Starting phenix.real_space_refine on Thu Mar 6 05:45:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ads_15369/03_2025/8ads_15369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ads_15369/03_2025/8ads_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_15369/03_2025/8ads_15369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ads_15369/03_2025/8ads_15369.map" model { file = "/net/cci-nas-00/data/ceres_data/8ads_15369/03_2025/8ads_15369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ads_15369/03_2025/8ads_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-5624/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: 2.04, per 1000 atoms: 0.39 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: 1.24 Conformation dependent library (CDL) restraints added in 640.2 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: 0.93 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: 1.37 Time building geometry restraints manager: 1.48 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' 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: 5.600 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.410 Find NCS groups from input model: 0.120 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.450 ------------------------------------------------------------------------------- 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 : 0.597 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: 0.2749 time to fit residues: 28.6437 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 : 0.535 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.107615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095292 restraints weight = 7059.539| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.22 r_work: 0.3492 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.583 Fit side-chains REVERT: A 35 GLU cc_start: 0.7519 (mp0) cc_final: 0.7313 (mp0) REVERT: A 57 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7054 (tm-30) REVERT: B 57 GLU cc_start: 0.7650 (tm-30) cc_final: 0.7430 (tm-30) REVERT: B 58 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8132 (mttm) REVERT: D 24 GLN cc_start: 0.6716 (mp10) cc_final: 0.6156 (mp10) REVERT: F 43 LYS cc_start: 0.7931 (tttp) cc_final: 0.7726 (ttmt) REVERT: H 46 GLU cc_start: 0.8369 (tt0) cc_final: 0.8003 (tm-30) REVERT: J 57 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7853 (tm-30) outliers start: 17 outliers final: 16 residues processed: 88 average time/residue: 0.2567 time to fit residues: 27.6255 Evaluate side-chains 85 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 9 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 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 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** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.105789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093483 restraints weight = 7199.601| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.21 r_work: 0.3462 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 5180 Z= 0.507 Angle : 0.609 5.544 6980 Z= 0.337 Chirality : 0.056 0.147 920 Planarity : 0.003 0.016 860 Dihedral : 4.917 13.568 740 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.27 % Allowed : 7.88 % Favored : 88.85 % 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: -3.44 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS E 50 PHE 0.005 0.001 PHE J 94 TYR 0.016 0.004 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 104 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.181 Fit side-chains REVERT: A 35 GLU cc_start: 0.7685 (mp0) cc_final: 0.7318 (mp0) REVERT: A 57 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: B 57 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7468 (tm-30) REVERT: B 58 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8264 (mttm) REVERT: B 83 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 57 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7084 (tm-30) REVERT: D 24 GLN cc_start: 0.6860 (mp10) cc_final: 0.6331 (mp10) REVERT: H 46 GLU cc_start: 0.8397 (tt0) cc_final: 0.7962 (tm-30) outliers start: 17 outliers final: 16 residues processed: 93 average time/residue: 0.2477 time to fit residues: 28.5996 Evaluate side-chains 96 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR 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 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 62 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.113986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.101812 restraints weight = 7037.516| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.24 r_work: 0.3575 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5180 Z= 0.188 Angle : 0.448 7.155 6980 Z= 0.245 Chirality : 0.053 0.126 920 Planarity : 0.002 0.010 860 Dihedral : 4.341 14.344 740 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.85 % Allowed : 9.81 % Favored : 86.35 % 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 0.002 0.001 PHE J 94 TYR 0.009 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 101 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.613 Fit side-chains REVERT: A 57 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7167 (tm-30) REVERT: B 57 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 58 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8321 (mttm) REVERT: C 57 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7128 (tm-30) REVERT: C 72 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8300 (m) REVERT: D 24 GLN cc_start: 0.7021 (mp10) cc_final: 0.6489 (mp10) REVERT: D 35 GLU cc_start: 0.7580 (mp0) cc_final: 0.6950 (mp0) outliers start: 20 outliers final: 15 residues processed: 90 average time/residue: 0.2293 time to fit residues: 25.4949 Evaluate side-chains 91 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 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 49 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 