Starting phenix.real_space_refine on Fri Dec 27 13:01:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xyp_10651/12_2024/6xyp_10651.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xyp_10651/12_2024/6xyp_10651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xyp_10651/12_2024/6xyp_10651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xyp_10651/12_2024/6xyp_10651.map" model { file = "/net/cci-nas-00/data/ceres_data/6xyp_10651/12_2024/6xyp_10651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xyp_10651/12_2024/6xyp_10651.cif" } resolution = 3.29 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 3085 2.51 5 N 865 2.21 5 O 1005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4955 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "B" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 442 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Restraints were copied for chains: D, F, H, J, C, E, G, I Time building chain proxies: 2.06, per 1000 atoms: 0.42 Number of scatterers: 4955 At special positions: 0 Unit cell: (105.8, 80.5, 41.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1005 8.00 N 865 7.00 C 3085 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 717.7 milliseconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 34.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 16 through 18 removed outlier: 6.542A pdb=" N VAL A 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL G 16 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 30 removed outlier: 6.717A pdb=" N GLY C 25 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLU E 28 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA C 27 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA E 30 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA C 29 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 25 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLU I 28 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA A 27 " --> pdb=" O GLU I 28 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA I 30 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA A 29 " --> pdb=" O ALA I 30 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.254A pdb=" N LEU A 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU G 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 45 through 52 removed outlier: 9.001A pdb=" N LYS C 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N VAL E 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLY C 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N HIS E 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL C 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU A 46 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY E 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N LYS A 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N VAL I 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N HIS I 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL I 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY A 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N GLU G 46 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY I 47 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL G 52 " --> pdb=" O GLY I 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.475A pdb=" N THR C 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLN E 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU C 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR A 59 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLN I 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU A 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS G 58 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU I 61 " --> pdb=" O LYS G 58 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS G 60 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL I 63 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN G 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 71 removed outlier: 6.365A pdb=" N ALA A 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA G 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 81 removed outlier: 6.332A pdb=" N ALA C 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLN E 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA A 76 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLN I 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA A 78 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR I 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS A 80 " --> pdb=" O THR I 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.258A pdb=" N ALA C 90 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ALA A 90 " --> pdb=" O ALA I 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 38 through 40 removed outlier: 6.496A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR B 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 45 through 52 removed outlier: 6.880A pdb=" N VAL D 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL F 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N HIS D 