Starting phenix.real_space_refine on Sun Feb 8 10:49:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9myg_48737/02_2026/9myg_48737.cif Found real_map, /net/cci-nas-00/data/ceres_data/9myg_48737/02_2026/9myg_48737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9myg_48737/02_2026/9myg_48737.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9myg_48737/02_2026/9myg_48737.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9myg_48737/02_2026/9myg_48737.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9myg_48737/02_2026/9myg_48737.map" } resolution = 3.8 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= 0.019 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: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 13968 2.51 5 N 3552 2.21 5 O 5256 1.98 5 H 22032 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 216 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44904 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1871 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 134} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 4.15, per 1000 atoms: 0.09 Number of scatterers: 44904 At special positions: 0 Unit cell: (113.4, 113.4, 218.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 5256 8.00 N 3552 7.00 C 13968 6.00 H 22032 1.00 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: 4.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 48 sheets defined 33.1% alpha, 30.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A 49 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER A 120 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 49 " --> pdb=" O ASP B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 95 removed outlier: 3.752A pdb=" N ASN B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER B 120 " --> pdb=" O SER B 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER C 120 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 95 removed outlier: 3.752A pdb=" N ASN D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER D 120 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN E 94 " --> pdb=" O GLY E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER E 120 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA F 41 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER F 49 " --> pdb=" O ASP F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN F 94 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER F 120 " --> pdb=" O SER F 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER G 49 " --> pdb=" O ASP G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN G 94 " --> pdb=" O GLY G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER G 120 " --> pdb=" O SER G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER H 49 " --> pdb=" O ASP H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN H 94 " --> pdb=" O GLY H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 121 removed outlier: 4.122A pdb=" N SER H 120 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA I 41 " --> pdb=" O ALA I 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE I 42 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 49 " --> pdb=" O ASP I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN I 94 " --> pdb=" O GLY I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER I 120 " --> pdb=" O SER I 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA J 41 " --> pdb=" O ALA J 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER J 49 " --> pdb=" O ASP J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER J 120 " --> pdb=" O SER J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA K 41 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE K 42 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER K 49 " --> pdb=" O ASP K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN K 94 " --> pdb=" O GLY K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER K 120 " --> pdb=" O SER K 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA L 41 " --> pdb=" O ALA L 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE L 42 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER L 49 " --> pdb=" O ASP L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 95 removed outlier: 3.752A pdb=" N ASN L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 121 removed outlier: 4.122A pdb=" N SER L 120 " --> pdb=" O SER L 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE M 42 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER M 49 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN M 94 " --> pdb=" O GLY M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 121 removed outlier: 4.122A pdb=" N SER M 120 " --> pdb=" O SER M 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA N 41 " --> pdb=" O ALA N 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE N 42 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER N 49 " --> pdb=" O ASP N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN N 94 " --> pdb=" O GLY N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 121 removed outlier: 4.122A pdb=" N SER N 120 " --> pdb=" O SER N 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA O 41 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE O 42 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER O 49 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN O 94 " --> pdb=" O GLY O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER O 120 " --> pdb=" O SER O 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE P 42 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER P 49 " --> pdb=" O ASP P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 95 removed outlier: 3.752A pdb=" N ASN P 94 " --> pdb=" O GLY P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER P 120 " --> pdb=" O SER P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA Q 41 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE Q 42 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER Q 49 " --> pdb=" O ASP Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN Q 94 " --> pdb=" O GLY Q 90 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER Q 120 " --> pdb=" O SER Q 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE R 42 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER R 49 " --> pdb=" O ASP R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 95 removed outlier: 3.752A pdb=" N ASN R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER R 120 " --> pdb=" O SER R 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER S 49 " --> pdb=" O ASP S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN S 94 " --> pdb=" O GLY S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER S 120 " --> pdb=" O SER S 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA T 41 " --> pdb=" O ALA T 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE T 42 " --> pdb=" O VAL T 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER T 49 " --> pdb=" O ASP T 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN T 94 " --> pdb=" O GLY T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER T 120 " --> pdb=" O SER T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA U 41 " --> pdb=" O ALA U 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE U 42 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER U 49 " --> pdb=" O ASP U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN U 94 " --> pdb=" O GLY U 90 " (cutoff:3.500A) Processing helix chain 'U' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER U 120 " --> pdb=" O SER U 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA V 41 " --> pdb=" O ALA V 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE V 42 " --> pdb=" O VAL V 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN V 94 " --> pdb=" O GLY V 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER V 120 " --> pdb=" O SER V 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA W 41 " --> pdb=" O ALA W 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE W 42 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER W 49 " --> pdb=" O ASP W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN W 94 " --> pdb=" O GLY W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER W 120 " --> pdb=" O SER W 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 49 removed outlier: 3.748A pdb=" N ALA X 41 " --> pdb=" O ALA X 37 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE X 42 " --> pdb=" O VAL X 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER X 49 " --> pdb=" O ASP X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 95 removed outlier: 3.753A pdb=" N ASN X 94 " --> pdb=" O GLY X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 121 removed outlier: 