Starting phenix.real_space_refine on Tue Feb 3 17:22:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8u_47731/02_2026/9e8u_47731.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8u_47731/02_2026/9e8u_47731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9e8u_47731/02_2026/9e8u_47731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8u_47731/02_2026/9e8u_47731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9e8u_47731/02_2026/9e8u_47731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8u_47731/02_2026/9e8u_47731.map" } resolution = 2.6 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 3435 2.51 5 N 970 2.21 5 O 1120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s 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: 5525 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 556 Classifications: {'peptide': 82} Link IDs: {'TRANS': 81} Chain: "B" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 549 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Restraints were copied for chains: C, E, G, I, D, F, H, J Time building chain proxies: 0.72, per 1000 atoms: 0.13 Number of scatterers: 5525 At special positions: 0 Unit cell: (110.92, 93.06, 46.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1120 8.00 N 970 7.00 C 3435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 306.1 milliseconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1360 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 61.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 15 through 20 removed outlier: 6.395A pdb=" N VAL A 15 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ALA E 18 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLU E 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL E 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ALA I 18 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA E 17 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N GLU I 20 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA E 19 " --> pdb=" O GLU I 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 24 through 34 removed outlier: 6.233A pdb=" N GLN C 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ALA G 27 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL C 26 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA G 29 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C 28 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY G 31 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ALA C 30 " --> pdb=" O GLY G 31 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR G 33 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N LYS C 32 " --> pdb=" O THR G 33 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ALA C 27 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 26 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA C 29 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU A 28 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N GLY C 31 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N ALA A 30 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR C 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N LYS A 32 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS E 32 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 33 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS E 34 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS I 32 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR E 33 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS I 34 " --> pdb=" O THR E 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 38 through 40 removed outlier: 6.495A pdb=" N LEU C 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 43 through 66 removed outlier: 6.904A pdb=" N THR C 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS G 45 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU C 46 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY G 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 52 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA G 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR C 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL G 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA C 56 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU G 57 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR A 44 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS C 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU A 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY C 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ALA C 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR A 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA A 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU C 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N LYS A 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N GLU E 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N LYS A 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N VAL E 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY A 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N HIS E 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL E 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N GLY A 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N THR E 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 8.942A pdb=" N ALA A 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N ALA E 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N VAL A 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LYS E 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU A 