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY F 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LYS B 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL F 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY B 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 10.011A pdb=" N HIS F 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N VAL B 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL F 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY B 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 48 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL J 49 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N HIS B 50 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY J 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS H 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL J 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 9.649A pdb=" N HIS J 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N VAL H 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N VAL J 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY H 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 55 through 57 removed outlier: 6.386A pdb=" N ALA D 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 56 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 62 through 66 removed outlier: 6.284A pdb=" N GLN B 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASN F 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR B 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN H 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.627A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL B 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 77 removed outlier: 6.539A pdb=" N ALA D 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA B 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.787A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.278A pdb=" N VAL B 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL H 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 33 through 34 removed outlier: 6.655A pdb=" N THR G 33 " --> pdb=" O LYS I 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 79 hydrogen bonds defined for protein. 237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 885 1.28 - 1.35: 775 1.35 - 1.41: 170 1.41 - 1.48: 830 1.48 - 1.54: 2315 Bond restraints: 4975 Sorted by residual: bond pdb=" CB VAL J 37 " pdb=" CG2 VAL J 37 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.03e+00 bond pdb=" CB VAL F 37 " pdb=" CG2 VAL F 37 " 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 H 37 " pdb=" CG2 VAL H 37 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB VAL B 37 " pdb=" CG2 VAL B 37 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 1.99e+00 bond pdb=" CB VAL D 37 " pdb=" CG2 VAL D 37 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.89e+00 ... (remaining 4970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.86: 5807 0.86 - 1.71: 755 1.71 - 2.57: 118 2.57 - 3.43: 35 3.43 - 4.28: 5 Bond angle restraints: 6720 Sorted by residual: angle pdb=" N LYS E 23 " pdb=" CA LYS E 23 " pdb=" C LYS E 23 " ideal model delta sigma weight residual 113.88 110.65 3.23 1.23e+00 6.61e-01 6.89e+00 angle pdb=" N LYS G 23 " pdb=" CA LYS G 23 " pdb=" C LYS G 23 " ideal model delta sigma weight residual 113.88 110.66 3.22 1.23e+00 6.61e-01 6.84e+00 angle pdb=" N LYS I 23 " pdb=" CA LYS I 23 " pdb=" C LYS I 23 " ideal model delta sigma weight residual 113.88 110.67 3.21 1.23e+00 6.61e-01 6.79e+00 angle pdb=" N LYS A 23 " pdb=" CA LYS A 23 " pdb=" C LYS A 23 " ideal model delta sigma weight residual 113.88 110.69 3.19 1.23e+00 6.61e-01 6.75e+00 angle pdb=" N LYS C 23 " pdb=" CA LYS C 23 " pdb=" C LYS C 23 " ideal model delta sigma weight residual 113.88 110.71 3.17 1.23e+00 6.61e-01 6.65e+00 ... (remaining 6715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.88: 2545 13.88 - 27.76: 275 27.76 - 41.63: 50 41.63 - 55.51: 28 55.51 - 69.39: 12 Dihedral angle restraints: 2910 sinusoidal: 965 harmonic: 1945 Sorted by residual: 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 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ALA A 78 " pdb=" C ALA A 78 " pdb=" N GLN A 79 " pdb=" CA GLN A 79 " ideal model delta harmonic sigma weight residual -180.00 -163.79 -16.21 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA ALA E 78 " pdb=" C ALA E 78 " pdb=" N GLN E 79 " pdb=" CA GLN E 79 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 580 0.047 - 0.094: 216 0.094 - 0.142: 69 0.142 - 0.189: 0 0.189 - 0.236: 5 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB VAL H 37 " pdb=" CA VAL H 37 " pdb=" CG1 VAL H 37 " pdb=" CG2 VAL H 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB VAL J 37 " pdb=" CA VAL J 37 " pdb=" CG1 VAL J 37 " pdb=" CG2 VAL J 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB VAL F 37 " pdb=" CA VAL F 37 " pdb=" CG1 VAL F 37 " pdb=" CG2 VAL F 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 867 not shown) Planarity restraints: 845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.009 2.00e-02 2.50e+03 6.85e-03 8.21e-01 