Starting phenix.real_space_refine on Sat Apr 4 22:47:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rb3_53884/04_2026/9rb3_53884.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rb3_53884/04_2026/9rb3_53884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rb3_53884/04_2026/9rb3_53884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rb3_53884/04_2026/9rb3_53884.map" model { file = "/net/cci-nas-00/data/ceres_data/9rb3_53884/04_2026/9rb3_53884.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rb3_53884/04_2026/9rb3_53884.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 3240 2.51 5 N 900 2.21 5 O 1060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5200 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 520 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.64, per 1000 atoms: 0.12 Number of scatterers: 5200 At special positions: 0 Unit cell: (104.85, 126.659, 43.6176, 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 1060 8.00 N 900 7.00 C 3240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 282.5 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 removed outlier: 6.526A pdb=" N ALA A 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR C 22 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS A 21 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR E 22 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS C 21 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA E 19 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR G 22 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS E 21 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA G 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR I 22 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS G 21 " --> pdb=" O THR I 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.540A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY C 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY E 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY G 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 57 removed outlier: 5.825A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU C 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU E 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA C 56 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR E 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU G 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA E 56 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR G 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU I 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA G 56 " --> pdb=" O GLU I 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.290A pdb=" N LYS A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL C 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN A 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ASN C 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR A 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS C 60 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL E 63 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLN C 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASN E 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR C 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS E 60 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL G 63 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN E 62 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ASN G 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR E 64 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS G 60 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL I 63 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN G 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ASN I 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR G 64 " --> pdb=" O ASN I 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 70 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 79 removed outlier: 6.532A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA C 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR C 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA E 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL C 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL E 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR G 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA I 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 23 removed outlier: 6.526A pdb=" N ALA B 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N THR D 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS B 21 " --> pdb=" O THR D 22 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA D 19 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR F 22 