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LYS E 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR A 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLN E 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU A 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N THR E 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL E 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN A 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N LYS E 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 10.002A pdb=" N GLU I 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N LYS E 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N VAL I 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY E 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N HIS I 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL E 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL I 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLY E 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.950A pdb=" N THR I 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N ALA E 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N ALA I 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N VAL E 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N LYS I 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLU E 57 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LYS I 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR E 59 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLN I 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU E 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR I 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL E 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL I 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN E 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 69 through 72 removed outlier: 6.567A pdb=" N ALA C 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N THR G 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL C 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 75 through 78 removed outlier: 6.647A pdb=" N THR C 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ALA G 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL C 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA C 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 89 through 93 removed outlier: 6.495A pdb=" N ALA C 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR G 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ALA C 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA A 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR C 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA A 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 23 through 24 removed outlier: 6.433A pdb=" N LYS D 23 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS B 23 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 27 through 32 removed outlier: 6.242A pdb=" N ALA B 27 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ALA F 30 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA B 29 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N LYS F 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY B 31 " --> pdb=" O LYS F 32 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA F 27 " --> pdb=" O GLU J 28 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ALA J 30 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA F 29 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N LYS J 32 " --> pdb=" O ALA F 29 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLY F 31 " --> pdb=" O LYS J 32 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 35 through 42 removed outlier: 6.192A pdb=" N GLU D 35 " --> pdb=" O GLY H 36 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU H 38 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 37 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL H 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR D 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER H 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY D 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLU B 35 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU D 38 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL D 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR B 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER D 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY B 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 45 through 57 removed outlier: 6.957A pdb=" N GLU D 46 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY H 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL D 52 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA H 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR D 54 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL H 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA D 56 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU H 57 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU B 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLY D 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA D 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR B 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL D 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA B 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU D 57 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LYS B 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N VAL F 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY B 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N