pdb=" CG PHE F 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " 0.009 2.00e-02 2.50e+03 6.77e-03 8.03e-01 pdb=" CG PHE D 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " 0.009 2.00e-02 2.50e+03 6.72e-03 7.91e-01 pdb=" CG PHE B 94 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " 0.001 2.00e-02 2.50e+03 ... (remaining 842 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 213 2.70 - 3.25: 4728 3.25 - 3.80: 7594 3.80 - 4.35: 9574 4.35 - 4.90: 18788 Nonbonded interactions: 40897 Sorted by model distance: nonbonded pdb=" OE1 GLU C 28 " pdb=" NZ LYS F 60 " model vdw 2.151 3.120 nonbonded pdb=" OE2 GLU A 28 " pdb=" NZ LYS H 60 " model vdw 2.165 3.120 nonbonded pdb=" OE1 GLU A 28 " pdb=" NZ LYS J 60 " model vdw 2.270 3.120 nonbonded pdb=" NZ LYS B 60 " pdb=" OE1 GLU E 28 " model vdw 2.293 3.120 nonbonded pdb=" NZ LYS H 60 " pdb=" OE1 GLU I 28 " model vdw 2.337 3.120 ... (remaining 40892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.850 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.650 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.008 0.047 4975 Z= 0.570 Angle : 0.643 4.284 6720 Z= 0.388 Chirality : 0.055 0.236 870 Planarity : 0.002 0.007 845 Dihedral : 13.985 69.389 1690 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % 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: -5.04 (0.22), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.16), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.015 0.003 PHE F 94 TYR 0.011 0.003 TYR G 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 71 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8604 (ttmm) REVERT: B 58 LYS cc_start: 0.8495 (mttt) cc_final: 0.8054 (mttt) REVERT: E 32 LYS cc_start: 0.8897 (ttmt) cc_final: 0.8469 (ttmm) REVERT: F 58 LYS cc_start: 0.8481 (mttt) cc_final: 0.8128 (mttt) REVERT: G 20 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7430 (mp0) REVERT: G 43 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7196 (mttt) REVERT: H 60 LYS cc_start: 0.8161 (mppt) cc_final: 0.7388 (mptt) REVERT: I 28 GLU cc_start: 0.7472 (tt0) cc_final: 0.7178 (mt-10) REVERT: I 35 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8158 (mm-30) REVERT: I 46 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8273 (mt-10) REVERT: J 60 LYS cc_start: 0.8933 (mppt) cc_final: 0.8419 (mptt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2377 time to fit residues: 20.5342 Evaluate side-chains 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 4.9990 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS C 50 HIS D 62 GLN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 4975 Z= 0.265 Angle : 0.471 5.470 6720 Z= 0.265 Chirality : 0.051 0.122 870 Planarity : 0.002 0.008 845 Dihedral : 5.066 16.223 725 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.41 % Allowed : 11.22 % Favored : 88.37 % 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: -4.42 (0.24), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 50 PHE 0.012 0.002 PHE F 94 TYR 0.013 0.002 TYR E 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 62 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.577 Fit side-chains REVERT: C 35 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7145 (pt0) REVERT: E 32 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8430 (ttmm) REVERT: G 43 LYS cc_start: 0.7791 (mtpt) cc_final: 0.7141 (mttt) REVERT: H 60 LYS cc_start: 0.9029 (mppt) cc_final: 0.8636 (mptt) REVERT: H 97 LYS cc_start: 0.8547 (mttt) cc_final: 0.8286 (mttt) REVERT: J 60 LYS cc_start: 0.8968 (mppt) cc_final: 0.8610 (mptt) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 0.3033 time to fit residues: 22.0700 Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4975 Z= 0.290 Angle : 0.469 6.104 6720 Z= 0.260 Chirality : 0.051 0.121 870 Planarity : 0.001 0.006 845 Dihedral : 4.959 15.536 725 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.43 % Allowed : 12.24 % Favored : 86.33 % 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: -4.06 (0.24), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS D 50 PHE 0.012 0.002 PHE F 94 TYR 0.013 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.571 Fit side-chains REVERT: E 32 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8419 (ttmm) REVERT: E 35 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7979 (mm-30) REVERT: G 43 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7172 (mttt) REVERT: H 60 LYS cc_start: 0.8943 (mppt) cc_final: 0.8378 (mptt) REVERT: H 97 LYS cc_start: 0.8573 (mttt) cc_final: 0.8307 (mttt) REVERT: I 28 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6823 (mt-10) REVERT: J 60 LYS cc_start: 0.8928 (mppt) cc_final: 0.8564 (mptt) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.2492 time to fit residues: 17.6796 Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain I residue 28 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 18 optimal weight: 0.3980 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 overall best weight: 8.