4.121A pdb=" N SER X 120 " --> pdb=" O SER X 117 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY A 57 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU A 81 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY A 129 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU A 150 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE A 131 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A 148 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA A 133 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY B 57 " --> pdb=" O THR B 74 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU B 81 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY B 129 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU B 150 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE B 131 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 148 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA B 133 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 57 through 63 removed outlier: 6.799A pdb=" N GLY C 57 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU C 81 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY C 129 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU C 150 " --> pdb=" O GLY C 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 131 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER C 148 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA C 133 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY D 57 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU D 81 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY D 129 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU D 150 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE D 131 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER D 148 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA D 133 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY E 57 " --> pdb=" O THR E 74 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU E 81 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY E 129 " --> pdb=" O GLU E 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU E 150 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE E 131 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER E 148 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA E 133 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY F 57 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU F 81 " --> pdb=" O VAL F 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY F 129 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU F 150 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE F 131 " --> pdb=" O SER F 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER F 148 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA F 133 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'G' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY G 57 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'G' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU G 81 " --> pdb=" O VAL G 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY G 129 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU G 150 " --> pdb=" O GLY G 129 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE G 131 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER G 148 " --> pdb=" O ILE G 131 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA G 133 " --> pdb=" O VAL G 146 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY H 57 " --> pdb=" O THR H 74 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'H' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU H 81 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY H 129 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU H 150 " --> pdb=" O GLY H 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE H 131 " --> pdb=" O SER H 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER H 148 " --> pdb=" O ILE H 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA H 133 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'I' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY I 57 " --> pdb=" O THR I 74 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU I 81 " --> pdb=" O VAL I 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY I 129 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU I 150 " --> pdb=" O GLY I 129 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE I 131 " --> pdb=" O SER I 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER I 148 " --> pdb=" O ILE I 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA I 133 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'J' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY J 57 " --> pdb=" O THR J 74 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'J' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU J 81 " --> pdb=" O VAL J 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY J 129 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU J 150 " --> pdb=" O GLY J 129 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE J 131 " --> pdb=" O SER J 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER J 148 " --> pdb=" O ILE J 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA J 133 " --> pdb=" O VAL J 146 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'K' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY K 57 " --> pdb=" O THR K 74 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'K' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU K 81 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY K 129 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU K 150 " --> pdb=" O GLY K 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE K 131 " --> pdb=" O SER K 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER K 148 " --> pdb=" O ILE K 131 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA K 133 " --> pdb=" O VAL K 146 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'L' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY L 57 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'L' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU L 81 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY L 129 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU L 150 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE L 131 " --> pdb=" O SER L 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER L 148 " --> pdb=" O ILE L 131 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA L 133 " --> pdb=" O VAL L 146 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'M' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY M 57 " --> pdb=" O THR M 74 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'M' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU M 81 " --> pdb=" O VAL M 136 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY M 129 " --> pdb=" O GLU M 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU M 150 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE M 131 " --> pdb=" O SER M 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER M 148 " --> pdb=" O ILE M 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA M 133 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'N' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY N 57 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'N' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU N 81 " --> pdb=" O VAL N 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY N 129 " --> pdb=" O GLU N 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU N 150 " --> pdb=" O GLY N 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE N 131 " --> pdb=" O SER N 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER N 148 " --> pdb=" O ILE N 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA N 133 " --> pdb=" O VAL N 146 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'O' and resid 57 through 63 removed outlier: 6.799A pdb=" N GLY O 57 " --> pdb=" O THR O 74 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'O' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU O 81 " --> pdb=" O VAL O 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY O 129 " --> pdb=" O GLU O 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU O 150 " --> pdb=" O GLY O 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE O 131 " --> pdb=" O SER O 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER O 148 " --> pdb=" O ILE O 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA O 133 " --> pdb=" O VAL O 146 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'P' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY P 57 " --> pdb=" O THR P 74 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'P' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU P 81 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY P 129 " --> pdb=" O GLU P 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU P 150 " --> pdb=" O GLY P 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE P 131 " --> pdb=" O SER P 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER P 148 " --> pdb=" O ILE P 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA P 133 " --> pdb=" O VAL P 146 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'Q' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY Q 57 " --> pdb=" O THR Q 74 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'Q' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU Q 81 " --> pdb=" O VAL Q 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY Q 129 " --> pdb=" O GLU Q 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU Q 150 " --> pdb=" O GLY Q 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE Q 131 " --> pdb=" O SER Q 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER Q 148 " --> pdb=" O ILE Q 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA Q 133 " --> pdb=" O VAL Q 146 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'R' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY R 57 " --> pdb=" O THR R 74 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'R' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU R 81 " --> pdb=" O VAL R 136 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY R 129 " --> pdb=" O GLU R 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU R 150 " --> pdb=" O GLY R 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE R 131 " --> pdb=" O SER R 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER R 148 " --> pdb=" O ILE R 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA R 133 " --> pdb=" O VAL R 146 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'S' and resid 57 through 63 removed outlier: 6.799A pdb=" N GLY S 57 " --> pdb=" O THR S 74 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'S' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU S 81 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLY S 129 " --> pdb=" O GLU S 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU S 150 " --> pdb=" O GLY S 129 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE S 131 " --> pdb=" O SER S 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER S 148 " --> pdb=" O ILE S 131 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA S 133 " --> pdb=" O VAL S 146 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'T' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY T 57 " --> pdb=" O THR T 74 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'T' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU T 81 " --> pdb=" O VAL T 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY T 129 " --> pdb=" O GLU T 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU T 150 " --> pdb=" O GLY T 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE T 131 " --> pdb=" O SER T 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER T 148 " --> pdb=" O ILE T 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA T 133 " --> pdb=" O VAL T 146 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'U' and resid 57 through 63 removed outlier: 6.799A pdb=" N GLY U 57 " --> pdb=" O THR U 74 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'U' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU U 81 " --> pdb=" O VAL U 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY U 129 " --> pdb=" O GLU U 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU U 150 " --> pdb=" O GLY U 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE U 131 " --> pdb=" O SER U 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER U 148 " --> pdb=" O ILE U 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA U 133 " --> pdb=" O VAL U 146 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'V' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY V 57 " --> pdb=" O THR V 74 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'V' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU V 81 " --> pdb=" O VAL V 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY V 129 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU V 150 " --> pdb=" O GLY V 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE V 131 " --> pdb=" O SER V 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER V 148 " --> pdb=" O ILE V 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA V 133 " --> pdb=" O VAL V 146 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'W' and resid 57 through 63 removed outlier: 6.800A pdb=" N GLY W 57 " --> pdb=" O THR W 74 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'W' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU W 81 " --> pdb=" O VAL W 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY W 129 " --> pdb=" O GLU W 150 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU W 150 " --> pdb=" O GLY W 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE W 131 " --> pdb=" O SER W 148 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER W 148 " --> pdb=" O ILE W 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA W 133 " --> pdb=" O VAL W 146 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'X' and resid 57 through 63 removed outlier: 6.799A pdb=" N GLY X 57 " --> pdb=" O THR X 74 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.833A pdb=" N LEU X 81 " --> pdb=" O VAL X 136 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY X 129 " --> pdb=" O GLU X 150 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU X 150 " --> pdb=" O GLY X 129 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE X 131 " --> pdb=" O SER X 148 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER X 148 " --> pdb=" O ILE X 131 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA X 133 " --> pdb=" O VAL X 146 " (cutoff:3.500A) 1248 hydrogen bonds defined for protein. 3528 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: 13.56 Time building geometry restraints manager: 5.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 22032 1.03 - 1.23: 0 1.23 - 1.42: 9144 1.42 - 1.62: 13680 1.62 - 1.81: 192 Bond restraints: 45048 Sorted by residual: bond pdb=" N VAL U 19 " pdb=" CA VAL U 19 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N VAL B 19 " pdb=" CA VAL B 19 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" N VAL K 19 " pdb=" CA VAL K 19 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N VAL T 19 " pdb=" CA VAL T 19 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.73e+00 bond pdb=" N VAL H 19 " pdb=" CA VAL H 19 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.71e+00 ... (remaining 45043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 77270 1.16 - 2.33: 3722 2.33 - 3.49: 176 3.49 - 4.65: 144 4.65 - 5.82: 24 Bond angle restraints: 81336 Sorted by residual: angle pdb=" CA SER K 97 " pdb=" C SER K 97 " pdb=" N THR K 98 " ideal model delta sigma weight residual 118.59 122.30 -3.71 1.63e+00 3.76e-01 5.17e+00 angle pdb=" CA SER J 97 " pdb=" C SER J 97 " pdb=" N THR J 98 " ideal model delta sigma weight residual 118.59 122.28 -3.69 1.63e+00 3.76e-01 5.14e+00 angle pdb=" CA SER D 97 " pdb=" C SER D 97 " pdb=" N THR D 98 " ideal model delta sigma weight residual 118.59 122.28 -3.69 1.63e+00 3.76e-01 5.12e+00 angle pdb=" CA SER S 97 " pdb=" C SER S 97 " pdb=" N THR S 98 " ideal model delta sigma weight residual 118.59 122.27 -3.68 1.63e+00 3.76e-01 5.10e+00 angle pdb=" CA SER W 97 " pdb=" C SER W 97 " pdb=" N THR W 98 " ideal model delta sigma weight residual 118.59 122.27 -3.68 1.63e+00 3.76e-01 5.08e+00 ... (remaining 81331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.61: 18528 14.61 - 29.22: 1680 29.22 - 43.83: 600 43.83 - 58.45: 360 58.45 - 73.06: 96 Dihedral angle restraints: 21264 sinusoidal: 11640 harmonic: 9624 Sorted by residual: dihedral pdb=" CB MET W 106 " pdb=" CG MET W 106 " pdb=" SD MET W 106 " pdb=" CE MET W 106 " ideal model delta sinusoidal sigma weight residual -60.00 -12.40 -47.60 3 1.50e+01 4.44e-03 8.52e+00 dihedral pdb=" CB MET N 106 " pdb=" CG MET N 106 " pdb=" SD MET N 106 " pdb=" CE MET N 106 " ideal model delta sinusoidal sigma weight residual -60.00 -12.40 -47.60 3 1.50e+01 4.44e-03 8.52e+00 dihedral pdb=" CB MET C 106 " pdb=" CG MET C 106 " pdb=" SD MET C 106 " pdb=" CE MET C 106 " ideal model delta sinusoidal sigma weight residual -60.00 -12.41 -47.59 3 1.50e+01 4.44e-03 8.52e+00 ... (remaining 21261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2184 0.027 - 0.054: 1043 0.054 - 0.080: 397 0.080 - 0.107: 189 0.107 - 0.134: 243 Chirality restraints: 4056 Sorted by residual: chirality pdb=" CA