20.0000 chunk 64 optimal weight: 0.2980 chunk 39 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094832 restraints weight = 7240.144| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.16 r_work: 0.3465 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 5180 Z= 0.439 Angle : 0.563 6.250 6980 Z= 0.311 Chirality : 0.055 0.135 920 Planarity : 0.002 0.014 860 Dihedral : 4.801 16.253 740 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.23 % Allowed : 10.38 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (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 0.014 0.003 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 102 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.482 Fit side-chains REVERT: A 35 GLU cc_start: 0.7808 (mp0) cc_final: 0.7420 (mp0) REVERT: A 57 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7061 (tm-30) REVERT: B 57 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7505 (tm-30) REVERT: B 83 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7895 (mt-10) REVERT: C 57 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7122 (tm-30) REVERT: D 24 GLN cc_start: 0.7022 (mp10) cc_final: 0.6523 (mp10) REVERT: H 46 GLU cc_start: 0.8414 (tt0) cc_final: 0.8000 (tm-30) REVERT: H 80 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8526 (mttm) outliers start: 22 outliers final: 22 residues processed: 93 average time/residue: 0.3316 time to fit residues: 38.6104 Evaluate side-chains 101 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 66 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.110778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098700 restraints weight = 7006.785| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.21 r_work: 0.3573 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5180 Z= 0.240 Angle : 0.467 5.480 6980 Z= 0.258 Chirality : 0.053 0.127 920 Planarity : 0.002 0.014 860 Dihedral : 4.503 16.762 740 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.23 % Allowed : 10.96 % Favored : 84.81 % 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 A 50 PHE 0.003 0.001 PHE J 94 TYR 0.010 0.002 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 99 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.573 Fit side-chains REVERT: A 57 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7011 (tm-30) REVERT: B 57 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7436 (tm-30) REVERT: C 57 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7010 (tm-30) REVERT: C 72 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8264 (m) REVERT: D 24 GLN cc_start: 0.7084 (mp10) cc_final: 0.6556 (mp10) REVERT: E 80 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8789 (mtpp) REVERT: F 24 GLN cc_start: 0.7194 (mp10) cc_final: 0.6907 (mp10) REVERT: H 46 GLU cc_start: 0.8377 (tt0) cc_final: 0.7947 (tm-30) REVERT: H 80 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8592 (mttm) outliers start: 22 outliers final: 21 residues processed: 89 average time/residue: 0.1848 time to fit residues: 20.6837 Evaluate side-chains 93 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 29 optimal weight: 0.0770 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 overall best weight: 3.5744 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.108052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.096002 restraints weight = 7193.802| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.21 r_work: 0.3490 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5180 Z= 0.326 Angle : 0.502 5.242 6980 Z= 0.279 Chirality : 0.053 0.131 920 Planarity : 0.002 0.012 860 Dihedral : 4.630 16.728 740 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.00 % Allowed : 10.77 % Favored : 84.23 % 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: -3.39 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 PHE 0.003 0.001 PHE J 94 TYR 0.011 0.003 TYR F 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 104 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.708 Fit side-chains REVERT: A 57 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7007 (tm-30) REVERT: B 57 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7508 (tm-30) REVERT: C 57 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7075 (tm-30) REVERT: D 24 GLN cc_start: 0.7125 (mp10) cc_final: 0.6604 (mp10) REVERT: D 35 GLU cc_start: 0.7772 (mp0) cc_final: 0.7091 (mp0) REVERT: E 80 LYS cc_start: 0.9046 (mtpt) cc_final: 0.8809 (mtpp) REVERT: F 24 GLN cc_start: 0.7301 (mp10) cc_final: 0.7032 (mp10) REVERT: H 46 GLU cc_start: 0.8424 (tt0) cc_final: 0.7999 (tm-30) REVERT: I 43 LYS cc_start: 0.7871 (tttp) cc_final: 0.7654 (tttt) outliers start: 26 outliers final: 26 residues processed: 94 average time/residue: 0.2921 time to fit residues: 34.0891 Evaluate side-chains 100 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 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 15 VAL 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 37 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 3 optimal weight: 0.0060 chunk 53 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 overall best weight: 4.8004 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.106267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.094262 restraints weight = 7233.177| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.18 r_work: 0.3467 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 5180 Z= 0.417 Angle : 0.550 5.191 6980 Z= 0.306 Chirality : 0.054 0.134 920 Planarity : 0.002 0.015 860 Dihedral : 4.829 16.634 740 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.81 % Allowed : 10.96 % Favored : 84.23 % 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: -3.48 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (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 F 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 100 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.554 