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS D 21 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA F 19 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR H 22 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS F 21 " --> pdb=" O THR H 22 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA H 19 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N THR J 22 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS H 21 " --> pdb=" O THR J 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.540A pdb=" N GLY B 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY F 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 57 removed outlier: 5.824A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR D 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU F 57 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA D 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N THR F 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU H 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA F 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N THR H 54 " --> pdb=" O VAL J 55 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLU J 57 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA H 56 " --> pdb=" O GLU J 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 66 removed outlier: 6.291A pdb=" N LYS B 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL D 63 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN B 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ASN D 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR B 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS D 60 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL F 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN D 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ASN F 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR D 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS F 60 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL H 63 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN F 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ASN H 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR F 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS H 60 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL J 63 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN H 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ASN J 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N THR H 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 70 through 72 Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 79 removed outlier: 6.531A pdb=" N THR B 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA D 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR D 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA F 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR F 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA H 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL F 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR H 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA J 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL H 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 88 through 90 32 hydrogen bonds defined for protein. 96 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.67 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 930 1.29 - 1.35: 799 1.35 - 1.42: 168 1.42 - 1.48: 853 1.48 - 1.54: 2460 Bond restraints: 5210 Sorted by residual: bond pdb=" C GLY J 36 " pdb=" O GLY J 36 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.30e-03 1.16e+04 7.15e-01 bond pdb=" C GLY B 36 " pdb=" O GLY B 36 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.30e-03 1.16e+04 7.01e-01 bond pdb=" CA GLU A 61 " pdb=" C GLU A 61 " ideal model delta sigma weight residual 1.532 1.524 0.008 9.60e-03 1.09e+04 6.86e-01 bond pdb=" C GLY I 36 " pdb=" O GLY I 36 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.30e-03 1.16e+04 6.79e-01 bond pdb=" C GLY C 36 " pdb=" O GLY C 36 " ideal model delta sigma weight residual 1.243 1.235 0.008 9.30e-03 1.16e+04 6.63e-01 ... (remaining 5205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.67: 5908 0.67 - 1.34: 801 1.34 - 2.01: 224 2.01 - 2.68: 57 2.68 - 3.35: 30 Bond angle restraints: 7020 Sorted by residual: angle pdb=" CA GLU I 61 " pdb=" C GLU I 61 " pdb=" N GLN I 62 " ideal model delta sigma weight residual 114.17 117.52 -3.35 1.45e+00 4.76e-01 5.33e+00 angle pdb=" CA GLU J 61 " pdb=" C GLU J 61 " pdb=" N GLN J 62 " ideal model delta sigma weight residual 114.17 117.51 -3.34 1.45e+00 4.76e-01 5.30e+00 angle pdb=" CA GLU E 61 " pdb=" C GLU E 61 " pdb=" N GLN E 62 " ideal model delta sigma weight residual 114.17 117.51 -3.34 1.45e+00 4.76e-01 5.30e+00 angle pdb=" CA GLU D 61 " pdb=" C GLU D 61 " pdb=" N GLN D 62 " ideal model delta sigma weight residual 114.17 117.50 -3.33 1.45e+00 4.76e-01 5.28e+00 angle pdb=" CA GLU G 61 " pdb=" C GLU G 61 " pdb=" N GLN G 62 " ideal model delta sigma weight residual 114.17 117.49 -3.32 1.45e+00 4.76e-01 5.25e+00 ... (remaining 7015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.12: 2810 12.12 - 24.24: 130 24.24 - 36.36: 90 36.36 - 48.49: 10 48.49 - 60.61: 30 Dihedral angle restraints: 3070 sinusoidal: 1050 harmonic: 2020 Sorted by residual: dihedral pdb=" CB LYS E 96 " pdb=" CG LYS E 96 " pdb=" CD LYS E 96 " pdb=" CE LYS E 96 " ideal model delta sinusoidal sigma weight residual -60.00 -99.00 39.00 3 1.50e+01 4.44e-03 6.89e+00 dihedral pdb=" CB LYS G 96 " pdb=" CG LYS G 96 " pdb=" CD LYS G 96 " pdb=" CE LYS G 96 " ideal model delta sinusoidal sigma weight residual -60.00 -98.96 38.96 3 1.50e+01 4.44e-03 6.88e+00 dihedral pdb=" CB LYS B 96 " pdb=" CG LYS B 96 " pdb=" CD LYS B 96 " pdb=" CE LYS B 96 " ideal model delta sinusoidal sigma weight residual -60.00 -98.95 38.95 3 1.50e+01 4.44e-03 6.88e+00 ... (remaining 3067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 516 0.023 - 0.046: 193 0.046 - 0.069: 61 0.069 - 0.092: 30 0.092 - 0.116: 120 Chirality restraints: 920 Sorted by residual: chirality pdb=" CA ILE G 88 " pdb=" N ILE G 88 " pdb=" C ILE G 88 " pdb=" CB ILE G 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.34e-01 chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.33e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 917 not shown) Planarity restraints: 870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 39 " -0.002 2.00e-02 2.50e+03 6.17e-03 7.61e-01 pdb=" CG TYR H 39 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR H 39 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR H 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR H 39 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 39 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 39 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 39 " 0.002 2.00e-02 2.50e+03 6.09e-03 7.43e-01 pdb=" CG TYR C 39 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR C 39 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 39 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 39 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 39 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 39 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 39 " -0.002 2.00e-02 2.50e+03 6.05e-03 7.31e-01 pdb=" CG TYR F 39 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR F 39 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR F 39 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR F 39 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR F 39 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR F 39 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 39 " 0.001 2.00e-02 2.50e+03 ... (remaining 867 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1860 2.91 - 3.41: 4414 3.41 - 3.91: 8181 3.91 - 4.40: 7926 4.40 - 4.90: 14263 Nonbonded interactions: 36644 Sorted by model distance: nonbonded pdb=" O THR A 59 " pdb=" OG1 THR C 59 " model vdw 2.414 3.040 nonbonded pdb=" O THR F 59 " pdb=" OG1 THR H 59 " model vdw 2.414 3.040 nonbonded pdb=" O THR E 59 " pdb=" OG1 THR G 59 " model vdw 2.414 3.040 nonbonded pdb=" O THR G 59 " pdb=" OG1 THR I 59 " model vdw 2.414 3.040 nonbonded pdb=" O THR D 59 " pdb=" OG1 THR F 59 " model vdw 2.414 3.040 ... (remaining 36639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.480 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.002 0.017 5210 Z= 0.151 Angle : 0.573 3.346 7020 Z= 0.382 Chirality : 0.047 0.116 920 Planarity : 0.001 0.006 870 Dihedral : 12.168 60.606 1790 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.29), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.004 TYR H 39 PHE 0.003 0.002 PHE G 94 HIS 0.000 0.000 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 5210) covalent geometry : angle 0.57346 ( 7020) hydrogen bonds : bond 0.21301 ( 32) hydrogen bonds : angle 8.98345 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.227 Fit side-chains REVERT: F 96 LYS cc_start: 0.6942 (ttmt) cc_final: 0.6178 (ttpt) REVERT: G 96 LYS cc_start: 0.6938 (ttmt) cc_final: 0.6153 (ttpt) REVERT: H 96 LYS cc_start: 0.6956 (ttmt) cc_final: 0.6203 (ttpt) REVERT: I 96 LYS cc_start: 0.7073 (ttmt) cc_final: 0.6433 (ttpt) REVERT: J 96 LYS cc_start: 0.6993 (ttmt) cc_final: 0.6381 (ttpt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1188 time to fit residues: 14.9325 Evaluate side-chains 101 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.135254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.107462 restraints weight = 