HIS F 50 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL B 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL F 52 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY B 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N THR F 54 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ALA B 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N ALA F 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N VAL B 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LYS F 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N VAL J 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY F 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N HIS J 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL F 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL J 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY F 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N THR J 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ALA F 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N ALA J 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N VAL F 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 60 through 66 removed outlier: 6.440A pdb=" N LYS D 60 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL H 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN D 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASN H 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR D 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS B 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL D 63 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN B 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASN D 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR B 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 69 through 71 removed outlier: 6.455A pdb=" N ALA D 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 74 through 82 removed outlier: 6.364A pdb=" N VAL B 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL F 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA B 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLN F 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N THR F 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS B 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL F 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL J 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA F 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N GLN J 79 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA F 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N THR J 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS F 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 88 through 96 removed outlier: 7.440A pdb=" N ALA D 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N THR H 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ALA D 91 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N PHE H 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY D 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LYS H 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL D 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA B 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N THR D 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ALA B 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N PHE D 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA B 90 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA F 91 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR B 92 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY F 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 94 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA F 90 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA J 91 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR F 92 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY J 93 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE F 94 " --> pdb=" O GLY J 93 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.70 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 990 1.29 - 1.35: 870 1.35 - 1.42: 170 1.42 - 1.48: 905 1.48 - 1.54: 2610 Bond restraints: 5545 Sorted by residual: bond pdb=" CA GLY E 25 " pdb=" C GLY E 25 " ideal model delta sigma weight residual 1.516 1.511 0.004 8.10e-03 1.52e+04 2.64e-01 bond pdb=" CA GLY C 25 " pdb=" C GLY C 25 " ideal model delta sigma weight residual 1.516 1.511 0.004 8.10e-03 1.52e+04 2.58e-01 bond pdb=" CA GLY A 25 " pdb=" C GLY A 25 " ideal model delta sigma weight residual 1.516 1.512 0.004 8.10e-03 1.52e+04 2.53e-01 bond pdb=" C VAL F 40 " pdb=" N GLY F 41 " ideal model delta sigma weight residual 1.325 1.331 -0.006 1.33e-02 5.65e+03 2.36e-01 bond pdb=" C VAL J 40 " pdb=" N GLY J 41 " ideal model delta sigma weight residual 1.325 1.331 -0.006 1.33e-02 5.65e+03 2.23e-01 ... (remaining 5540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 7429 1.67 - 3.34: 41 3.34 - 5.00: 0 5.00 - 6.67: 0 6.67 - 8.34: 5 Bond angle restraints: 7475 Sorted by residual: angle pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " ideal model delta sigma weight residual 116.30 124.64 -8.34 3.50e+00 8.16e-02 5.68e+00 angle pdb=" CA LEU I 38 " pdb=" CB LEU I 38 " pdb=" CG LEU I 38 " ideal model delta sigma weight residual 116.30 124.64 -8.34 3.50e+00 8.16e-02 5.67e+00 angle pdb=" CA LEU E 38 " pdb=" CB LEU E 38 " pdb=" CG LEU E 38 " ideal model delta sigma weight residual 116.30 124.62 -8.32 3.50e+00 8.16e-02 5.65e+00 angle pdb=" CA LEU G 38 " pdb=" CB LEU G 38 " pdb=" CG LEU G 38 " ideal model delta sigma weight