Starting phenix.real_space_refine on Fri Dec 27 13:33:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ads_15369/12_2024/8ads_15369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ads_15369/12_2024/8ads_15369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ads_15369/12_2024/8ads_15369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ads_15369/12_2024/8ads_15369.map" model { file = "/net/cci-nas-00/data/ceres_data/8ads_15369/12_2024/8ads_15369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ads_15369/12_2024/8ads_15369.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 3230 2.51 5 N 900 2.21 5 O 1040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5170 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 3.32, per 1000 atoms: 0.64 Number of scatterers: 5170 At special positions: 0 Unit cell: (116.55, 105, 43.05, 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 1040 8.00 N 900 7.00 C 3230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 889.7 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 54.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 removed outlier: 6.633A pdb=" N VAL A 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA B 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS B 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU A 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LYS B 23 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR A 22 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 16 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA C 19 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 18 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS C 21 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU B 20 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS C 23 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR B 22 " --> pdb=" O LYS C 23 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 16 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA D 19 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA C 18 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LYS D 21 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU C 20 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS D 23 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR C 22 " --> pdb=" O LYS D 23 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL D 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA E 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA D 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LYS E 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU D 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS E 23 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR D 22 " --> pdb=" O LYS E 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 5.917A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS B 34 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS C 34 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS D 34 " --> pdb=" O GLU E 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 49 removed outlier: 6.389A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU B 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS A 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N VAL B 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER C 42 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY B 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR C 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU C 46 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS B 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N VAL C 48 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N GLY B 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER D 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLY C 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR D 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU D 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LYS C 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N VAL D 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU E 46 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LYS D 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N VAL E 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N GLY D 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.504A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL C 66 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN B 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL D 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN C 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 72 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA8, first strand: chain 'A' and resid 85 through 92 Processing sheet with id=AA9, first strand: chain 'F' and resid 15 through 23 removed outlier: 6.633A pdb=" N VAL F 16 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA G 19 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA F 18 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LYS G 21 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU F 20 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS G 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR F 22 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL G 16 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA H 19 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA G 18 " --> pdb=" O ALA H 19 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS H 21 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU G 20 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS H 23 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR G 22 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL H 16 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ALA I 19 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA H 18 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LYS I 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU H 20 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LYS I 23 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR H 22 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL I 16 