Starting phenix.real_space_refine on Tue Feb 11 09:38:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ads_15369/02_2025/8ads_15369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ads_15369/02_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_15369/02_2025/8ads_15369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ads_15369/02_2025/8ads_15369.map" model { file = "/net/cci-nas-00/data/ceres_data/8ads_15369/02_2025/8ads_15369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ads_15369/02_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-5592/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: 2.17, per 1000 atoms: 0.42 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: 1.29 Conformation dependent library (CDL) restraints added in 909.2 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: 0.95 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: 1.55 Time building geometry restraints manager: 1.49 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:5.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.180 ------------------------------------------------------------------------------- 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: 0.2474 time to fit residues: 25.8582 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 : 0.615 ------------------------------------------------------------------------------- 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: 0.7525 (mp0) cc_final: 0.7318 (mp0) REVERT: A 57 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7051 (tm-30) REVERT: B 57 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7425 (tm-30) REVERT: B 58 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8127 (mttm) REVERT: D 24 GLN cc_start: 0.6711 (mp10) cc_final: 0.6152 (mp10) REVERT: F 43 LYS cc_start: 0.7930 (tttp) cc_final: 0.7724 (ttmt) REVERT: H 46 GLU cc_start: 0.8373 (tt0) cc_final: 0.8005 (tm-30) REVERT: J 57 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7852 (tm-30) outliers start: 17 outliers final: 16 residues processed: 88 average time/residue: 0.2400 time to fit residues: 25.7776 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 : 0.555 ------------------------------------------------------------------------------- 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: 4.9990 chunk 43 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 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 = 0.093482 restraints weight = 7199.601| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.21 r_work: 0.3464 rms_B_bonded: 2.37 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 : 0.603 Fit side-chains REVERT: A 35 GLU cc_start: 0.7682 (mp0) cc_final: 0.7317 (mp0) REVERT: A 57 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: B 57 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 58 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8266 (mttm) REVERT: B 83 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7680 (mt-10) REVERT: C 57 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7084 (tm-30) REVERT: D 24 GLN cc_start: 0.6862 (mp10) cc_final: 0.6332 (mp10) REVERT: H 46 GLU cc_start: 0.8396 (tt0) cc_final: 0.7962 (tm-30) outliers start: 17 outliers final: 16 residues processed: 93 average time/residue: 0.2201 time to fit residues: 25.2073 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 : 0.577 ------------------------------------------------------------------------------- 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: 9.9990 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: 2.9990 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 = 0.113765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.101539 restraints weight = 7044.241| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.26 r_work: 0.3575 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 7.156 6980 Z= 0.245 Chirality : 0.053 0.126 920 Planarity : 0.002 0.010 860 Dihedral : 4.341 14.343 740 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.53 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 : 0.531 Fit side-chains REVERT: A 57 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7160 (tm-30) REVERT: B 57 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7528 (tm-30) REVERT: B 58 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8313 (mttm) REVERT: C 57 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7117 (tm-30) REVERT: C 72 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8298 (m) REVERT: D 24 GLN cc_start: 0.7013 (mp10) cc_final: 0.6479 (mp10) REVERT: D 35 GLU cc_start: 0.7578 (mp0) cc_final: 0.6947 (mp0) outliers start: 20 outliers final: 15 residues processed: 90 average time/residue: 0.2135 time to fit residues: 23.6587 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 : 0.541 ------------------------------------------------------------------------------- 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: 10.0000 chunk 7 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.105109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.093065 restraints weight = 7361.270| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.16 r_work: 0.3474 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.045 5180 Z= 0.568 Angle : 0.631 6.303 6980 Z= 0.350 