VAL U 19 " pdb=" N VAL U 19 " pdb=" C VAL U 19 " pdb=" CB VAL U 19 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL X 19 " pdb=" N VAL X 19 " pdb=" C VAL X 19 " pdb=" CB VAL X 19 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL D 19 " pdb=" N VAL D 19 " pdb=" C VAL D 19 " pdb=" CB VAL D 19 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 4053 not shown) Planarity restraints: 7320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU F 138 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.07e+00 pdb=" CD GLU F 138 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU F 138 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU F 138 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU S 138 " -0.005 2.00e-02 2.50e+03 1.03e-02 1.07e+00 pdb=" CD GLU S 138 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU S 138 " -0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU S 138 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 138 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.06e+00 pdb=" CD GLU K 138 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLU K 138 " 0.006 2.00e-02 2.50e+03 pdb=" OE2 GLU K 138 " 0.006 2.00e-02 2.50e+03 ... (remaining 7317 not shown) Histogram of nonbonded interaction distances: 0.49 - 1.31: 253 1.31 - 2.13: 1779 2.13 - 2.95: 121683 2.95 - 3.78: 177448 3.78 - 4.60: 309818 Warning: very small nonbonded interaction distances. Nonbonded interactions: 610981 Sorted by model distance: nonbonded pdb=" HA SER C 65 " pdb=" OE2 GLU I 138 " model vdw 0.486 2.620 nonbonded pdb=" HA SER J 65 " pdb=" OE2 GLU Q 138 " model vdw 0.486 2.620 nonbonded pdb=" HA SER A 65 " pdb=" OE2 GLU N 138 " model vdw 0.486 2.620 nonbonded pdb=" HA SER G 65 " pdb=" OE2 GLU M 138 " model vdw 0.486 2.620 nonbonded pdb=" HA SER L 65 " pdb=" OE2 GLU S 138 " model vdw 0.486 2.620 ... (remaining 610976 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: 0.11 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' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 group one per residue 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: 1.550 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: 0.310 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 42.440 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.003 0.032 23016 Z= 0.134 Angle : 0.573 5.817 31392 Z= 0.327 Chirality : 0.046 0.134 4056 Planarity : 0.001 0.010 4104 Dihedral : 13.444 66.598 7800 Min Nonbonded Distance : 0.785 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.00 % Allowed : 13.21 % Favored : 86.79 % 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: 0.95 (0.16), residues: 3216 helix: 3.14 (0.17), residues: 696 sheet: 0.55 (0.16), residues: 1008 loop : -0.52 (0.18), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR O 151 PHE 0.001 0.000 PHE Q 153 TRP 0.003 0.001 TRP W 119 HIS 0.001 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00256 (23016) covalent geometry : angle 0.57347 (31392) hydrogen bonds : bond 0.22961 ( 1248) hydrogen bonds : angle 7.22392 ( 3528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1230 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 TRP cc_start: 0.8768 (m-10) cc_final: 0.8387 (m-10) REVERT: A 141 GLU cc_start: 0.8559 (tp30) cc_final: 0.8044 (tp30) REVERT: B 72 GLU cc_start: 0.8287 (pm20) cc_final: 0.8008 (pm20) REVERT: B 145 GLN cc_start: 0.8316 (tt0) cc_final: 0.7419 (pm20) REVERT: C 59 THR cc_start: 0.8796 (m) cc_final: 0.8001 (p) REVERT: C 145 GLN cc_start: 0.8509 (tt0) cc_final: 0.7522 (pm20) REVERT: D 72 GLU cc_start: 0.8455 (pm20) cc_final: 0.8170 (pm20) REVERT: D 145 GLN cc_start: 0.8610 (tt0) cc_final: 0.7803 (pm20) REVERT: E 59 THR cc_start: 0.8445 (m) cc_final: 0.7538 (p) REVERT: E 72 GLU cc_start: 0.8463 (pm20) cc_final: 0.7882 (pm20) REVERT: F 59 THR cc_start: 0.8560 (m) cc_final: 0.7742 (p) REVERT: F 72 GLU cc_start: 0.8204 (pm20) cc_final: 0.7904 (pm20) REVERT: G 141 GLU cc_start: 0.8684 (tp30) cc_final: 0.8270 (tp30) REVERT: I 52 GLN cc_start: 0.7785 (tt0) cc_final: 0.7533 (tp-100) REVERT: J 28 MET cc_start: 0.7696 (tpp) cc_final: 0.7433 (tpp) REVERT: J 72 GLU cc_start: 0.8484 (pm20) cc_final: 0.8014 (pm20) REVERT: M 23 ILE cc_start: 0.9318 (mt) cc_final: 0.9009 (tp) REVERT: N 23 ILE cc_start: 0.8999 (mt) cc_final: 0.8775 (tp) REVERT: N 70 GLN cc_start: 0.8178 (tt0) cc_final: 0.7947 (tt0) REVERT: N 78 ASN cc_start: 0.8334 (p0) cc_final: 0.7410 (p0) REVERT: Q 102 ASP cc_start: 0.7846 (t0) cc_final: 0.7476 (t70) REVERT: R 63 ASP cc_start: 0.8037 (t70) cc_final: 0.7733 (t0) REVERT: S 23 ILE cc_start: 0.8927 (mt) cc_final: 0.8685 (tp) REVERT: S 63 ASP cc_start: 0.8085 (t70) cc_final: 0.7844 (t0) REVERT: T 76 MET cc_start: 0.6665 (mmm) cc_final: 0.6411 (mmm) REVERT: U 76 MET cc_start: 0.7020 (mmm) cc_final: 0.6800 (tpp) REVERT: V 63 ASP cc_start: 0.7770 (t70) cc_final: 0.7363 (t0) REVERT: W 63 ASP cc_start: 0.7271 (t70) cc_final: 0.7070 (t0) REVERT: X 63 ASP cc_start: 0.7275 (t70) cc_final: 0.7011 (t70) outliers start: 0 outliers final: 0 residues processed: 1230 average time/residue: 0.2675 time to fit residues: 567.2517 Evaluate side-chains 844 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 844 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 70 GLN U 70 GLN U 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.083591 restraints weight = 165004.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086715 restraints weight = 61071.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088668 restraints weight = 29004.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089783 restraints weight = 15888.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.090457 restraints weight = 10023.886| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23016 Z= 0.208 Angle : 0.578 5.335 31392 Z= 0.329 Chirality : 0.048 0.176 4056 Planarity : 0.003 0.015 4104 Dihedral : 4.277 14.613 3288 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.46 % Allowed : 19.54 % Favored : 77.00 % 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: 1.04 (0.16), residues: 3216 helix: 2.52 (0.17), residues: 720 sheet: 0.85 (0.18), residues: 1008 loop : -0.31 (0.19), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 151 PHE 0.014 0.002 PHE V 42 TRP 0.006 0.001 TRP N 119 HIS 0.005 0.001 HIS J 103 Details of bonding type rmsd covalent geometry : bond 0.00428 (23016) covalent geometry : angle 0.57820 (31392) hydrogen bonds : bond 0.05544 ( 1248) hydrogen bonds : angle 5.92077 ( 3528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 858 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8559 (tp30) cc_final: 0.8187 (tp30) REVERT: B 60 ILE cc_start: 0.8616 (mt) cc_final: 0.8270 (tt) REVERT: B 72 GLU cc_start: 0.8335 (pm20) cc_final: 0.7948 (pm20) REVERT: B 145 GLN cc_start: 0.8445 (tt0) cc_final: 0.7309 (pm20) REVERT: C 59 THR cc_start: 0.8517 (m) cc_final: 0.7505 (m) REVERT: C 72 GLU cc_start: 0.8409 (pm20) cc_final: 0.8068 (pm20) REVERT: C 145 GLN cc_start: 0.8704 (tt0) cc_final: 0.7527 (pm20) REVERT: D 59 THR cc_start: 0.8166 (m) cc_final: 0.7740 (m) REVERT: D 145 GLN cc_start: 0.8789 (tt0) cc_final: 0.8046 (pm20) REVERT: E 59 THR cc_start: 0.8170 (m) cc_final: 0.7949 (m) REVERT: F 59 THR cc_start: 0.8241 (m) cc_final: 0.8029 (m) REVERT: F 64 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7909 (mm-30) REVERT: F 65 SER cc_start: 0.8653 (p) cc_final: 0.8264 (t) REVERT: G 61 GLU cc_start: 0.8027 (tp30) cc_final: 0.7633 (tp30) REVERT: G 65 SER cc_start: 0.8799 (p) cc_final: 0.8018 (t) REVERT: G 141 GLU cc_start: 0.8763 (tp30) cc_final: 0.8557 (tp30) REVERT: H 65 SER cc_start: 0.9166 (p) cc_final: 0.8694 (p) REVERT: I 52 GLN cc_start: 0.8130 (tt0) cc_final: 0.7795 (tp40) REVERT: I 64 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: J 28 MET cc_start: 0.8096 (tpp) cc_final: 0.7713 (tpp) REVERT: J 64 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: K 140 ASP cc_start: 0.8853 (p0) cc_final: 0.8584 (p0) REVERT: L 28 MET cc_start: 0.8389 (tpp) cc_final: 0.8149 (tpp) REVERT: L 63 ASP cc_start: 0.7954 (t0) cc_final: 0.7658 (t0) REVERT: M 52 GLN cc_start: 0.8010 (tt0) cc_final: 0.7756 (tt0) REVERT: M 65 SER cc_start: 0.9101 (p) cc_final: 0.8513 (p) REVERT: N 53 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7728 (mt-10) REVERT: N 72 GLU cc_start: 0.8167 (pm20) cc_final: 0.7861 (pm20) REVERT: N 115 ASP cc_start: 0.8502 (t0) cc_final: 0.8236 (p0) REVERT: O 65 SER cc_start: 0.9205 (p) cc_final: 0.8562 (p) REVERT: P 76 MET cc_start: 0.6700 (mmm) cc_final: 0.6220 (mmm) REVERT: Q 63 ASP cc_start: 0.8219 (t0) cc_final: 0.7933 (t0) REVERT: R 63 ASP cc_start: 0.8000 (t70) cc_final: 0.7721 (t0) REVERT: S 63 ASP cc_start: 0.8506 (t70) cc_final: 0.8057 (t0) REVERT: U 72 GLU cc_start: 0.8475 (pm20) cc_final: 0.8141 (pm20) REVERT: U 137 ILE cc_start: 0.8206 (mt) cc_final: 0.7967 (mt) REVERT: W 76 MET cc_start: 0.7227 (mmm) cc_final: 0.6829 (mmm) REVERT: W 115 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.7823 (p0) REVERT: X 63 ASP cc_start: 0.7882 (t70) cc_final: 0.7458 (t0) REVERT: X 102 ASP cc_start: 0.8670 (t0) cc_final: 0.8426 (t0) outliers start: 88 outliers final: 69 residues processed: 881 average time/residue: 0.2609 time to fit residues: 398.4442 Evaluate side-chains 757 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 685 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 114 MET Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 53 GLU Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 146 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 136 VAL Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 146 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 118 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.092000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.081624 restraints weight = 165646.