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ALA J 19 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA I 18 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N LYS J 21 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU I 20 " --> pdb=" O LYS J 21 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LYS J 23 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR I 22 " --> pdb=" O LYS J 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 34 through 35 removed outlier: 5.916A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS I 34 " --> pdb=" O GLU J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 38 through 49 removed outlier: 6.389A pdb=" N TYR F 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER G 42 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY F 41 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR G 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS F 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU G 46 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS F 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N VAL G 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER H 42 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY G 41 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR H 44 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N GLU H 46 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS G 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N VAL H 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N GLY G 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER I 42 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY H 41 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N THR I 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU I 46 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS H 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N VAL I 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N GLY H 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N TYR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N SER J 42 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY I 41 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N THR J 44 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS I 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU J 46 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LYS I 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N VAL J 48 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 53 through 57 Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 66 removed outlier: 6.503A pdb=" N VAL F 63 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL G 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN F 65 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL G 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL H 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN G 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL H 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL I 66 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN H 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL I 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL J 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN I 65 " --> pdb=" O VAL J 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 69 through 72 Processing sheet with id=AB6, first strand: chain 'F' and resid 75 through 79 Processing sheet with id=AB7, first strand: chain 'F' and resid 85 through 92 144 hydrogen bonds defined for protein. 432 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 910 1.29 - 1.35: 799 1.35 - 1.42: 171 1.42 - 1.48: 873 1.48 - 1.55: 2427 Bond restraints: 5180 Sorted by residual: bond pdb=" CB THR B 72 " pdb=" CG2 THR B 72 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CB THR E 72 " pdb=" CG2 THR E 72 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CB THR H 72 " pdb=" CG2 THR H 72 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.79e+00 bond pdb=" CB THR J 72 " pdb=" CG2 THR J 72 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CB THR D 72 " pdb=" CG2 THR D 72 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 ... (remaining 5175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.67: 6057 0.67 - 1.33: 784 1.33 - 2.00: 99 2.00 - 2.67: 20 2.67 - 3.33: 20 Bond angle restraints: 6980 Sorted by residual: angle pdb=" N THR G 72 " pdb=" CA THR G 72 " pdb=" C THR G 72 " ideal model delta sigma weight residual 108.99 110.97 -1.98 1.57e+00 4.06e-01 1.59e+00 angle pdb=" N THR B 72 " pdb=" CA THR B 72 " pdb=" C THR B 72 " ideal model delta sigma weight residual 108.99 110.95 -1.96 1.57e+00 4.06e-01 1.57e+00 angle pdb=" N THR E 72 " pdb=" CA THR E 72 " pdb=" C THR E 72 " ideal model delta sigma weight residual 108.99 110.92 -1.93 1.57e+00 4.06e-01 1.50e+00 angle pdb=" N THR J 72 " pdb=" CA THR J 72 " pdb=" C THR J 72 " ideal model delta sigma weight residual 108.99 110.92 -1.93 1.57e+00 4.06e-01 1.50e+00 angle pdb=" N THR D 72 " pdb=" CA THR D 72 " pdb=" C THR D 72 " ideal model delta sigma weight residual 108.99 110.91 -1.92 1.57e+00 4.06e-01 1.50e+00 ... (remaining 6975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 2830 15.13 - 30.26: 150 30.26 - 45.39: 40 45.39 - 60.52: 20 60.52 - 75.66: 10 Dihedral angle restraints: 3050 sinusoidal: 1030 harmonic: 2020 Sorted by residual: dihedral pdb=" CB GLU J 46 " pdb=" CG GLU J 46 " pdb=" CD GLU J 46 " pdb=" OE1 GLU J 46 " ideal model delta sinusoidal sigma weight residual 0.00 -75.66 75.66 1 3.00e+01 1.11e-03 8.02e+00 dihedral pdb=" CB GLU G 46 " pdb=" CG GLU G 46 " pdb=" CD GLU G 46 " pdb=" OE1 GLU G 46 " ideal model delta sinusoidal sigma weight residual 0.00 -75.65 75.65 1 3.00e+01 1.11e-03 8.02e+00 dihedral pdb=" CB GLU C 46 " pdb=" CG GLU C 46 " pdb=" CD GLU C 46 " pdb=" OE1 GLU C 46 " ideal model delta sinusoidal sigma weight residual 0.00 -75.65 75.65 1 3.00e+01 1.11e-03 8.02e+00 ... (remaining 3047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 504 0.034 - 0.068: 209 0.068 - 0.102: 113 0.102 - 0.136: 84 0.136 - 0.170: 10 Chirality restraints: 920 Sorted by residual: chirality pdb=" CB THR I 72 " pdb=" CA THR