8128.067| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.89 r_work: 0.3772 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 5210 Z= 0.360 Angle : 0.712 5.252 7020 Z= 0.423 Chirality : 0.054 0.139 920 Planarity : 0.004 0.010 870 Dihedral : 5.115 14.742 740 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 2.08 % Allowed : 8.87 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.004 TYR B 39 PHE 0.023 0.005 PHE F 94 HIS 0.003 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00794 ( 5210) covalent geometry : angle 0.71154 ( 7020) hydrogen bonds : bond 0.07200 ( 32) hydrogen bonds : angle 4.56394 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.219 Fit side-chains REVERT: A 83 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7210 (tm-30) REVERT: D 83 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6752 (tm-30) REVERT: F 83 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6867 (tm-30) REVERT: F 87 SER cc_start: 0.7992 (p) cc_final: 0.7727 (t) REVERT: G 35 GLU cc_start: 0.5520 (mp0) cc_final: 0.5229 (mp0) REVERT: G 96 LYS cc_start: 0.6936 (ttmt) cc_final: 0.6166 (ttpt) REVERT: H 35 GLU cc_start: 0.5592 (mp0) cc_final: 0.5379 (mp0) REVERT: H 96 LYS cc_start: 0.6832 (ttmt) cc_final: 0.6094 (ttpt) REVERT: I 96 LYS cc_start: 0.7005 (ttmt) cc_final: 0.6364 (ttpt) REVERT: J 57 GLU cc_start: 0.8075 (pt0) cc_final: 0.7780 (pt0) REVERT: J 96 LYS cc_start: 0.6827 (ttmt) cc_final: 0.6336 (ttpt) outliers start: 11 outliers final: 10 residues processed: 143 average time/residue: 0.1022 time to fit residues: 17.5513 Evaluate side-chains 133 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.137578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.109973 restraints weight = 7978.291| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.87 r_work: 0.3797 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5210 Z= 0.177 Angle : 0.536 4.589 7020 Z= 0.308 Chirality : 0.050 0.139 920 Planarity : 0.002 0.010 870 Dihedral : 4.306 12.843 740 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 2.26 % Allowed : 16.42 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.24 (0.28), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 39 PHE 0.013 0.003 PHE E 94 HIS 0.001 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 5210) covalent geometry : angle 0.53576 ( 7020) hydrogen bonds : bond 0.05171 ( 32) hydrogen bonds : angle 4.69893 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.198 Fit side-chains REVERT: C 83 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6718 (tm-30) REVERT: C 87 SER cc_start: 0.8300 (p) cc_final: 0.8089 (p) REVERT: D 83 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6779 (tm-30) REVERT: D 87 SER cc_start: 0.8253 (p) cc_final: 0.8050 (p) REVERT: E 83 GLU cc_start: 0.6912 (tm-30) cc_final: 0.6457 (tm-30) REVERT: F 83 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6974 (tm-30) REVERT: G 96 LYS cc_start: 0.6894 (ttmt) cc_final: 0.6202 (ttpt) REVERT: H 35 GLU cc_start: 0.5718 (mp0) cc_final: 0.5427 (mp0) REVERT: H 96 LYS cc_start: 0.6939 (ttmt) cc_final: 0.6260 (ttpt) REVERT: I 96 LYS cc_start: 0.7028 (ttmt) cc_final: 0.6341 (ttpt) REVERT: J 57 GLU cc_start: 0.8223 (pt0) cc_final: 0.7924 (pt0) REVERT: J 96 LYS cc_start: 0.6867 (ttmt) cc_final: 0.6407 (ttpt) outliers start: 12 outliers final: 11 residues processed: 128 average time/residue: 0.0983 time to fit residues: 15.2696 Evaluate side-chains 128 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 9 optimal weight: 0.0270 chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 overall best weight: 4.8046 ------------------------------------------------------------------------------- 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 = 0.4246 r_free = 0.4246 target = 0.135427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.107843 restraints weight = 8016.769| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.85 r_work: 0.3810 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 5210 Z= 0.210 Angle : 0.552 4.277 7020 Z= 0.321 Chirality : 0.051 0.145 920 Planarity : 0.002 0.008 870 Dihedral : 4.301 12.103 740 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 4.72 % Allowed : 17.55 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR F 39 PHE 0.013 0.003 PHE E 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 5210) covalent geometry : angle 0.55206 ( 7020) hydrogen bonds : bond 0.05742 ( 32) hydrogen bonds : angle 4.62619 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.206 Fit side-chains REVERT: C 83 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6768 (tm-30) REVERT: C 87 SER cc_start: 0.8335 (p) cc_final: 0.8101 (p) REVERT: D 83 GLU cc_start: 0.7157 (tm-30) cc_final: 0.6823 (tm-30) REVERT: D 87 SER cc_start: 0.8353 (p) cc_final: 0.8119 (p) REVERT: E 83 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6490 (tm-30) REVERT: F 83 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6887 (tm-30) REVERT: G 96 LYS cc_start: 0.6857 (ttmt) cc_final: 0.6206 (ttpt) REVERT: H 35 GLU cc_start: 0.5466 (mp0) cc_final: 0.5101 (mp0) REVERT: H 96 LYS cc_start: 0.6823 (ttmt) cc_final: 0.6144 (ttpt) REVERT: I 96 LYS cc_start: 0.6912 (ttmt) cc_final: 0.6239 (ttpt) REVERT: J 57 GLU cc_start: 0.8177 (pt0) cc_final: 0.7872 (pt0) REVERT: J 96 LYS cc_start: 0.6773 (ttmt) cc_final: 0.6307 (ttpt) outliers start: 25 outliers final: 25 residues processed: 122 average time/residue: 0.0985 time to fit residues: 14.7807 Evaluate side-chains 136 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 72 THR 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 14 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 60 optimal weight: 0.0170 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 overall best weight: 5.2026 ------------------------------------------------------------------------------- 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 = 0.4230 r_free = 0.4230 target = 0.134421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.106701 restraints weight = 8141.164| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.87 r_work: 0.3790 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5210 Z= 0.220 Angle : 0.561 4.446 7020 Z= 0.327 Chirality : 0.052 0.144 920 Planarity : 0.002 0.006 870 Dihedral : 4.363 11.852 740 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 5.28 % Allowed : 17.17 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.013 0.003 PHE E 94 HIS 0.002 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 5210) covalent geometry : angle 0.56134 ( 7020) hydrogen bonds : bond 0.05907 ( 32) hydrogen bonds : angle 4.51799 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.189 Fit side-chains REVERT: C 83 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6784 (tm-30) REVERT: C 87 SER cc_start: 0.8360 (p) cc_final: 0.8105 (p) REVERT: D 83 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6840 (tm-30) REVERT: D 87 SER cc_start: 0.8364 (p) cc_final: 0.8113 (p) REVERT: E 83 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6713 (tm-30) REVERT: F 83 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6937 (tm-30) REVERT: G 96 LYS cc_start: 0.6896 (ttmt) cc_final: 0.6352 (ttpt) REVERT: H 96 LYS cc_start: 0.6942 (ttmt) cc_final: 0.6290 (ttpt) REVERT: I 96 LYS cc_start: 0.6936 (ttmt) cc_final: 0.6307 (ttpt) REVERT: J 57 GLU cc_start: 0.8209 (pt0) cc_final: 0.7891 (pt0) REVERT: J 96 LYS cc_start: 0.6857 (ttmt) cc_final: 0.6388 (ttpt) outliers start: 28 outliers final: 28 residues processed: 122 average time/residue: 0.0904 time to fit residues: 13.6289 Evaluate side-chains 134 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 72 THR 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 59 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 11 optimal weight: 0.0070 chunk 17 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.135179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.107217 restraints weight = 8086.636| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 3.88 r_work: 0.3804 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5210 Z= 0.191 Angle : 0.518 4.492 7020 Z= 0.302 Chirality : 0.052 0.142 920 Planarity : 0.002 0.011 870 Dihedral : 4.143 11.549 740 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 5.66 % Allowed : 18.30 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 39 PHE 0.011 0.003 PHE E 94 HIS 0.001 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 5210) covalent geometry : angle 0.51812 ( 7020) hydrogen bonds : bond 0.05357 ( 32) hydrogen bonds : angle 4.51668 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.217 Fit side-chains REVERT: C 83 GLU cc_start: 0.7096 (tm-30) cc_final: 0.6772 (tm-30) REVERT: C 87 SER cc_start: 0.8375 (p) cc_final: 0.8152 (p) REVERT: D 83 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6894 (tm-30) REVERT: D 87 SER cc_start: 0.8353 (p) cc_final: 0.8102 (p) REVERT: E 83 GLU cc_start: 0.7055 (tm-30) cc_final: 0.6733 (tm-30) REVERT: F 83 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: G 96 LYS cc_start: 0.6935 (ttmt) cc_final: 0.6408 (ttpt) REVERT: H 96 LYS cc_start: 0.7002 (ttmt) cc_final: 0.6335 (ttpt) REVERT: I 96 LYS cc_start: 0.6914 (ttmt) cc_final: 0.6285 (ttpt) REVERT: J 57 GLU cc_start: 0.8224 (pt0) cc_final: 0.7907 (pt0) REVERT: J 96 LYS cc_start: 0.6857 (ttmt) cc_final: 0.6373 (ttpt) outliers start: 30 outliers final: 28 residues processed: 120 average time/residue: 0.0888 time to fit residues: 13.1637 Evaluate side-chains 141 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 