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.084667 restraints weight = 63014.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.086615 restraints weight = 30733.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087690 restraints weight = 17153.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088401 restraints weight = 11040.852| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23016 Z= 0.160 Angle : 0.514 4.973 31392 Z= 0.289 Chirality : 0.047 0.172 4056 Planarity : 0.002 0.019 4104 Dihedral : 4.055 14.497 3288 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.09 % Allowed : 20.91 % Favored : 75.00 % 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: 0.95 (0.16), residues: 3216 helix: 2.39 (0.16), residues: 720 sheet: 0.78 (0.18), residues: 1008 loop : -0.33 (0.19), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR V 151 PHE 0.016 0.002 PHE I 42 TRP 0.005 0.001 TRP Q 119 HIS 0.004 0.001 HIS C 103 Details of bonding type rmsd covalent geometry : bond 0.00337 (23016) covalent geometry : angle 0.51440 (31392) hydrogen bonds : bond 0.04953 ( 1248) hydrogen bonds : angle 5.63661 ( 3528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 751 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8629 (tp30) cc_final: 0.8255 (tp30) REVERT: B 145 GLN cc_start: 0.8412 (tt0) cc_final: 0.7235 (pm20) REVERT: C 29 VAL cc_start: 0.9670 (t) cc_final: 0.9392 (t) REVERT: C 59 THR cc_start: 0.8381 (m) cc_final: 0.8102 (m) REVERT: C 145 GLN cc_start: 0.8734 (tt0) cc_final: 0.7604 (pm20) REVERT: D 145 GLN cc_start: 0.8768 (tt0) cc_final: 0.8009 (pm20) REVERT: G 61 GLU cc_start: 0.8033 (tp30) cc_final: 0.7658 (tp30) REVERT: G 141 GLU cc_start: 0.8876 (tp30) cc_final: 0.8622 (tp30) REVERT: I 52 GLN cc_start: 0.8120 (tt0) cc_final: 0.7507 (tp-100) REVERT: I 139 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7473 (mm-30) REVERT: J 28 MET cc_start: 0.8172 (tpp) cc_final: 0.7845 (tpp) REVERT: J 61 GLU cc_start: 0.7602 (tp30) cc_final: 0.7398 (tp30) REVERT: J 89 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8533 (t0) REVERT: K 140 ASP cc_start: 0.8980 (p0) cc_final: 0.8740 (p0) REVERT: N 55 GLN cc_start: 0.8446 (pm20) cc_final: 0.8203 (pm20) REVERT: N 61 GLU cc_start: 0.7925 (tp30) cc_final: 0.7544 (tt0) REVERT: P 76 MET cc_start: 0.6825 (mmm) cc_final: 0.6315 (mmm) REVERT: Q 63 ASP cc_start: 0.8192 (t0) cc_final: 0.7965 (t0) REVERT: R 63 ASP cc_start: 0.8019 (t70) cc_final: 0.7718 (t0) REVERT: R 134 ILE cc_start: 0.9082 (mp) cc_final: 0.8618 (tp) REVERT: S 63 ASP cc_start: 0.8523 (t70) cc_final: 0.8131 (t0) REVERT: W 76 MET cc_start: 0.7286 (mmm) cc_final: 0.6985 (mmm) REVERT: X 61 GLU cc_start: 0.7614 (mp0) cc_final: 0.7188 (mp0) REVERT: X 63 ASP cc_start: 0.7695 (t70) cc_final: 0.7340 (t0) REVERT: X 102 ASP cc_start: 0.8693 (t0) cc_final: 0.8369 (t0) REVERT: X 150 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7830 (tm-30) outliers start: 104 outliers final: 86 residues processed: 793 average time/residue: 0.2663 time to fit residues: 367.7702 Evaluate side-chains 740 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 653 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 114 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 114 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 150 GLU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 136 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain P residue 26 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 146 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 60 ILE Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 115 ASP Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 47 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 203 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 HIS M 52 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.092077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081657 restraints weight = 166925.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.084673 restraints weight = 64001.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.086626 restraints weight = 31269.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.087801 restraints weight = 17477.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088423 restraints weight = 11004.872| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23016 Z= 0.135 Angle : 0.493 4.989 31392 Z= 0.274 Chirality : 0.047 0.169 4056 Planarity : 0.002 0.017 4104 Dihedral : 3.920 15.096 3288 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.69 % Allowed : 22.41 % Favored : 73.90 % 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: 0.89 (0.16), residues: 3216 helix: 2.40 (0.16), residues: 720 sheet: 0.72 (0.18), residues: 1008 loop : -0.37 (0.19), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR V 151 PHE 0.013 0.001 PHE I 42 TRP 0.004 0.001 TRP L 119 HIS 0.003 0.001 HIS L 103 Details of bonding type rmsd covalent geometry : bond 0.00286 (23016) covalent geometry : angle 0.49306 (31392) hydrogen bonds : bond 0.04483 ( 1248) hydrogen bonds : angle 5.41852 ( 3528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 687 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.7715 (t0) cc_final: 0.7085 (t0) REVERT: A 141 GLU cc_start: 0.8656 (tp30) cc_final: 0.8354 (tp30) REVERT: B 72 GLU cc_start: 0.8469 (pm20) cc_final: 0.8024 (pm20) REVERT: C 145 GLN cc_start: 0.8761 (tt0) cc_final: 0.7690 (pm20) REVERT: D 145 GLN cc_start: 0.8815 (tt0) cc_final: 0.8006 (pm20) REVERT: G 28 MET cc_start: 0.8538 (tpp) cc_final: 0.8028 (tpp) REVERT: G 61 GLU cc_start: 0.8088 (tp30) cc_final: 0.7728 (tp30) REVERT: G 141 GLU cc_start: 0.8884 (tp30) cc_final: 0.8640 (tp30) REVERT: I 52 GLN cc_start: 0.8100 (tt0) cc_final: 0.7476 (tp-100) REVERT: J 28 MET cc_start: 0.8111 (tpp) cc_final: 0.7795 (tpp) REVERT: K 72 GLU cc_start: 0.8120 (pm20) cc_final: 0.7751 (pm20) REVERT: K 140 ASP cc_start: 0.8980 (p0) cc_final: 0.8751 (p0) REVERT: L 63 ASP cc_start: 0.7930 (t0) cc_final: 0.7665 (t0) REVERT: L 140 ASP cc_start: 0.8490 (p0) cc_final: 0.8234 (p0) REVERT: N 53 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7841 (mt-10) REVERT: N 55 GLN cc_start: 0.8522 (pm20) cc_final: 0.7910 (pm20) REVERT: N 139 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7933 (mm-30) REVERT: P 76 MET cc_start: 0.6905 (mmm) cc_final: 0.6447 (mmm) REVERT: Q 63 ASP cc_start: 0.8225 (t0) cc_final: 0.7886 (t0) REVERT: R 63 ASP cc_start: 0.8034 (t70) cc_final: 0.7468 (t0) REVERT: S 63 ASP cc_start: 0.8494 (t70) cc_final: 0.8125 (t0) REVERT: W 69 ILE cc_start: 0.9308 (mp) cc_final: 0.9088 (mm) REVERT: W 76 MET cc_start: 0.7310 (mmm) cc_final: 0.7094 (mmm) REVERT: X 61 GLU cc_start: 0.7545 (mp0) cc_final: 0.7093 (mp0) REVERT: X 63 ASP cc_start: 0.7589 (t70) cc_final: 0.7243 (t0) REVERT: X 102 ASP cc_start: 0.8744 (t0) cc_final: 0.8374 (t0) REVERT: X 150 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7804 (tm-30) outliers start: 94 outliers final: 78 residues processed: 724 average time/residue: 0.2693 time to fit residues: 338.7460 Evaluate side-chains 691 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 613 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 114 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 28 MET Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 150 GLU Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 114 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 25 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 146 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 146 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 31 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 275 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 212 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.089825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.079618 restraints weight = 168278.