Chirality : 0.057 0.146 920 Planarity : 0.003 0.015 860 Dihedral : 5.012 16.243 740 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.46 % Allowed : 11.35 % 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: -3.49 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 50 PHE 0.005 0.001 PHE J 94 TYR 0.016 0.004 TYR J 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 104 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.586 Fit side-chains REVERT: A 35 GLU cc_start: 0.7866 (mp0) cc_final: 0.7458 (mp0) REVERT: A 57 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7017 (tm-30) REVERT: B 57 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7544 (tm-30) REVERT: C 57 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7124 (tm-30) REVERT: D 24 GLN cc_start: 0.7052 (mp10) cc_final: 0.6555 (mp10) REVERT: H 46 GLU cc_start: 0.8448 (tt0) cc_final: 0.8010 (tm-30) REVERT: H 80 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8680 (mttt) outliers start: 18 outliers final: 17 residues processed: 95 average time/residue: 0.2039 time to fit residues: 24.2300 Evaluate side-chains 102 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.110774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.098727 restraints weight = 7051.563| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.22 r_work: 0.3534 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5180 Z= 0.237 Angle : 0.468 5.678 6980 Z= 0.258 Chirality : 0.053 0.130 920 Planarity : 0.002 0.013 860 Dihedral : 4.518 16.797 740 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.42 % Allowed : 11.15 % 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: -3.43 (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 0.003 0.001 HIS G 50 PHE 0.003 0.001 PHE J 94 TYR 0.009 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 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 102 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.545 Fit side-chains REVERT: A 57 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7048 (tm-30) REVERT: B 57 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7532 (tm-30) REVERT: C 57 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7066 (tm-30) REVERT: C 72 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8289 (m) REVERT: D 24 GLN cc_start: 0.7124 (mp10) cc_final: 0.6599 (mp10) REVERT: D 35 GLU cc_start: 0.7699 (mp0) cc_final: 0.7060 (mp0) REVERT: F 24 GLN cc_start: 0.7290 (mp10) cc_final: 0.7027 (mp10) REVERT: H 46 GLU cc_start: 0.8408 (tt0) cc_final: 0.7959 (tm-30) REVERT: H 58 LYS cc_start: 0.8021 (mtpp) cc_final: 0.7814 (mtpp) outliers start: 23 outliers final: 22 residues processed: 92 average time/residue: 0.2034 time to fit residues: 23.3290 Evaluate side-chains 95 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 29 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 overall best weight: 7.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.103587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.091530 restraints weight = 7449.968| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.19 r_work: 0.3457 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.048 5180 Z= 0.602 Angle : 0.651 5.738 6980 Z= 0.363 Chirality : 0.058 0.152 920 Planarity : 0.003 0.014 860 Dihedral : 5.145 17.804 740 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.85 % Allowed : 12.31 % Favored : 83.85 % 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: -3.59 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 50 PHE 0.006 0.001 PHE J 94 TYR 0.016 0.004 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 110 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.485 Fit side-chains REVERT: A 35 GLU cc_start: 0.7991 (mp0) cc_final: 0.7697 (mp0) REVERT: A 57 GLU cc_start: 0.7816 (tm-30) cc_final: 0.6978 (tm-30) REVERT: B 45 LYS cc_start: 0.7952 (tttm) cc_final: 0.7572 (tppt) REVERT: B 57 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 57 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7075 (tm-30) REVERT: D 24 GLN cc_start: 0.7204 (mp10) cc_final: 0.6640 (mp10) REVERT: D 45 LYS cc_start: 0.7813 (tttm) cc_final: 0.7528 (tppt) REVERT: E 45 LYS cc_start: 0.7986 (tttm) cc_final: 0.7673 (tppt) REVERT: H 46 GLU cc_start: 0.8524 (tt0) cc_final: 0.7988 (tm-30) REVERT: J 46 GLU cc_start: 0.8469 (tt0) cc_final: 0.8264 (tm-30) outliers start: 20 outliers final: 20 residues processed: 101 average time/residue: 0.2334 time to fit residues: 29.3941 Evaluate side-chains 109 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.109518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.097579 restraints weight = 7110.803| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.21 r_work: 0.3521 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5180 Z= 0.253 Angle : 0.489 5.092 6980 Z= 0.270 Chirality : 0.053 0.132 920 Planarity : 0.002 0.016 860 Dihedral : 4.631 17.894 740 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 4.04 % Allowed : 12.31 % 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: -3.52 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS J 50 PHE 0.003 0.001 PHE J 94 TYR 0.009 0.002 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 103 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.532 Fit side-chains REVERT: A 