residual 116.30 124.62 -8.32 3.50e+00 8.16e-02 5.64e+00 angle pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " pdb=" CG LEU C 38 " ideal model delta sigma weight residual 116.30 124.60 -8.30 3.50e+00 8.16e-02 5.62e+00 ... (remaining 7470 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 2751 14.13 - 28.25: 279 28.25 - 42.37: 120 42.37 - 56.49: 95 56.49 - 70.62: 30 Dihedral angle restraints: 3275 sinusoidal: 1110 harmonic: 2165 Sorted by residual: dihedral pdb=" CA LYS D 43 " pdb=" CB LYS D 43 " pdb=" CG LYS D 43 " pdb=" CD LYS D 43 " ideal model delta sinusoidal sigma weight residual -60.00 -120.00 60.00 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS J 43 " pdb=" CB LYS J 43 " pdb=" CG LYS J 43 " pdb=" CD LYS J 43 " ideal model delta sinusoidal sigma weight residual 180.00 -120.01 -59.99 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA LYS F 43 " pdb=" CB LYS F 43 " pdb=" CG LYS F 43 " pdb=" CD LYS F 43 " ideal model delta sinusoidal sigma weight residual -60.00 -119.99 59.99 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 447 0.023 - 0.046: 230 0.046 - 0.070: 120 0.070 - 0.093: 13 0.093 - 0.116: 150 Chirality restraints: 960 Sorted by residual: chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.36e-01 chirality pdb=" CA ILE F 88 " pdb=" N ILE F 88 " pdb=" C ILE F 88 " pdb=" CB ILE F 88 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.34e-01 chirality pdb=" CA VAL J 82 " pdb=" N VAL J 82 " pdb=" C VAL J 82 " pdb=" CB VAL J 82 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 957 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " -0.004 2.00e-02 2.50e+03 3.13e-03 1.72e-01 pdb=" CG PHE D 94 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " -0.004 2.00e-02 2.50e+03 3.11e-03 1.70e-01 pdb=" CG PHE F 94 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 94 " -0.004 2.00e-02 2.50e+03 2.96e-03 1.53e-01 pdb=" CG PHE H 94 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE H 94 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE H 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE H 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 94 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE H 94 " -0.002 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1573 2.84 - 3.35: 3965 3.35 - 3.87: 9230 3.87 - 4.38: 10003 4.38 - 4.90: 19745 Nonbonded interactions: 44516 Sorted by model distance: nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS G 80 " model vdw 2.323 3.120 nonbonded pdb=" NZ LYS A 80 " pdb=" OE1 GLU E 46 " model vdw 2.324 3.120 nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS C 80 " model vdw 2.325 3.120 nonbonded pdb=" NZ LYS E 80 " pdb=" OE1 GLU I 46 " model vdw 2.325 3.120 nonbonded pdb=" NZ LYS B 96 " pdb=" OD2 ASP F 98 " model vdw 2.333 3.120 ... (remaining 44511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 5545 Z= 0.081 Angle : 0.437 8.340 7475 Z= 0.233 Chirality : 0.050 0.116 960 Planarity : 0.001 0.003 940 Dihedral : 18.307 70.618 1915 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.75 % Allowed : 25.69 % Favored : 71.56 % 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: -1.74 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.007 0.001 PHE F 94 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00156 ( 5545) covalent geometry : angle 0.43742 ( 7475) hydrogen bonds : bond 0.16719 ( 146) hydrogen bonds : angle 7.58739 ( 438) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.211 Fit side-chains REVERT: A 62 GLN cc_start: 0.7980 (tt0) cc_final: 0.7503 (mt0) REVERT: C 62 GLN cc_start: 0.8061 (tt0) cc_final: 0.7606 (mt0) REVERT: C 83 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7624 (mt-10) REVERT: D 99 GLN cc_start: 0.7610 (mt0) cc_final: 0.7209 (mt0) REVERT: E 62 GLN cc_start: 0.8061 (tt0) cc_final: 0.7600 (mt0) REVERT: G 34 LYS cc_start: 0.8559 (tmtt) cc_final: 0.7909 (ttmt) REVERT: G 62 GLN cc_start: 0.8361 (tt0) cc_final: 0.7936 (mt0) REVERT: G 83 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: I 62 GLN cc_start: 0.7984 (tt0) cc_final: 0.7665 (mt0) REVERT: J 99 GLN cc_start: 0.7813 (mt0) cc_final: 0.7536 (mt0) outliers start: 15 outliers final: 11 residues processed: 114 average time/residue: 0.6424 time to fit residues: 75.5913 Evaluate side-chains 114 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN B 24 GLN C 62 GLN D 24 GLN E 62 GLN F 24 GLN G 62 GLN H 24 GLN I 62 GLN J 24 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.104442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.081372 restraints weight = 6020.838| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.51 r_work: 0.2978 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 5545 Z= 0.274 Angle : 0.610 11.897 7475 Z= 0.323 Chirality : 0.053 0.141 960 Planarity : 0.002 0.008 940 Dihedral : 6.567 35.896 828 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.32 % Allowed : 24.40 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR F 39 PHE 0.015 0.002 PHE D 94 HIS 0.008 0.002 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 5545) covalent geometry : angle 0.60986 ( 7475) hydrogen bonds : bond 0.03694 ( 146) hydrogen bonds : angle 5.37128 ( 438) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.175 Fit side-chains REVERT: A 62 GLN cc_start: 0.7920 (tt0) cc_final: 0.7271 (mt0) REVERT: B 35 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8173 (mt-10) REVERT: C 34 LYS cc_start: 0.8448 (tmtt) cc_final: 0.7849 (tmtm) REVERT: C 62 GLN cc_start: 0.7889 (tt0) cc_final: 0.7275 (mt0) REVERT: C 64 THR cc_start: 0.9065 (m) cc_final: 0.8852 (m) REVERT: D 99 GLN cc_start: 0.7253 (mt0) cc_final: 0.6889 (mt0) REVERT: E 62 GLN cc_start: 0.8188 (tt0) cc_final: 0.7557 (mt0) REVERT: G 34 LYS cc_start: 0.8544 (tmtt) cc_final: 0.7767 (ttmt) REVERT: G 58 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8549 (mtpp) REVERT: G 62 GLN cc_start: 0.8436 (tt0) cc_final: 0.7879 (mt0) REVERT: H 99 GLN cc_start: 0.7732 (mt0) cc_final: 0.7525 (mt0) REVERT: I 34 LYS cc_start: 0.8682 (tmtt) cc_final: 0.8463 (tttt) REVERT: I 35 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: I 62 GLN cc_start: 0.8044 (tt0) cc_final: 0.7502 (mt0) REVERT: J 99 GLN cc_start: 0.7457 (mt0) cc_final: 0.7162 (mt0) outliers start: 29 outliers final: 24 residues processed: 146 average time/residue: 0.5460 time to fit residues: 82.5764 Evaluate side-chains 152 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 0.0570 chunk 28 optimal weight: 9.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.079215 restraints weight = 6140.653| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.57 r_work: 0.2982 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 5545 Z= 0.164 Angle : 0.517 11.135 7475 Z= 0.272 Chirality : 0.051 0.129 960 Planarity : 0.002 0.006 940 Dihedral : 4.796 21.068 807 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 5.50 % Allowed : 27.16 % Favored : 67.34 % 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: -1.93 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR F 39 PHE 0.012 0.002 PHE H 94 HIS 0.005 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5545) covalent geometry : angle 0.51708 ( 7475) hydrogen bonds : bond 0.02642 ( 146) hydrogen bonds : angle 5.01673 ( 438) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.245 Fit side-chains REVERT: B 35 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8095 (mt-10) REVERT: C 34 LYS cc_start: 0.8384 (tmtt) cc_final: 0.7782 (tmtm) REVERT: C 57 GLU cc_start: 0.8217 (tt0) cc_final: 0.7769 (tp30) REVERT: C 62 GLN cc_start: 0.7894 (tt0) cc_final: 0.7266 (mt0) REVERT: C 64 THR cc_start: 0.8980 (m) cc_final: 0.8772 (m) REVERT: D 99 GLN cc_start: 0.7174 (mt0) cc_final: 0.6810 (mt0) REVERT: E 62 GLN cc_start: 0.8126 (tt0) cc_final: 0.7433 (mt0) REVERT: G 58 LYS cc_start: 0.8803 (ttmm) cc_final: 0.8517 (mtpp) REVERT: G 62 GLN cc_start: 0.8423 (tt0) cc_final: 0.7837 (mt0) REVERT: H 99 GLN cc_start: 0.7666 (mt0) cc_final: 0.7463 (mt0) REVERT: I 62 GLN cc_start: 0.8017 (tt0) cc_final: 0.7416 (mt0) REVERT: J 57 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: J 99 GLN cc_start: 0.7352 (mt0) cc_final: 0.7072 (mt0) outliers start: 30 outliers final: 24 residues processed: 133 average time/residue: 0.6361 time to fit residues: 87.4916 Evaluate side-chains 142 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.0270 chunk 48 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 overall best weight: 6.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079524 restraints weight = 6056.864| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.59 r_work: 0.2945 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.040 5545 Z= 0.356 Angle : 0.679 13.578 7475 Z= 0.356 Chirality : 0.056 0.143 960 Planarity : 0.003 0.009 940 Dihedral : 5.166 13.544 805 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.79 % Allowed : 26.79 % Favored : 66.42 % 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: -2.06 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR F 39 PHE 0.018 0.003 PHE D 94 HIS 0.008 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00854 ( 5545) covalent geometry : angle 0.67859 ( 7475) hydrogen bonds : bond 0.03759 ( 146) hydrogen bonds : angle 5.11831 ( 438) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.218 Fit side-chains REVERT: A 62 GLN cc_start: 0.7938 (tt0) cc_final: 0.7430 (mt0) REVERT: B 35 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8186 (mt-10) REVERT: C 34 LYS cc_start: 0.8479 (tmtt) cc_final: 0.7900 (tmtm) REVERT: C 62 GLN cc_start: 0.7966 (tt0) cc_final: 0.7285 (mt0) REVERT: D 99 GLN cc_start: 0.7347 (mt0) cc_final: 0.7059 (mt0) REVERT: G 34 LYS cc_start: 0.8595 (tmtt) cc_final: 0.7817 (ttmt) REVERT: G 58 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8564 (mtpp) REVERT: G 62 GLN cc_start: 0.8486 (tt0) cc_final: 0.7896 (mt0) REVERT: I 35 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: I 62 GLN cc_start: 0.8183 (tt0) cc_final: 0.7528 (mt0) REVERT: J 57 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: J 99 GLN cc_start: 0.7283 (mt0) cc_final: 0.6993 (mt0) outliers start: 37 outliers final: 31 residues processed: 141 average time/residue: 0.6276 time to fit residues: 91.4184 Evaluate side-chains 158 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.082367 restraints weight = 6059.610| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.50 r_work: 0.3037 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 5545 Z= 0.112 Angle : 0.497 11.121 7475 Z= 0.257 Chirality : 0.051 0.126 960 Planarity : 0.001 0.005 940 Dihedral : 4.699 12.886 805 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.49 % Allowed : 29.17 % Favored : 67.34 % 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: -2.02 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYR F 39 PHE 0.010 0.002 PHE D 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5545) covalent geometry : angle 0.49690 ( 7475) hydrogen bonds : bond 0.02023 ( 146) hydrogen bonds : angle 4.72415 ( 438) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.132 Fit side-chains REVERT: A 34 LYS cc_start: 0.8510 (tmtt) cc_final: 0.7902 (tmtm) REVERT: B 35 