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082571 restraints weight = 64024.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.084415 restraints weight = 31195.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.085538 restraints weight = 17435.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.086118 restraints weight = 11007.694| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23016 Z= 0.232 Angle : 0.552 5.794 31392 Z= 0.314 Chirality : 0.047 0.167 4056 Planarity : 0.002 0.019 4104 Dihedral : 4.221 16.024 3288 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.64 % Allowed : 22.56 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.00 (0.15), residues: 3216 helix: 1.23 (0.16), residues: 864 sheet: 0.67 (0.17), residues: 984 loop : -1.33 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR B 151 PHE 0.014 0.002 PHE S 42 TRP 0.007 0.001 TRP T 119 HIS 0.004 0.001 HIS M 103 Details of bonding type rmsd covalent geometry : bond 0.00490 (23016) covalent geometry : angle 0.55158 (31392) hydrogen bonds : bond 0.05029 ( 1248) hydrogen bonds : angle 5.66199 ( 3528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 598 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.7708 (t0) cc_final: 0.6243 (t0) REVERT: A 141 GLU cc_start: 0.8715 (tp30) cc_final: 0.8435 (tp30) REVERT: C 61 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7355 (mm-30) REVERT: G 28 MET cc_start: 0.8560 (tpp) cc_final: 0.8022 (tpp) REVERT: G 141 GLU cc_start: 0.8870 (tp30) cc_final: 0.8661 (tp30) REVERT: I 52 GLN cc_start: 0.8130 (tt0) cc_final: 0.7347 (tp-100) REVERT: I 64 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: J 28 MET cc_start: 0.8283 (tpp) cc_final: 0.7976 (tpp) REVERT: J 89 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8532 (t0) REVERT: L 140 ASP cc_start: 0.8633 (p0) cc_final: 0.8425 (p0) REVERT: M 63 ASP cc_start: 0.8129 (t0) cc_final: 0.7920 (t0) REVERT: N 53 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7895 (mt-10) REVERT: N 55 GLN cc_start: 0.8608 (pm20) cc_final: 0.8281 (pm20) REVERT: N 139 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7944 (mm-30) REVERT: P 76 MET cc_start: 0.7031 (mmm) cc_final: 0.6532 (mmm) REVERT: Q 63 ASP cc_start: 0.8247 (t0) cc_final: 0.7899 (t0) REVERT: R 63 ASP cc_start: 0.8280 (t70) cc_final: 0.7734 (t0) REVERT: S 63 ASP cc_start: 0.8627 (t70) cc_final: 0.8256 (t0) REVERT: U 32 THR cc_start: 0.9309 (OUTLIER) cc_final: 0.9059 (p) REVERT: V 32 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8954 (p) REVERT: X 61 GLU cc_start: 0.7682 (mp0) cc_final: 0.7200 (mp0) REVERT: X 63 ASP cc_start: 0.7644 (t70) cc_final: 0.7313 (t0) REVERT: X 102 ASP cc_start: 0.8855 (t0) cc_final: 0.8575 (t0) REVERT: X 150 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7847 (tm-30) outliers start: 118 outliers final: 90 residues processed: 657 average time/residue: 0.2716 time to fit residues: 310.5256 Evaluate side-chains 646 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 552 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 32 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 114 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 64 GLU Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 53 GLU Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 114 MET Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 114 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 146 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain V residue 23 ILE Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 97 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 236 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 134 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 271 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.091903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.081668 restraints weight = 165209.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.084675 restraints weight = 62440.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.086596 restraints weight = 30183.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.087661 restraints weight = 16612.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.088325 restraints weight = 10596.084| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23016 Z= 0.117 Angle : 0.494 6.082 31392 Z= 0.270 Chirality : 0.047 0.176 4056 Planarity : 0.002 0.017 4104 Dihedral : 3.911 14.643 3288 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.50 % Allowed : 24.14 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.68 (0.16), residues: 3216 helix: 2.52 (0.17), residues: 720 sheet: 0.51 (0.17), residues: 1008 loop : -0.61 (0.18), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 151 PHE 0.012 0.001 PHE T 42 TRP 0.004 0.001 TRP L 119 HIS 0.002 0.000 HIS L 103 Details of bonding type rmsd covalent geometry : bond 0.00254 (23016) covalent geometry : angle 0.49362 (31392) hydrogen bonds : bond 0.04261 ( 1248) hydrogen bonds : angle 5.27820 ( 3528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 627 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.7720 (t0) cc_final: 0.6338 (t0) REVERT: A 141 GLU cc_start: 0.8708 (tp30) cc_final: 0.8443 (tp30) REVERT: A 150 GLU cc_start: 0.8482 (pm20) cc_final: 0.8139 (pp20) REVERT: D 145 GLN cc_start: 0.8856 (tt0) cc_final: 0.7976 (pm20) REVERT: G 76 MET cc_start: 0.7450 (mmm) cc_final: 0.7201 (mmt) REVERT: I 52 GLN cc_start: 0.8477 (tt0) cc_final: 0.7334 (tp-100) REVERT: J 28 MET cc_start: 0.8122 (tpp) cc_final: 0.7858 (tpp) REVERT: J 134 ILE cc_start: 0.8634 (mm) cc_final: 0.8426 (mm) REVERT: K 61 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7477 (mm-30) REVERT: L 63 ASP cc_start: 0.7933 (t0) cc_final: 0.7693 (t0) REVERT: L 140 ASP cc_start: 0.8664 (p0) cc_final: 0.8397 (p0) REVERT: M 63 ASP cc_start: 0.8147 (t0) cc_final: 0.7747 (t0) REVERT: N 53 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7813 (mt-10) REVERT: N 55 GLN cc_start: 0.8521 (pm20) cc_final: 0.8253 (pm20) REVERT: N 139 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7937 (mm-30) REVERT: P 76 MET cc_start: 0.7008 (mmm) cc_final: 0.6564 (mmm) REVERT: Q 63 ASP cc_start: 0.8171 (t0) cc_final: 0.7794 (t0) REVERT: R 63 ASP cc_start: 0.8249 (t70) cc_final: 0.7744 (t0) REVERT: R 76 MET cc_start: 0.7316 (mmm) cc_final: 0.6636 (mmm) REVERT: S 63 ASP cc_start: 0.8576 (t70) cc_final: 0.8233 (t0) REVERT: U 32 THR cc_start: 0.9257 (OUTLIER) cc_final: 0.9009 (p) REVERT: X 22 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8542 (t) REVERT: X 61 GLU cc_start: 0.7601 (mp0) cc_final: 0.7113 (mp0) REVERT: X 63 ASP cc_start: 0.7657 (t70) cc_final: 0.7340 (t0) REVERT: X 102 ASP cc_start: 0.8841 (t0) cc_final: 0.8548 (t0) REVERT: X 150 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7765 (tm-30) outliers start: 89 outliers final: 71 residues processed: 668 average time/residue: 0.2695 time to fit residues: 312.9318 Evaluate side-chains 646 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 573 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 114 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 136 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 28 MET Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 114 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 146 VAL Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 22 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 146 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 9.9990 chunk 246 optimal weight: 0.0050 chunk 269 optimal weight: 9.9990 chunk 233 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 308 optimal weight: 9.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.092586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082330 restraints weight = 163583.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.085356 restraints weight = 61995.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.087287 restraints weight = 29942.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.088355 restraints weight = 16595.