_final: 0.8823 (mt) REVERT: E 22 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8335 (m) REVERT: E 60 LYS cc_start: 0.8000 (tttt) cc_final: 0.7070 (tptp) REVERT: H 62 GLN cc_start: 0.9046 (mt0) cc_final: 0.8770 (mt0) REVERT: I 35 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7739 (mm-30) REVERT: I 60 LYS cc_start: 0.8039 (tttt) cc_final: 0.7779 (ttmt) outliers start: 11 outliers final: 8 residues processed: 72 average time/residue: 0.2099 time to fit residues: 19.2901 Evaluate side-chains 75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 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 18 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.0170 chunk 40 optimal weight: 6.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100838 restraints weight = 5309.766| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.67 r_work: 0.3331 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4975 Z= 0.120 Angle : 0.411 5.481 6720 Z= 0.227 Chirality : 0.049 0.126 870 Planarity : 0.001 0.010 845 Dihedral : 4.018 13.197 725 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.43 % Allowed : 17.96 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.30 (0.28), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS J 50 PHE 0.006 0.001 PHE J 94 TYR 0.006 0.001 TYR B 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8204 (mp0) cc_final: 0.7711 (mp0) REVERT: A 35 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 60 LYS cc_start: 0.7689 (tttt) cc_final: 0.7224 (ttmt) REVERT: C 60 LYS cc_start: 0.8397 (tttt) cc_final: 0.8082 (ttmt) REVERT: D 88 ILE cc_start: 0.9014 (mp) cc_final: 0.8779 (mt) REVERT: D 99 GLN cc_start: 0.6392 (tm-30) cc_final: 0.6125 (pm20) REVERT: E 60 LYS cc_start: 0.7989 (tttt) cc_final: 0.7054 (tptp) REVERT: H 62 GLN cc_start: 0.8918 (mt0) cc_final: 0.8621 (mt0) REVERT: I 35 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7702 (mm-30) REVERT: I 60 LYS cc_start: 0.8030 (tttt) cc_final: 0.7748 (ttmt) outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 0.1866 time to fit residues: 16.4638 Evaluate side-chains 68 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain C residue 37 VAL 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 57 optimal weight: 0.6980 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: 0.9990 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 HIS I 50 HIS J 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.122871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097079 restraints weight = 5343.510| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.70 r_work: 0.3259 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4975 Z= 0.204 Angle : 0.439 7.118 6720 Z= 0.240 Chirality : 0.049 0.120 870 Planarity : 0.001 0.009 845 Dihedral : 4.108 14.183 725 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.22 % Allowed : 18.37 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.28), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS J 50 PHE 0.005 0.001 PHE B 94 TYR 0.011 0.002 TYR G 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3893.10 seconds wall clock time: 70 minutes 38.94 seconds (4238.94 seconds total)