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8172 (mt-10) REVERT: C 62 GLN cc_start: 0.7983 (tt0) cc_final: 0.7370 (mt0) REVERT: D 99 GLN cc_start: 0.7272 (mt0) cc_final: 0.6931 (mt0) REVERT: G 58 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8501 (mtpp) REVERT: G 62 GLN cc_start: 0.8498 (tt0) cc_final: 0.7926 (mt0) REVERT: G 83 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: I 62 GLN cc_start: 0.8133 (tt0) cc_final: 0.7506 (mt0) REVERT: J 99 GLN cc_start: 0.7280 (mt0) cc_final: 0.6998 (mt0) outliers start: 19 outliers final: 15 residues processed: 127 average time/residue: 0.6830 time to fit residues: 89.4761 Evaluate side-chains 131 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 23 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN H 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082373 restraints weight = 5989.616| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.49 r_work: 0.3038 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 5545 Z= 0.115 Angle : 0.492 11.403 7475 Z= 0.254 Chirality : 0.051 0.126 960 Planarity : 0.001 0.005 940 Dihedral : 4.586 12.733 805 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.40 % Allowed : 28.62 % Favored : 66.97 % 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: -2.02 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR G 39 PHE 0.010 0.001 PHE D 94 HIS 0.003 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5545) covalent geometry : angle 0.49195 ( 7475) hydrogen bonds : bond 0.02009 ( 146) hydrogen bonds : angle 4.60838 ( 438) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.209 Fit side-chains REVERT: A 34 LYS cc_start: 0.8492 (tmtt) cc_final: 0.7869 (tmtm) REVERT: A 57 GLU cc_start: 0.8339 (tt0) cc_final: 0.7943 (tp30) REVERT: B 35 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8218 (mt-10) REVERT: C 57 GLU cc_start: 0.8283 (tt0) cc_final: 0.7855 (tp30) REVERT: C 62 GLN cc_start: 0.7916 (tt0) cc_final: 0.7338 (mt0) REVERT: D 99 GLN cc_start: 0.7272 (mt0) cc_final: 0.6928 (mt0) REVERT: E 62 GLN cc_start: 0.8048 (tt0) cc_final: 0.7357 (mt0) REVERT: G 62 GLN cc_start: 0.8435 (tt0) cc_final: 0.7865 (mt0) REVERT: G 83 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: I 34 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8459 (tttt) REVERT: I 35 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: I 62 GLN cc_start: 0.8108 (tt0) cc_final: 0.7512 (mt0) REVERT: J 57 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8459 (tt0) REVERT: J 99 GLN cc_start: 0.7212 (mt0) cc_final: 0.6928 (mt0) outliers start: 24 outliers final: 19 residues processed: 122 average time/residue: 0.6288 time to fit residues: 79.3213 Evaluate side-chains 133 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 34 LYS Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 57 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN H 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.078573 restraints weight = 6125.805| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.49 r_work: 0.2982 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.043 5545 Z= 0.413 Angle : 0.717 14.044 7475 Z= 0.377 Chirality : 0.057 0.146 960 Planarity : 0.003 0.010 940 Dihedral : 5.293 13.633 805 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 7.52 % Allowed : 26.24 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR G 39 PHE 0.019 0.003 PHE D 94 HIS 0.010 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00990 ( 5545) covalent geometry : angle 0.71688 ( 7475) hydrogen bonds : bond 0.03987 ( 146) hydrogen bonds : angle 5.03829 ( 438) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.202 Fit side-chains REVERT: A 62 GLN cc_start: 0.7975 (tt0) cc_final: 0.7312 (mt0) REVERT: B 35 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8257 (mt-10) REVERT: C 34 LYS cc_start: 0.8521 (tmtt) cc_final: 0.7927 (tmtm) REVERT: C 62 GLN cc_start: 0.8036 (tt0) cc_final: 0.7388 (mt0) REVERT: D 99 GLN cc_start: 0.7417 (mt0) cc_final: 0.7092 (mt0) REVERT: G 34 LYS cc_start: 0.8607 (tmtt) cc_final: 0.8051 (tmtm) REVERT: G 62 GLN cc_start: 0.8510 (tt0) cc_final: 0.7918 (mt0) REVERT: G 83 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: I 34 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8516 (tttt) REVERT: I 35 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: I 62 GLN cc_start: 0.8224 (tt0) cc_final: 0.7526 (mt0) REVERT: J 57 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: J 99 GLN cc_start: 0.7338 (mt0) cc_final: 0.7066 (mt0) outliers start: 41 outliers final: 33 residues processed: 145 average time/residue: 0.6466 time to fit residues: 96.8256 Evaluate side-chains 164 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 34 LYS Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN F 79 GLN H 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.104324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081656 restraints weight = 6013.401| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.49 r_work: 0.3015 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 5545 Z= 0.114 Angle : 0.505 11.763 7475 Z= 0.259 Chirality : 0.051 0.126 960 Planarity : 0.001 0.006 940 Dihedral : 4.745 12.879 805 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.59 % Allowed : 29.36 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR J 39 PHE 0.010 0.001 PHE H 94 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5545) covalent geometry : angle 0.50541 ( 7475) hydrogen bonds : bond 0.01998 ( 146) hydrogen bonds : angle 4.65346 ( 438) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.206 Fit side-chains