I 72 " pdb=" OG1 THR I 72 " pdb=" CG2 THR I 72 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CB THR E 72 " pdb=" CA THR E 72 " pdb=" OG1 THR E 72 " pdb=" CG2 THR E 72 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CB THR C 72 " pdb=" CA THR C 72 " pdb=" OG1 THR C 72 " pdb=" CG2 THR C 72 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 917 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 73 " -0.003 2.00e-02 2.50e+03 5.96e-03 3.55e-01 pdb=" C GLY C 73 " 0.010 2.00e-02 2.50e+03 pdb=" O GLY C 73 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL C 74 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 73 " -0.003 2.00e-02 2.50e+03 5.92e-03 3.50e-01 pdb=" C GLY B 73 " 0.010 2.00e-02 2.50e+03 pdb=" O GLY B 73 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL B 74 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 73 " 0.003 2.00e-02 2.50e+03 5.91e-03 3.50e-01 pdb=" C GLY H 73 " -0.010 2.00e-02 2.50e+03 pdb=" O GLY H 73 " 0.004 2.00e-02 2.50e+03 pdb=" N VAL H 74 " 0.003 2.00e-02 2.50e+03 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 323 2.75 - 3.29: 4874 3.29 - 3.83: 9037 3.83 - 4.36: 11148 4.36 - 4.90: 19858 Nonbonded interactions: 45240 Sorted by model distance: nonbonded pdb=" NZ LYS C 80 " pdb=" OE2 GLU D 83 " model vdw 2.218 3.120 nonbonded pdb=" NZ LYS D 80 " pdb=" OE2 GLU E 83 " model vdw 2.218 3.120 nonbonded pdb=" NZ LYS I 80 " pdb=" OE2 GLU J 83 " model vdw 2.218 3.120 nonbonded pdb=" NZ LYS B 80 " pdb=" OE2 GLU C 83 " model vdw 2.218 3.120 nonbonded pdb=" NZ LYS G 80 " pdb=" OE2 GLU H 83 " model vdw 2.218 3.120 ... (remaining 45235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.160 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.004 0.044 5180 Z= 0.237 Angle : 0.487 3.332 6980 Z= 0.275 Chirality : 0.055 0.170 920 Planarity : 0.001 0.006 860 Dihedral : 13.377 75.655 1770 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS G 50 PHE 0.003 0.001 PHE A 94 TYR 0.007 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.530 Fit side-chains REVERT: B 58 LYS cc_start: 0.8472 (mtpp) cc_final: 0.8175 (mttm) REVERT: C 35 GLU cc_start: 0.6283 (mp0) cc_final: 0.5886 (mp0) REVERT: D 58 LYS cc_start: 0.8269 (mtpp) cc_final: 0.7966 (mttm) REVERT: E 35 GLU cc_start: 0.6122 (mp0) cc_final: 0.5797 (mp0) REVERT: H 58 LYS cc_start: 0.8157 (mtpp) cc_final: 0.7952 (mtpp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2486 time to fit residues: 26.1018 Evaluate side-chains 63 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 HIS ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 5180 Z= 0.477 Angle : 0.614 6.667 6980 Z= 0.337 Chirality : 0.056 0.142 920 Planarity : 0.003 0.014 860 Dihedral : 4.815 12.961 740 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.27 % Allowed : 6.15 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.26), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS E 50 PHE 0.006 0.001 PHE J 94 TYR 0.016 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.635 Fit side-chains REVERT: A 57 GLU cc_start: 0.7716 (tm-30) cc_final: 0.6954 (tm-30) REVERT: B 58 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8242 (mttm) REVERT: D 24 GLN cc_start: 0.6919 (mp10) cc_final: 0.6390 (mp10) REVERT: J 57 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7491 (tm-30) outliers start: 17 outliers final: 16 residues processed: 88 average time/residue: 0.2478 time to fit residues: 26.7928 Evaluate side-chains 86 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 0.0070 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 5180 Z= 0.400 Angle : 0.549 5.358 6980 Z= 0.303 Chirality : 0.055 0.133 920 Planarity : 0.002 0.013 860 Dihedral : 4.701 13.645 740 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.08 % Allowed : 7.88 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS E 50 PHE 0.004 0.001 PHE J 94 TYR 0.014 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.722 Fit side-chains REVERT: A 57 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6945 (tm-30) REVERT: B 58 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8300 (mtpt) REVERT: B 83 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7164 (mt-10) REVERT: C 57 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7010 (tm-30) REVERT: D 24 GLN cc_start: 0.7061 (mp10) cc_final: 0.6543 (mp10) REVERT: G 43 LYS cc_start: 0.7758 (tttp) cc_final: 0.7532 (tttt) REVERT: G 80 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8490 (mtpt) REVERT: H 46 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7516 (tm-30) outliers start: 16 outliers final: 16 residues processed: 87 average time/residue: 0.2475 time to fit residues: 26.2258 Evaluate side-chains 87 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 5180 Z= 0.247 Angle : 0.472 7.287 6980 Z= 0.258 Chirality : 0.053 0.129 920 Planarity : 0.002 0.010 860 Dihedral : 4.423 14.084 740 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.04 % Allowed : 9.23 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 PHE 0.003 0.001 PHE J 94 TYR 0.011 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.682 Fit side-chains REVERT: A 57 GLU cc_start: 0.7637 (tm-30) cc_final: 0.6938 (tm-30) REVERT: B 58 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8308 (mttm) REVERT: C 57 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7014 (tm-30) REVERT: C 72 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8169 (m) REVERT: D 24 GLN cc_start: 0.7126 (mp10) cc_final: 0.6658 (mp10) REVERT: D 35 GLU cc_start: 0.7195 (mp0) cc_final: 0.6656 (mp0) REVERT: G 80 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8272 (mtpt) outliers start: 21 outliers final: 17 residues processed: 85 average time/residue: 0.2641 time to fit residues: 27.5346 Evaluate side-chains 88 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 5180 Z= 0.508 Angle : 0.601 6.468 6980 Z= 0.333 Chirality : 0.056 0.139 920 Planarity : 0.003 0.015 860 Dihedral : 4.888 14.979 740 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.42 % Allowed : 10.38 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 50 PHE 0.004 0.001 PHE J 94 TYR 0.015 