Fit side-chains REVERT: A 35 GLU cc_start: 0.7908 (mp0) cc_final: 0.7491 (mp0) REVERT: A 57 GLU cc_start: 0.7774 (tm-30) cc_final: 0.6986 (tm-30) REVERT: B 57 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7479 (tm-30) REVERT: C 24 GLN cc_start: 0.7423 (mp10) cc_final: 0.7052 (mp10) REVERT: C 35 GLU cc_start: 0.7636 (mp0) cc_final: 0.6777 (mp0) REVERT: C 57 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7104 (tm-30) REVERT: D 24 GLN cc_start: 0.7246 (mp10) cc_final: 0.6663 (mp10) REVERT: E 35 GLU cc_start: 0.7940 (mp0) cc_final: 0.7649 (mp0) REVERT: E 80 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8835 (mtpp) REVERT: F 24 GLN cc_start: 0.7253 (mp10) cc_final: 0.7002 (mp10) REVERT: H 46 GLU cc_start: 0.8462 (tt0) cc_final: 0.8028 (tm-30) outliers start: 25 outliers final: 25 residues processed: 90 average time/residue: 0.1782 time to fit residues: 20.5021 Evaluate side-chains 100 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 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 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 15 VAL 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 17 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** 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 = 0.3744 r_free = 0.3744 target = 0.105784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.093749 restraints weight = 7342.216| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.17 r_work: 0.3480 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 5180 Z= 0.463 Angle : 0.581 5.138 6980 Z= 0.324 Chirality : 0.055 0.137 920 Planarity : 0.002 0.013 860 Dihedral : 4.962 16.438 740 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.42 % Allowed : 11.35 % Favored : 84.23 % 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: -3.60 (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 0.005 0.002 HIS A 50 PHE 0.004 0.001 PHE G 94 TYR 0.014 0.003 TYR F 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 110 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.189 Fit side-chains REVERT: A 35 GLU cc_start: 0.7938 (mp0) cc_final: 0.7646 (mp0) REVERT: A 57 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7043 (tm-30) REVERT: B 45 LYS cc_start: 0.8013 (tttm) cc_final: 0.7693 (tppt) REVERT: B 57 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7509 (tm-30) REVERT: C 24 GLN cc_start: 0.7530 (mp10) cc_final: 0.7203 (mp10) REVERT: C 57 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7205 (tm-30) REVERT: D 24 GLN cc_start: 0.7417 (mp10) cc_final: 0.6777 (mp10) REVERT: D 45 LYS cc_start: 0.7910 (tttm) cc_final: 0.7622 (tppt) REVERT: E 45 LYS cc_start: 0.8038 (tttm) cc_final: 0.7775 (tppt) REVERT: E 80 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8824 (mtpp) REVERT: F 24 GLN cc_start: 0.7385 (mp10) cc_final: 0.7147 (mp10) REVERT: H 46 GLU cc_start: 0.8499 (tt0) cc_final: 0.8068 (tm-30) REVERT: H 58 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7838 (mtpp) outliers start: 23 outliers final: 23 residues processed: 100 average time/residue: 0.2597 time to fit residues: 32.7398 Evaluate side-chains 107 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 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 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 71 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 46 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.0030 chunk 66 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.110535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.098410 restraints weight = 7137.511| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.26 r_work: 0.3545 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5180 Z= 0.227 Angle : 0.474 4.580 6980 Z= 0.263 Chirality : 0.053 0.129 920 Planarity : 0.002 0.018 860 Dihedral : 4.519 15.196 740 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.62 % Allowed : 11.35 % 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: -3.50 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (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 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 109 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.584 Fit side-chains REVERT: A 57 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7037 (tm-30) REVERT: B 57 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7382 (tm-30) REVERT: C 35 GLU cc_start: 0.7601 (mp0) cc_final: 0.6669 (mp0) REVERT: C 72 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8304 (m) REVERT: D 24 GLN cc_start: 0.7425 (mp10) cc_final: 0.6803 (mp10) REVERT: D 35 GLU cc_start: 0.7742 (mp0) cc_final: 0.7072 (mp0) REVERT: F 24 GLN cc_start: 0.7332 (mp10) cc_final: 0.7098 (mp10) REVERT: H 46 GLU cc_start: 0.8422 (tt0) cc_final: 0.7981 (tm-30) outliers start: 24 outliers final: 23 residues processed: 98 average time/residue: 0.2299 time to fit residues: 28.1365 Evaluate side-chains 104 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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 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 71 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 16 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.104751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.092463 restraints weight = 7375.020| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.19 r_work: 0.3472 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 5180 Z= 0.520 Angle : 0.618 5.154 6980 Z= 0.344 Chirality : 0.056 0.138 920 Planarity : 0.003 0.012 860 Dihedral : 5.024 16.760 740 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.23 % Allowed : 11.54 % Favored : 84.23 % 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: -3.65 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 50 PHE 0.005 0.001 PHE F 94 TYR 0.015 0.004 TYR J 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3210.97 seconds wall clock time: 59 minutes 27.56 seconds (3567.56 seconds total)