REVERT: A 34 LYS cc_start: 0.8476 (tmtt) cc_final: 0.7850 (tmtm) REVERT: B 35 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8130 (mt-10) REVERT: C 62 GLN cc_start: 0.7964 (tt0) cc_final: 0.7377 (mt0) REVERT: D 99 GLN cc_start: 0.7330 (mt0) cc_final: 0.6967 (mt0) REVERT: G 62 GLN cc_start: 0.8408 (tt0) cc_final: 0.7845 (mt0) REVERT: G 83 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7817 (mt-10) REVERT: I 62 GLN cc_start: 0.8146 (tt0) cc_final: 0.7504 (mt0) REVERT: J 57 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8471 (tt0) REVERT: J 99 GLN cc_start: 0.7292 (mt0) cc_final: 0.6995 (mt0) outliers start: 25 outliers final: 21 residues processed: 125 average time/residue: 0.5385 time to fit residues: 69.7816 Evaluate side-chains 138 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 57 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 1 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN H 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.100411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.078137 restraints weight = 6157.959| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.45 r_work: 0.2983 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.046 5545 Z= 0.447 Angle : 0.746 14.596 7475 Z= 0.393 Chirality : 0.059 0.148 960 Planarity : 0.003 0.011 940 Dihedral : 5.388 13.965 805 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 6.42 % Allowed : 27.89 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.13 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR F 39 PHE 0.019 0.003 PHE D 94 HIS 0.011 0.004 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.01069 ( 5545) covalent geometry : angle 0.74609 ( 7475) hydrogen bonds : bond 0.04186 ( 146) hydrogen bonds : angle 5.07562 ( 438) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.212 Fit side-chains REVERT: A 62 GLN cc_start: 0.7981 (tt0) cc_final: 0.7285 (mt0) REVERT: B 35 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8332 (mt-10) REVERT: C 62 GLN cc_start: 0.8001 (tt0) cc_final: 0.7349 (mt0) REVERT: D 99 GLN cc_start: 0.7444 (mt0) cc_final: 0.7139 (mt0) REVERT: G 34 LYS cc_start: 0.8615 (tmtt) cc_final: 0.8106 (tmtm) REVERT: G 62 GLN cc_start: 0.8472 (tt0) cc_final: 0.7874 (mt0) REVERT: G 83 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7782 (mt-10) REVERT: I 35 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: I 62 GLN cc_start: 0.8187 (tt0) cc_final: 0.7529 (mt0) REVERT: J 57 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: J 99 GLN cc_start: 0.7339 (mt0) cc_final: 0.7048 (mt0) outliers start: 35 outliers final: 31 residues processed: 145 average time/residue: 0.6657 time to fit residues: 99.7624 Evaluate side-chains 165 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 57 GLU Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 68 optimal weight: 10.0000 chunk 54 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN H 50 HIS H 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.080668 restraints weight = 6137.624| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.57 r_work: 0.3016 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 5545 Z= 0.083 Angle : 0.483 11.759 7475 Z= 0.246 Chirality : 0.051 0.131 960 Planarity : 0.001 0.006 940 Dihedral : 4.640 12.417 805 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.04 % Allowed : 31.01 % Favored : 64.95 % 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: -2.05 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR J 39 PHE 0.009 0.001 PHE H 94 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 5545) covalent geometry : angle 0.48286 ( 7475) hydrogen bonds : bond 0.01546 ( 146) hydrogen bonds : angle 4.52556 ( 438) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.127 Fit side-chains REVERT: A 57 GLU cc_start: 0.8325 (tt0) cc_final: 0.7966 (tp30) REVERT: B 35 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8093 (mt-10) REVERT: C 62 GLN cc_start: 0.7801 (tt0) cc_final: 0.7239 (mt0) REVERT: D 99 GLN cc_start: 0.7202 (mt0) cc_final: 0.6850 (mt0) REVERT: G 62 GLN cc_start: 0.8422 (tt0) cc_final: 0.7821 (mt0) REVERT: I 62 GLN cc_start: 0.8126 (tt0) cc_final: 0.7423 (mt0) REVERT: J 57 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: J 99 GLN cc_start: 0.7190 (mt0) cc_final: 0.6884 (mt0) outliers start: 22 outliers final: 18 residues processed: 122 average time/residue: 0.5954 time to fit residues: 75.1645 Evaluate side-chains 129 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 57 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 44 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN H 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.102044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.079476 restraints weight = 6099.404| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.49 r_work: 0.2998 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 5545 Z= 0.307 Angle : 0.645 13.698 7475 Z= 0.336 Chirality : 0.054 0.139 960 Planarity : 0.002 0.008 940 Dihedral : 5.130 13.458 805 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.95 % Allowed : 31.01 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.28), residues: 785 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR G 39 PHE 0.016 0.002 PHE D 94 HIS 0.008 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00733 ( 5545) covalent geometry : angle 0.64499 ( 7475) hydrogen bonds : bond 0.03365 ( 146) hydrogen bonds : angle 4.89788 ( 438) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2204.37 seconds wall clock time: 38 minutes 22.03 seconds (2302.03 seconds total)