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.690 Fit side-chains REVERT: A 57 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.6899 (tm-30) REVERT: B 83 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7436 (mt-10) REVERT: C 57 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7040 (tm-30) REVERT: D 24 GLN cc_start: 0.7219 (mp10) cc_final: 0.6702 (mp10) REVERT: I 43 LYS cc_start: 0.7837 (tttp) cc_final: 0.7620 (tttt) outliers start: 23 outliers final: 22 residues processed: 98 average time/residue: 0.2693 time to fit residues: 32.8815 Evaluate side-chains 104 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5180 Z= 0.418 Angle : 0.565 5.972 6980 Z= 0.312 Chirality : 0.055 0.136 920 Planarity : 0.002 0.014 860 Dihedral : 4.823 15.464 740 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.62 % Allowed : 10.96 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 50 PHE 0.004 0.001 PHE J 94 TYR 0.013 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.571 Fit side-chains REVERT: A 57 GLU cc_start: 0.7632 (tm-30) cc_final: 0.6893 (tm-30) REVERT: C 57 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7006 (tm-30) REVERT: D 24 GLN cc_start: 0.7276 (mp10) cc_final: 0.6793 (mp10) REVERT: H 46 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7665 (tm-30) outliers start: 24 outliers final: 23 residues processed: 94 average time/residue: 0.2019 time to fit residues: 23.8004 Evaluate side-chains 101 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 5180 Z= 0.235 Angle : 0.475 5.425 6980 Z= 0.262 Chirality : 0.053 0.129 920 Planarity : 0.002 0.011 860 Dihedral : 4.477 16.627 740 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.81 % Allowed : 11.73 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 PHE 0.003 0.001 PHE J 94 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7625 (tm-30) cc_final: 0.6919 (tm-30) REVERT: C 57 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6936 (tm-30) REVERT: C 72 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8179 (m) REVERT: D 24 GLN cc_start: 0.7426 (mp10) cc_final: 0.6923 (mp10) REVERT: D 35 GLU cc_start: 0.7296 (mp0) cc_final: 0.6696 (mp0) REVERT: D 80 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8500 (mtpp) REVERT: F 24 GLN cc_start: 0.7322 (mp10) cc_final: 0.7096 (mp10) outliers start: 25 outliers final: 23 residues processed: 88 average time/residue: 0.1902 time to fit residues: 21.3416 Evaluate side-chains 97 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 5180 Z= 0.627 Angle : 0.679 5.800 6980 Z= 0.379 Chirality : 0.059 0.155 920 Planarity : 0.003 0.016 860 Dihedral : 5.200 18.869 740 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.65 % Allowed : 12.69 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 50 PHE 0.006 0.001 PHE F 94 TYR 0.017 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.784 Fit side-chains REVERT: A 57 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: C 57 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6960 (tm-30) REVERT: D 24 GLN cc_start: 0.7527 (mp10) cc_final: 0.6924 (mp10) REVERT: E 35 GLU cc_start: 0.7575 (mp0) cc_final: 0.7253 (mp0) outliers start: 19 outliers final: 18 residues processed: 102 average time/residue: 0.2317 time to fit residues: 29.5533 Evaluate side-chains 110 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5180 Z= 0.215 Angle : 0.497 5.266 6980 Z= 0.274 Chirality : 0.053 0.129 920 Planarity : 0.002 0.011 860 Dihedral : 4.529 18.968 740 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.65 % Allowed : 12.31 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 PHE 0.003 0.001 PHE J 94 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.559 Fit side-chains REVERT: A 57 GLU cc_start: 0.7644 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 24 GLN cc_start: 0.7661 (mp10) cc_final: 0.7379 (mm110) REVERT: C 35 GLU cc_start: 0.7290 (mp0) cc_final: 0.6431 (mp0) REVERT: C 57 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6991 (tm-30) REVERT: C 72 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8192 (m) REVERT: D 24 GLN cc_start: 0.7572 (mp10) cc_final: 0.7026 (mp10) REVERT: D 35 GLU cc_start: 0.7282 (mp0) cc_final: 0.6691 (mp0) outliers start: 19 outliers final: 16 residues processed: 90 average time/residue: 0.2191 time to fit residues: 24.5249 Evaluate side-chains 95 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 0.0770 chunk 34 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 5180 Z= 0.542 Angle : 0.650 5.643 6980 Z= 0.361 Chirality : 0.057 0.140 920 Planarity : 0.003 0.019 860 Dihedral : 5.082 18.747 740 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.85 % Allowed : 13.08 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 50 PHE 0.004 0.001 PHE F 94 TYR 0.015 0.004 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.609 Fit side-chains REVERT: A 57 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: C 24 GLN cc_start: 0.7459 (mp10) cc_final: 0.7256 (mm110) REVERT: C 57 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6982 (tm-30) REVERT: D 24 GLN cc_start: 0.7593 (mp10) cc_final: 0.7092 (mp10) REVERT: E 24 GLN cc_start: 0.7914 (mp10) cc_final: 0.7491 (mp10) REVERT: E 35 GLU cc_start: 0.7541 (mp0) cc_final: 0.7246 (mp0) REVERT: H 80 LYS cc_start: 0.8939 (mttt) cc_final: 0.8379 (tttm) outliers start: 20 outliers final: 19 residues processed: 96 average time/residue: 0.2074 time to fit residues: 25.0619 Evaluate side-chains 106 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.107491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.095493 restraints weight = 7243.514| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.19 r_work: 0.3496 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5180 Z= 0.347 Angle : 0.568 5.223 6980 Z= 0.314 Chirality : 0.054 0.135 920 Planarity : 0.002 0.019 860 Dihedral : 4.839 20.028 740 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.65 % Allowed : 13.08 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 PHE 0.004 0.001 PHE J 94 TYR 0.011 0.003 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1416.53 seconds wall clock time: 27 minutes 40.80 seconds (1660.80 seconds total)