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.089046 restraints weight = 10600.968| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.5849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23016 Z= 0.116 Angle : 0.491 5.184 31392 Z= 0.269 Chirality : 0.047 0.160 4056 Planarity : 0.002 0.018 4104 Dihedral : 3.772 14.385 3288 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.26 % Allowed : 24.41 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.40 (0.16), residues: 3216 helix: 1.43 (0.17), residues: 888 sheet: 0.53 (0.17), residues: 1008 loop : -0.70 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR B 151 PHE 0.013 0.001 PHE S 42 TRP 0.004 0.001 TRP U 119 HIS 0.002 0.000 HIS L 103 Details of bonding type rmsd covalent geometry : bond 0.00251 (23016) covalent geometry : angle 0.49128 (31392) hydrogen bonds : bond 0.03990 ( 1248) hydrogen bonds : angle 5.12495 ( 3528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 622 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.7671 (t0) cc_final: 0.7185 (t0) REVERT: A 141 GLU cc_start: 0.8720 (tp30) cc_final: 0.8502 (tp30) REVERT: A 150 GLU cc_start: 0.8484 (pm20) cc_final: 0.8141 (pp20) REVERT: B 72 GLU cc_start: 0.8398 (pm20) cc_final: 0.8012 (pm20) REVERT: D 145 GLN cc_start: 0.8839 (tt0) cc_final: 0.7952 (pm20) REVERT: G 76 MET cc_start: 0.7377 (mmm) cc_final: 0.7111 (mmt) REVERT: J 28 MET cc_start: 0.8067 (tpp) cc_final: 0.7787 (tpp) REVERT: J 134 ILE cc_start: 0.8626 (mm) cc_final: 0.8413 (mm) REVERT: K 61 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7327 (mm-30) REVERT: K 72 GLU cc_start: 0.8059 (pm20) cc_final: 0.7683 (pm20) REVERT: L 63 ASP cc_start: 0.7920 (t0) cc_final: 0.7667 (t0) REVERT: M 140 ASP cc_start: 0.8452 (p0) cc_final: 0.8102 (p0) REVERT: N 53 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7799 (mt-10) REVERT: N 55 GLN cc_start: 0.8496 (pm20) cc_final: 0.8223 (pm20) REVERT: N 139 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7989 (mm-30) REVERT: P 76 MET cc_start: 0.6990 (mmm) cc_final: 0.6511 (mmm) REVERT: Q 63 ASP cc_start: 0.8152 (t0) cc_final: 0.7779 (t0) REVERT: R 63 ASP cc_start: 0.8220 (t70) cc_final: 0.7718 (t0) REVERT: R 76 MET cc_start: 0.7216 (mmm) cc_final: 0.6434 (mmm) REVERT: S 63 ASP cc_start: 0.8550 (t70) cc_final: 0.8263 (t0) REVERT: T 140 ASP cc_start: 0.8838 (p0) cc_final: 0.8599 (p0) REVERT: U 139 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8244 (mp0) REVERT: V 46 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8701 (tt) REVERT: W 28 MET cc_start: 0.8778 (mmp) cc_final: 0.8560 (mmp) REVERT: W 102 ASP cc_start: 0.9083 (t0) cc_final: 0.8864 (t0) REVERT: X 59 THR cc_start: 0.7898 (m) cc_final: 0.7573 (m) REVERT: X 61 GLU cc_start: 0.7558 (mp0) cc_final: 0.7024 (mp0) REVERT: X 63 ASP cc_start: 0.7711 (t70) cc_final: 0.7403 (t0) REVERT: X 102 ASP cc_start: 0.8810 (t0) cc_final: 0.8530 (t0) REVERT: X 150 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7745 (tm-30) outliers start: 83 outliers final: 68 residues processed: 657 average time/residue: 0.2525 time to fit residues: 288.7764 Evaluate side-chains 654 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 585 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 114 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 28 MET Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 114 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 139 GLU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 146 VAL Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 46 LEU Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 23 ILE Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 146 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 18 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 209 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3252 r_free = 0.3252 target = 0.091466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.081185 restraints weight = 166734.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084207 restraints weight = 63666.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086122 restraints weight = 30941.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087217 restraints weight = 17279.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.087925 restraints weight = 11104.033| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23016 Z= 0.144 Angle : 0.512 6.121 31392 Z= 0.281 Chirality : 0.047 0.181 4056 Planarity : 0.002 0.018 4104 Dihedral : 3.817 14.390 3288 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.42 % Allowed : 24.41 % Favored : 72.17 % 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: 0.28 (0.16), residues: 3216 helix: 1.42 (0.17), residues: 864 sheet: 0.51 (0.17), residues: 1008 loop : -0.84 (0.19), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR B 151 PHE 0.026 0.002 PHE D 42 TRP 0.005 0.001 TRP U 119 HIS 0.002 0.001 HIS L 103 Details of bonding type rmsd covalent geometry : bond 0.00313 (23016) covalent geometry : angle 0.51219 (31392) hydrogen bonds : bond 0.04093 ( 1248) hydrogen bonds : angle 5.17717 ( 3528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 601 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 GLU cc_start: 0.8755 (tp30) cc_final: 0.8550 (tp30) REVERT: G 76 MET cc_start: 0.7387 (mmm) cc_final: 0.7107 (mmt) REVERT: H 139 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7341 (mt-10) REVERT: J 76 MET cc_start: 0.7780 (mmm) cc_final: 0.7522 (mmt) REVERT: J 150 GLU cc_start: 0.8839 (pm20) cc_final: 0.8560 (mp0) REVERT: K 61 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7346 (mm-30) REVERT: L 140 ASP cc_start: 0.8647 (p0) cc_final: 0.8434 (p0) REVERT: N 53 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7835 (mt-10) REVERT: N 139 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7994 (mm-30) REVERT: O 76 MET cc_start: 0.7357 (mmm) cc_final: 0.7057 (mmt) REVERT: P 76 MET cc_start: 0.7066 (mmm) cc_final: 0.6569 (mmm) REVERT: Q 63 ASP cc_start: 0.8185 (t0) cc_final: 0.7812 (t0) REVERT: R 63 ASP cc_start: 0.8267 (t70) cc_final: 0.7750 (t0) REVERT: R 76 MET cc_start: 0.7146 (mmm) cc_final: 0.6398 (mmm) REVERT: S 63 ASP cc_start: 0.8536 (t70) cc_final: 0.8220 (t0) REVERT: U 139 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8273 (mp0) REVERT: U 140 ASP cc_start: 0.8779 (p0) cc_final: 0.8560 (p0) REVERT: V 46 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8741 (tt) REVERT: V 140 ASP cc_start: 0.8658 (p0) cc_final: 0.8438 (p0) REVERT: X 61 GLU cc_start: 0.7623 (mp0) cc_final: 0.7144 (mp0) REVERT: X 63 ASP cc_start: 0.7721 (t70) cc_final: 0.7409 (t0) REVERT: X 102 ASP cc_start: 0.8837 (t0) cc_final: 0.8553 (t0) REVERT: X 150 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7756 (tm-30) outliers start: 87 outliers final: 77 residues processed: 639 average time/residue: 0.2549 time to fit residues: 282.9379 Evaluate side-chains 651 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 573 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 114 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 GLU Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 28 MET Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 65 SER Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 137 ILE Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 114 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 146 VAL Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 46 LEU Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 146 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 149 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 284 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 269 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 chunk 291 optimal weight: 0.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.091012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.080782 restraints weight = 164667.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083761 restraints weight = 63048.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.085632 restraints weight = 30589.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086749 restraints weight = 17215.