57 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7023 (tm-30) REVERT: B 57 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7519 (tm-30) REVERT: C 35 GLU cc_start: 0.7621 (mp0) cc_final: 0.6689 (mp0) REVERT: C 57 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7023 (tm-30) REVERT: C 72 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8296 (m) REVERT: D 24 GLN cc_start: 0.7299 (mp10) cc_final: 0.6762 (mp10) REVERT: D 35 GLU cc_start: 0.7759 (mp0) cc_final: 0.7078 (mp0) REVERT: E 24 GLN cc_start: 0.7890 (mp10) cc_final: 0.7489 (mp10) REVERT: F 24 GLN cc_start: 0.7339 (mp10) cc_final: 0.7105 (mp10) REVERT: H 46 GLU cc_start: 0.8460 (tt0) cc_final: 0.7987 (tm-30) REVERT: H 57 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7903 (tm-30) outliers start: 21 outliers final: 20 residues processed: 93 average time/residue: 0.2026 time to fit residues: 23.7179 Evaluate side-chains 98 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.0470 chunk 46 optimal weight: 8.9990 overall best weight: 5.2086 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.105731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.093676 restraints weight = 7334.727| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.18 r_work: 0.3492 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 5180 Z= 0.450 Angle : 0.580 5.443 6980 Z= 0.322 Chirality : 0.055 0.136 920 Planarity : 0.002 0.012 860 Dihedral : 4.934 17.892 740 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.42 % Allowed : 12.31 % 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: -3.60 (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 0.004 0.002 HIS J 50 PHE 0.004 0.001 PHE G 94 TYR 0.013 0.003 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 104 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.531 Fit side-chains REVERT: A 35 GLU cc_start: 0.7969 (mp0) cc_final: 0.7657 (mp0) REVERT: A 57 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: B 57 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7476 (tm-30) REVERT: C 24 GLN cc_start: 0.7426 (mp10) cc_final: 0.7060 (mp10) REVERT: C 57 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7094 (tm-30) REVERT: D 24 GLN cc_start: 0.7265 (mp10) cc_final: 0.6716 (mp10) REVERT: E 24 GLN cc_start: 0.7892 (mp10) cc_final: 0.7482 (mp10) REVERT: F 24 GLN cc_start: 0.7391 (mp10) cc_final: 0.7146 (mp10) REVERT: H 46 GLU cc_start: 0.8498 (tt0) cc_final: 0.8020 (tm-30) REVERT: J 46 GLU cc_start: 0.8464 (tt0) cc_final: 0.8238 (tm-30) outliers start: 23 outliers final: 22 residues processed: 93 average time/residue: 0.1906 time to fit residues: 22.4209 Evaluate side-chains 103 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.109164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.097117 restraints weight = 7216.185| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.23 r_work: 0.3513 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5180 Z= 0.263 Angle : 0.491 5.141 6980 Z= 0.272 Chirality : 0.053 0.131 920 Planarity : 0.002 0.018 860 Dihedral : 4.635 16.848 740 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.23 % Allowed : 12.88 % Favored : 82.88 % 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: -3.52 (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 J 50 PHE 0.004 0.001 PHE J 94 TYR 0.010 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 102 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.528 Fit side-chains REVERT: A 57 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7002 (tm-30) REVERT: B 57 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7494 (tm-30) REVERT: C 35 GLU cc_start: 0.7645 (mp0) cc_final: 0.6649 (mp0) REVERT: C 57 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7067 (tm-30) REVERT: C 72 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8291 (m) REVERT: D 24 GLN cc_start: 0.7288 (mp10) cc_final: 0.6736 (mp10) REVERT: D 35 GLU cc_start: 0.7715 (mp0) cc_final: 0.6905 (mp0) REVERT: E 24 GLN cc_start: 0.7969 (mp10) cc_final: 0.7519 (mp10) REVERT: E 35 GLU cc_start: 0.7840 (mp0) cc_final: 0.7594 (mp0) REVERT: E 80 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8675 (tttt) REVERT: F 24 GLN cc_start: 0.7380 (mp10) cc_final: 0.7149 (mp10) REVERT: H 46 GLU cc_start: 0.8453 (tt0) cc_final: 0.7960 (tm-30) REVERT: H 57 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7901 (tm-30) outliers start: 22 outliers final: 20 residues processed: 91 average time/residue: 0.1893 time to fit residues: 21.9089 Evaluate side-chains 101 residues out of total 520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.104625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.092420 restraints weight = 7417.782| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.20 r_work: 0.3477 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 5180 Z= 0.520 Angle : 0.617 5.413 6980 Z= 0.343 Chirality : 0.056 0.138 920 Planarity : 0.003 0.013 860 Dihedral : 5.066 17.487 740 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.04 % Allowed : 12.88 % 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 0.005 0.002 HIS J 50 PHE 0.004 0.001 PHE F 94 TYR 0.015 0.004 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2496.42 seconds wall clock time: 45 minutes 29.73 seconds (2729.73 seconds total)