72 THR 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 24 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 0.0870 chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.9764 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.135805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.107650 restraints weight = 7984.343| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.88 r_work: 0.3814 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5210 Z= 0.174 Angle : 0.501 4.558 7020 Z= 0.291 Chirality : 0.052 0.142 920 Planarity : 0.002 0.008 870 Dihedral : 3.993 11.206 740 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 5.47 % Allowed : 19.25 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.001 TYR I 39 PHE 0.011 0.003 PHE F 94 HIS 0.001 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 5210) covalent geometry : angle 0.50109 ( 7020) hydrogen bonds : bond 0.05129 ( 32) hydrogen bonds : angle 4.55569 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.197 Fit side-chains REVERT: B 35 GLU cc_start: 0.5997 (mp0) cc_final: 0.5747 (mp0) REVERT: C 83 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6821 (tm-30) REVERT: C 87 SER cc_start: 0.8383 (p) cc_final: 0.8139 (p) REVERT: D 83 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6848 (tm-30) REVERT: D 87 SER cc_start: 0.8384 (p) cc_final: 0.8130 (p) REVERT: E 83 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6651 (tm-30) REVERT: F 83 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: G 83 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6305 (tm-30) REVERT: G 96 LYS cc_start: 0.6892 (ttmt) cc_final: 0.6371 (ttpt) REVERT: H 83 GLU cc_start: 0.6658 (tm-30) cc_final: 0.6433 (tm-30) REVERT: H 96 LYS cc_start: 0.6979 (ttmt) cc_final: 0.6317 (ttpt) REVERT: I 96 LYS cc_start: 0.6921 (ttmt) cc_final: 0.6291 (ttpt) REVERT: J 57 GLU cc_start: 0.8238 (pt0) cc_final: 0.7925 (pt0) REVERT: J 96 LYS cc_start: 0.6864 (ttmt) cc_final: 0.6377 (ttpt) outliers start: 29 outliers final: 28 residues processed: 126 average time/residue: 0.0910 time to fit residues: 14.0614 Evaluate side-chains 147 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 72 THR 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 46 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.134676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.106377 restraints weight = 8069.344| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.92 r_work: 0.3810 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 5210 Z= 0.218 Angle : 0.547 4.913 7020 Z= 0.320 Chirality : 0.053 0.143 920 Planarity : 0.002 0.006 870 Dihedral : 4.241 10.890 740 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.97 % Favored : 88.03 % Rotamer: Outliers : 5.66 % Allowed : 19.81 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 39 PHE 0.013 0.003 PHE E 94 HIS 0.002 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 5210) covalent geometry : angle 0.54665 ( 7020) hydrogen bonds : bond 0.05846 ( 32) hydrogen bonds : angle 4.53990 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.239 Fit side-chains REVERT: B 35 GLU cc_start: 0.5969 (mp0) cc_final: 0.5722 (mp0) REVERT: C 87 SER cc_start: 0.8378 (p) cc_final: 0.8156 (p) REVERT: D 83 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6858 (tm-30) REVERT: D 87 SER cc_start: 0.8386 (p) cc_final: 0.8182 (p) REVERT: E 83 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6657 (tm-30) REVERT: F 83 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: G 83 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6357 (tm-30) REVERT: G 96 LYS cc_start: 0.6933 (ttmt) cc_final: 0.6407 (ttpt) REVERT: H 83 GLU cc_start: 0.6667 (tm-30) cc_final: 0.6428 (tm-30) REVERT: H 96 LYS cc_start: 0.7077 (ttmt) cc_final: 0.6436 (ttpt) REVERT: I 96 LYS cc_start: 0.6933 (ttmt) cc_final: 0.6315 (ttpt) REVERT: J 57 GLU cc_start: 0.8259 (pt0) cc_final: 0.7926 (pt0) REVERT: J 96 LYS cc_start: 0.6913 (ttmt) cc_final: 0.6371 (ttpt) outliers start: 30 outliers final: 28 residues processed: 131 average time/residue: 0.0923 time to fit residues: 14.9163 Evaluate side-chains 140 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 72 THR 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 41 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 63 optimal weight: 0.0170 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 4.4824 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.135396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.107290 restraints weight = 8013.144| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.90 r_work: 0.3804 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5210 Z= 0.192 Angle : 0.528 5.135 7020 Z= 0.306 Chirality : 0.053 0.142 920 Planarity : 0.002 0.017 870 Dihedral : 4.036 10.095 740 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 5.47 % Allowed : 21.32 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.001 TYR J 39 PHE 0.011 0.003 PHE F 94 HIS 0.001 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 5210) covalent geometry : angle 0.52782 ( 7020) hydrogen bonds : bond 0.05377 ( 32) hydrogen bonds : angle 4.56699 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.184 Fit side-chains REVERT: B 35 GLU cc_start: 0.5915 (mp0) cc_final: 0.5664 (mp0) REVERT: C 87 SER cc_start: 0.8395 (p) cc_final: 0.8140 (p) REVERT: D 83 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6854 (tm-30) REVERT: D 87 SER cc_start: 0.8413 (p) cc_final: 0.8173 (p) REVERT: E 83 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6768 (tm-30) REVERT: F 83 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6792 (tm-30) REVERT: G 83 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6343 (tm-30) REVERT: G 96 LYS cc_start: 0.6899 (ttmt) cc_final: 0.6389 (ttpt) REVERT: H 83 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6429 (tm-30) REVERT: H 96 LYS cc_start: 0.7070 (ttmt) cc_final: 0.6430 (ttpt) REVERT: I 96 LYS cc_start: 0.6938 (ttmt) cc_final: 0.6293 (ttpt) REVERT: J 57 GLU cc_start: 0.8265 (pt0) cc_final: 0.7937 (pt0) REVERT: J 96 LYS cc_start: 0.6900 (ttmt) cc_final: 0.6368 (ttpt) outliers start: 29 outliers final: 28 residues processed: 128 average time/residue: 0.0883 time to fit residues: 13.8822 Evaluate side-chains 143 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 72 THR 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 41 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 13 optimal weight: 0.0060 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 67 optimal weight: 0.0040 chunk 51 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.4014 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.136304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.108157 restraints weight = 8051.747| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.90 r_work: 0.3820 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5210 Z= 0.152 Angle : 0.484 5.355 7020 Z= 0.280 Chirality : 0.052 0.139 920 Planarity : 0.002 0.015 870 Dihedral : 3.771 9.814 740 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 5.28 % Allowed : 21.32 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR J 39 PHE 0.010 0.002 PHE C 94 HIS 0.001 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5210) covalent geometry : angle 0.48403 ( 7020) hydrogen bonds : bond 0.04748 ( 32) hydrogen bonds : angle 4.55878 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.199 Fit side-chains REVERT: B 35 GLU cc_start: 0.5967 (mp0) cc_final: 0.5715 (mp0) REVERT: C 87 SER cc_start: 0.8346 (p) cc_final: 0.8091 (p) REVERT: D 83 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6845 (tm-30) REVERT: D 87 SER cc_start: 0.8375 (p) cc_final: 0.8140 (p) REVERT: E 83 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6753 (tm-30) REVERT: F 83 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6825 (tm-30) REVERT: G 83 GLU cc_start: 0.6645 (tm-30) cc_final: 0.6343 (tm-30) REVERT: G 96 LYS cc_start: 0.6851 (ttmt) cc_final: 0.6370 (ttpt) REVERT: H 83 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6451 (tm-30) REVERT: H 96 LYS cc_start: 0.6963 (ttmt) cc_final: 0.6324 (ttpt) REVERT: I 96 LYS cc_start: 0.6933 (ttmt) cc_final: 0.6273 (ttpt) REVERT: J 57 GLU cc_start: 0.8266 (pt0) cc_final: 0.7939 (pt0) REVERT: J 96 LYS cc_start: 0.6850 (ttmt) cc_final: 0.6330 (ttpt) outliers start: 28 outliers final: 28 residues processed: 124 average time/residue: 0.0987 time to fit residues: 15.0188 Evaluate side-chains 145 residues out of total 530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 72 THR 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 33 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.136082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.107874 restraints weight = 8070.732| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.90 r_work: 0.3812 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5210 Z= 0.167 Angle : 0.498 5.298 7020 Z= 0.288 Chirality : 0.052 0.140 920 Planarity : 0.002 0.015 870 Dihedral : 3.838 9.826 740 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 5.47 % Allowed : 21.32 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.001 TYR F 39 PHE 0.011 0.003 PHE F 94 HIS 0.001 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 5210) covalent geometry : angle 0.49832 ( 7020) hydrogen bonds : bond 0.05081 ( 32) hydrogen bonds : angle 4.59324 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1191.45 seconds wall clock time: 21 minutes 8.19 seconds (1268.19 seconds total)