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087427 restraints weight = 10866.351| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23016 Z= 0.151 Angle : 0.519 6.804 31392 Z= 0.285 Chirality : 0.047 0.178 4056 Planarity : 0.002 0.019 4104 Dihedral : 3.878 14.163 3288 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.38 % Allowed : 24.92 % Favored : 71.70 % 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: 0.21 (0.16), residues: 3216 helix: 1.36 (0.17), residues: 864 sheet: 0.47 (0.17), residues: 1008 loop : -0.90 (0.19), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 151 PHE 0.021 0.002 PHE D 42 TRP 0.005 0.001 TRP P 119 HIS 0.002 0.001 HIS M 103 Details of bonding type rmsd covalent geometry : bond 0.00326 (23016) covalent geometry : angle 0.51898 (31392) hydrogen bonds : bond 0.04125 ( 1248) hydrogen bonds : angle 5.19592 ( 3528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 580 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.7715 (t0) cc_final: 0.7350 (t0) REVERT: A 65 SER cc_start: 0.8679 (t) cc_final: 0.8444 (p) REVERT: A 141 GLU cc_start: 0.8719 (tp30) cc_final: 0.8506 (tp30) REVERT: A 150 GLU cc_start: 0.8473 (pm20) cc_final: 0.8129 (pp20) REVERT: G 76 MET cc_start: 0.7464 (mmm) cc_final: 0.7196 (mmt) REVERT: G 138 GLU cc_start: 0.6035 (tm-30) cc_final: 0.5780 (tm-30) REVERT: H 140 ASP cc_start: 0.8777 (p0) cc_final: 0.8566 (p0) REVERT: J 150 GLU cc_start: 0.8835 (pm20) cc_final: 0.8586 (mp0) REVERT: K 61 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7367 (mm-30) REVERT: K 72 GLU cc_start: 0.8095 (pm20) cc_final: 0.7741 (pm20) REVERT: L 63 ASP cc_start: 0.7943 (t0) cc_final: 0.7729 (t0) REVERT: N 139 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7921 (mm-30) REVERT: O 76 MET cc_start: 0.7348 (mmm) cc_final: 0.7064 (mmt) REVERT: P 76 MET cc_start: 0.7105 (mmm) cc_final: 0.6597 (mmm) REVERT: Q 63 ASP cc_start: 0.8202 (t0) cc_final: 0.7825 (t0) REVERT: R 63 ASP cc_start: 0.8228 (t70) cc_final: 0.7723 (t0) REVERT: R 134 ILE cc_start: 0.9042 (mp) cc_final: 0.8823 (pt) REVERT: S 63 ASP cc_start: 0.8495 (t70) cc_final: 0.8181 (t0) REVERT: U 28 MET cc_start: 0.8576 (mmt) cc_final: 0.8241 (mmt) REVERT: U 137 ILE cc_start: 0.8740 (mt) cc_final: 0.8383 (mt) REVERT: U 139 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8283 (mp0) REVERT: W 28 MET cc_start: 0.8861 (mmp) cc_final: 0.8659 (mmp) REVERT: X 61 GLU cc_start: 0.7544 (mp0) cc_final: 0.7072 (mp0) REVERT: X 63 ASP cc_start: 0.7874 (t70) cc_final: 0.7595 (t0) REVERT: X 102 ASP cc_start: 0.8858 (t0) cc_final: 0.8625 (t0) REVERT: X 139 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8428 (mp0) REVERT: X 150 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7752 (tm-30) outliers start: 86 outliers final: 74 residues processed: 618 average time/residue: 0.2462 time to fit residues: 264.6731 Evaluate side-chains 641 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 567 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 114 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 150 GLU Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 137 ILE Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 146 VAL Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 68 GLU Chi-restraints excluded: chain X residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 82 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 254 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 278 optimal weight: 0.8980 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.089962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079816 restraints weight = 166750.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.082746 restraints weight = 63704.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.084600 restraints weight = 31050.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.085702 restraints weight = 17500.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.086301 restraints weight = 11116.430| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.6242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23016 Z= 0.173 Angle : 0.538 6.467 31392 Z= 0.296 Chirality : 0.047 0.159 4056 Planarity : 0.002 0.017 4104 Dihedral : 3.977 14.270 3288 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.07 % Allowed : 25.24 % Favored : 71.70 % 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: 0.09 (0.16), residues: 3216 helix: 1.33 (0.17), residues: 864 sheet: 0.41 (0.17), residues: 1008 loop : -1.03 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR B 151 PHE 0.019 0.002 PHE D 42 TRP 0.005 0.001 TRP U 119 HIS 0.002 0.001 HIS M 103 Details of bonding type rmsd covalent geometry : bond 0.00371 (23016) covalent geometry : angle 0.53795 (31392) hydrogen bonds : bond 0.04296 ( 1248) hydrogen bonds : angle 5.28115 ( 3528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6432 Ramachandran restraints generated. 3216 Oldfield, 0 Emsley, 3216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 582 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.7710 (t0) cc_final: 0.7328 (t0) REVERT: A 65 SER cc_start: 0.8689 (t) cc_final: 0.8455 (p) REVERT: B 142 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8308 (m) REVERT: G 76 MET cc_start: 0.7533 (mmm) cc_final: 0.7244 (mmt) REVERT: H 139 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7289 (mt-10) REVERT: J 150 GLU cc_start: 0.8789 (pm20) cc_final: 0.8554 (mp0) REVERT: K 61 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7382 (mm-30) REVERT: K 72 GLU cc_start: 0.8049 (pm20) cc_final: 0.7677 (pm20) REVERT: L 63 ASP cc_start: 0.7987 (t0) cc_final: 0.7776 (t0) REVERT: N 139 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7983 (mm-30) REVERT: O 76 MET cc_start: 0.7443 (mmm) cc_final: 0.7145 (mmt) REVERT: P 76 MET cc_start: 0.7074 (mmm) cc_final: 0.6613 (mmm) REVERT: Q 63 ASP cc_start: 0.8237 (t0) cc_final: 0.7851 (t0) REVERT: R 63 ASP cc_start: 0.8217 (t70) cc_final: 0.7703 (t0) REVERT: R 76 MET cc_start: 0.7401 (mmm) cc_final: 0.6740 (mmm) REVERT: R 134 ILE cc_start: 0.9001 (mp) cc_final: 0.8774 (pt) REVERT: S 63 ASP cc_start: 0.8518 (t70) cc_final: 0.8093 (t0) REVERT: U 28 MET cc_start: 0.8485 (mmt) cc_final: 0.8258 (mmt) REVERT: U 137 ILE cc_start: 0.8861 (mt) cc_final: 0.8502 (mt) REVERT: U 139 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8293 (mp0) REVERT: V 32 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8923 (p) REVERT: W 28 MET cc_start: 0.8877 (mmp) cc_final: 0.8669 (mmp) REVERT: W 140 ASP cc_start: 0.8647 (p0) cc_final: 0.8437 (p0) REVERT: X 61 GLU cc_start: 0.7712 (mp0) cc_final: 0.7209 (mp0) REVERT: X 102 ASP cc_start: 0.8850 (t0) cc_final: 0.8645 (t0) REVERT: X 139 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8507 (mp0) REVERT: X 150 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7764 (tm-30) outliers start: 78 outliers final: 68 residues processed: 615 average time/residue: 0.2169 time to fit residues: 231.3491 Evaluate side-chains 624 residues out of total 2544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 554 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain H residue 23 ILE Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain H residue 114 MET Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 136 VAL Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 58 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain N residue 62 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain O residue 26 ILE Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 146 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 114 MET Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 146 VAL Chi-restraints excluded: chain T residue 46 LEU Chi-restraints excluded: chain T residue 146 VAL Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 146 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 146 VAL Chi-restraints excluded: chain W residue 23 ILE Chi-restraints excluded: chain W residue 31 ILE Chi-restraints excluded: chain W residue 68 GLU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 ILE Chi-restraints excluded: chain X residue 68 GLU Chi-restraints excluded: chain X residue 146 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 26 optimal weight: 2.9990 chunk 276 optimal weight: 0.4980 chunk 90 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 305 optimal weight: 9.9990 chunk 288 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.092072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.081846 restraints weight = 165388.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.084893 restraints weight = 62803.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.086829 restraints weight = 30234.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087951 restraints weight = 16748.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088571 restraints weight = 10546.037| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23016 Z= 0.120 Angle : 0.523 6.834 31392 Z= 0.282 Chirality : 0.048 0.199 4056 Planarity : 0.002 0.018 4104 Dihedral : 3.804 13.936 3288 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.67 % Allowed : 25.98 % Favored : 71.34 % 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: 0.26 (0.16), residues: 3216 helix: 1.42 (0.17), residues: 864 sheet: 0.53 (0.18), residues: 960 loop : -0.86 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR T 151 PHE 0.019 0.002 PHE D 42 TRP 0.004 0.001 TRP A 119 HIS 0.002 0.000 HIS M 103 Details of bonding type rmsd covalent geometry : bond 0.00267 (23016) covalent geometry : angle 0.52251 (31392) hydrogen bonds : bond 0.03900 ( 1248) hydrogen bonds : angle 5.09804 ( 3528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7017.05 seconds wall clock time: 120 minutes 23.89 seconds (7223.89 seconds total)