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN E 79 GLN F 62 GLN J 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.046 4975 Z= 0.650 Angle : 0.628 7.883 6720 Z= 0.351 Chirality : 0.055 0.124 870 Planarity : 0.002 0.008 845 Dihedral : 5.530 16.239 725 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.27 % Allowed : 15.31 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.24), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS D 50 PHE 0.018 0.003 PHE F 94 TYR 0.017 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.545 Fit side-chains REVERT: B 60 LYS cc_start: 0.8778 (mptt) cc_final: 0.8070 (mptt) REVERT: C 35 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7154 (pt0) REVERT: E 28 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6739 (mt-10) REVERT: E 32 LYS cc_start: 0.8895 (ttmt) cc_final: 0.8567 (ttmm) REVERT: G 43 LYS cc_start: 0.7865 (mtpt) cc_final: 0.7226 (mttt) REVERT: H 58 LYS cc_start: 0.8897 (mttt) cc_final: 0.8653 (mttt) REVERT: H 60 LYS cc_start: 0.8985 (mppt) cc_final: 0.8375 (mptt) REVERT: I 28 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: J 60 LYS cc_start: 0.9061 (mppt) cc_final: 0.8113 (mptt) outliers start: 16 outliers final: 13 residues processed: 71 average time/residue: 0.2330 time to fit residues: 20.2762 Evaluate side-chains 78 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 4975 Z= 0.399 Angle : 0.521 7.240 6720 Z= 0.288 Chirality : 0.051 0.122 870 Planarity : 0.002 0.008 845 Dihedral : 5.231 16.042 725 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.67 % Allowed : 16.33 % Favored : 80.00 % 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: -3.89 (0.25), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 50 PHE 0.014 0.002 PHE F 94 TYR 0.014 0.002 TYR A 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 79 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.580 Fit side-chains REVERT: B 38 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7793 (mp) REVERT: C 35 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7169 (pt0) REVERT: E 28 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6818 (mt-10) REVERT: E 32 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8501 (ttmm) REVERT: G 43 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7234 (mttt) REVERT: H 60 LYS cc_start: 0.8955 (mppt) cc_final: 0.8478 (mptt) REVERT: I 28 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6803 (mt-10) REVERT: J 60 LYS cc_start: 0.8954 (mppt) cc_final: 0.7919 (mptt) outliers start: 18 outliers final: 11 residues processed: 72 average time/residue: 0.2519 time to fit residues: 22.4474 Evaluate side-chains 74 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 0.004 0.022 4975 Z= 0.255 Angle : 0.456 6.537 6720 Z= 0.252 Chirality : 0.050 0.127 870 Planarity : 0.001 0.006 845 Dihedral : 4.902 15.348 725 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.27 % Allowed : 17.14 % Favored : 79.59 % 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: -3.66 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 50 PHE 0.011 0.002 PHE F 94 TYR 0.011 0.002 TYR A 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 74 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: B 38 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7908 (mp) REVERT: B 60 LYS cc_start: 0.8574 (mptt) cc_final: 0.8017 (mptt) REVERT: B 97 LYS cc_start: 0.8665 (mttt) cc_final: 0.8387 (mttt) REVERT: C 35 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7092 (pt0) REVERT: E 28 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: E 32 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8384 (ttmm) REVERT: G 43 LYS cc_start: 0.7829 (mtpt) cc_final: 0.7152 (mttt) REVERT: H 60 LYS cc_start: 0.8896 (mppt) cc_final: 0.8675 (mptt) REVERT: H 97 LYS cc_start: 0.8662 (mttt) cc_final: 0.7452 (mmmt) outliers start: 16 outliers final: 13 residues processed: 67 average time/residue: 0.2215 time to fit residues: 18.5208 Evaluate side-chains 72 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4975 Z= 0.195 Angle : 0.434 6.524 6720 Z= 0.237 Chirality : 0.050 0.128 870 Planarity : 0.001 0.005 845 Dihedral : 4.699 15.475 725 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.45 % Allowed : 17.76 % Favored : 79.80 % 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: -3.45 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 50 PHE 0.010 0.001 PHE F 94 TYR 0.009 0.002 TYR E 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 70 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: B 38 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7902 (mp) REVERT: B 97 LYS cc_start: 0.8665 (mttt) cc_final: 0.8400 (mttt) REVERT: C 35 GLU cc_start: 0.8161 (mm-30) cc_final: 0.6815 (pt0) REVERT: G 43 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7123 (mttt) REVERT: H 60 LYS cc_start: 0.8871 (mppt) cc_final: 0.8451 (mptt) REVERT: I 28 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6911 (mt-10) outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 0.2004 time to fit residues: 16.3982 Evaluate side-chains 67 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 4975 Z= 0.400 Angle : 0.511 7.501 6720 Z= 0.281 Chirality : 0.051 0.124 870 Planarity : 0.002 0.007 845 Dihedral : 5.019 15.969 725 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.67 % Allowed : 16.53 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.26), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS D 50 PHE 0.015 0.002 PHE F 94 TYR 0.013 0.002 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 77 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.575 Fit side-chains REVERT: B 38 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7897 (mp) REVERT: B 97 LYS cc_start: 0.8682 (mttt) cc_final: 0.8412 (mttt) REVERT: C 35 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7043 (pt0) REVERT: D 99 GLN cc_start: 0.7109 (mt0) cc_final: 0.6776 (pm20) REVERT: E 28 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6931 (mt-10) REVERT: E 32 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8447 (ttmm) REVERT: G 43 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7149 (mttt) REVERT: H 60 LYS cc_start: 0.8901 (mppt) cc_final: 0.8466 (mptt) REVERT: I 28 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: J 60 LYS cc_start: 0.8923 (mppt) cc_final: 0.7612 (mptt) outliers start: 18 outliers final: 14 residues processed: 71 average time/residue: 0.2242 time to fit residues: 19.6583 Evaluate side-chains 76 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.0070 chunk 49 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4975 Z= 0.215 Angle : 0.448 7.303 6720 Z= 0.243 Chirality : 0.050 0.130 870 Planarity : 0.001 0.005 845 Dihedral : 4.759 15.768 725 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.27 % Allowed : 16.53 % Favored : 80.20 % 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: -3.34 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 50 PHE 0.010 0.001 PHE F 94 TYR 0.011 0.002 TYR A 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 73 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: B 38 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7865 (mp) REVERT: B 97 LYS cc_start: 0.8642 (mttt) cc_final: 0.8374 (mttt) REVERT: C 35 GLU cc_start: 0.8296 (mm-30) cc_final: 0.6955 (pt0) REVERT: D 99 GLN cc_start: 0.7105 (mt0) cc_final: 0.6810 (pm20) REVERT: E 28 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6995 (mt-10) REVERT: G 43 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7139 (mttt) REVERT: H 60 LYS cc_start: 0.8858 (mppt) cc_final: 0.8458 (mptt) REVERT: I 28 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6877 (mt-10) outliers start: 16 outliers final: 12 residues processed: 68 average time/residue: 0.2469 time to fit residues: 21.5697 Evaluate side-chains 70 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 0.0030 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 0.0060 chunk 8 optimal weight: 6.9990 overall best weight: 3.8012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4975 Z= 0.321 Angle : 0.478 6.877 6720 Z= 0.261 Chirality : 0.050 0.127 870 Planarity : 0.001 0.006 845 Dihedral : 4.858 15.861 725 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.27 % Allowed : 16.73 % Favored : 80.00 % 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: -3.34 (0.27), residues: 705 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 50 PHE 0.013 0.002 PHE F 94 TYR 0.012 0.002 TYR A 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 74 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.454 Fit side-chains REVERT: B 38 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 97 LYS cc_start: 0.8694 (mttt) cc_final: 0.8412 (mttt) REVERT: C 35 GLU cc_start: 0.8318 (mm-30) cc_final: 0.6966 (pt0) REVERT: D 99 GLN cc_start: 0.7113 (mt0) cc_final: 0.6784 (pm20) REVERT: E 28 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6994 (mt-10) REVERT: E 32 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8403 (ttmm) REVERT: G 43 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7148 (mttt) REVERT: H 60 LYS cc_start: 0.8863 (mppt) cc_final: 0.8450 (mptt) REVERT: I 28 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6903 (mt-10) REVERT: J 60 LYS cc_start: 0.8852 (mppt) cc_final: 0.7487 (mptt) outliers start: 16 outliers final: 13 residues processed: 69 average time/residue: 0.2161 time to fit residues: 18.4728 Evaluate side-chains 74 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.122928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093379 restraints weight = 5421.940| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.75 r_work: 0.3267 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4975 Z= 0.244 Angle : 0.450 6.767 6720 Z= 0.245 Chirality : 0.050 0.129 870 Planarity : 0.001 0.006 845 Dihedral : 4.758 15.652 725 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.06 % Allowed : 17.55 % Favored : 79.39 % 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: -3.25 (0.27), 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 0.005 0.001 HIS F 50 PHE 0.012 0.002 PHE F 94 TYR 0.011 0.002 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1316.12 seconds wall clock time: 24 minutes 45.85 seconds (1485.85 seconds total)