Starting phenix.real_space_refine on Sun Mar 10 21:22:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ads_15369/03_2024/8ads_15369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ads_15369/03_2024/8ads_15369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ads_15369/03_2024/8ads_15369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ads_15369/03_2024/8ads_15369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ads_15369/03_2024/8ads_15369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ads_15369/03_2024/8ads_15369.pdb" } 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 Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5170 Number of models: 1 Model: "" Number of chains: 10 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Chain: "F" 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 Chain: "G" 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 Chain: "H" 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 Chain: "I" 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 Chain: "J" 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 Time building chain proxies: 3.02, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 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: 1.87 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.71 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: 1.41 Time building geometry restraints manager: 2.01 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: 106.12 - 111.14: 2299 111.14 - 116.17: 1401 116.17 - 121.19: 1667 121.19 - 126.21: 1603 126.21 - 131.23: 10 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 2.520 nonbonded pdb=" NZ LYS D 80 " pdb=" OE2 GLU E 83 " model vdw 2.218 2.520 nonbonded pdb=" NZ LYS I 80 " pdb=" OE2 GLU J 83 " model vdw 2.218 2.520 nonbonded pdb=" NZ LYS B 80 " pdb=" OE2 GLU C 83 " model vdw 2.218 2.520 nonbonded pdb=" NZ LYS G 80 " pdb=" OE2 GLU H 83 " model vdw 2.218 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 3.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.180 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.559 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: 0.2361 time to fit residues: 24.6774 Evaluate side-chains 63 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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: 0.9990 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 0.0060 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 0.0020 overall best weight: 3.0010 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5180 Z= 0.279 Angle : 0.481 7.058 6980 Z= 0.266 Chirality : 0.052 0.124 920 Planarity : 0.002 0.008 860 Dihedral : 4.406 12.720 740 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.27 % Allowed : 6.35 % Favored : 90.38 % 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: -3.06 (0.27), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 50 PHE 0.004 0.001 PHE J 94 TYR 0.013 0.003 TYR I 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 90 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.553 Fit side-chains REVERT: A 57 GLU cc_start: 0.7576 (tm-30) cc_final: 0.6830 (tm-30) REVERT: B 58 LYS cc_start: 0.8505 (mtpp) cc_final: 0.8105 (mtpt) REVERT: C 35 GLU cc_start: 0.6337 (mp0) cc_final: 0.5842 (mp0) REVERT: D 24 GLN cc_start: 0.6857 (mp10) cc_final: 0.6314 (mp10) REVERT: E 35 GLU cc_start: 0.6808 (mp0) cc_final: 0.6471 (mp0) outliers start: 17 outliers final: 15 residues processed: 80 average time/residue: 0.2207 time to fit residues: 21.8955 Evaluate side-chains 78 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 7.9188 ------------------------------------------------------------------------------- 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 50 HIS ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.051 5180 Z= 0.649 Angle : 0.679 6.137 6980 Z= 0.380 Chirality : 0.059 0.171 920 Planarity : 0.003 0.019 860 Dihedral : 5.113 13.275 740 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.08 % Allowed : 8.27 % Favored : 88.65 % 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: -3.37 (0.25), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS E 50 PHE 0.007 0.002 PHE J 94 TYR 0.019 0.004 TYR F 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 109 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.664 Fit side-chains REVERT: A 35 GLU cc_start: 0.7095 (mp0) cc_final: 0.6704 (mp0) REVERT: A 57 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.6723 (tm-30) REVERT: A 83 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7783 (mm-30) REVERT: B 58 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8189 (mtpt) REVERT: B 83 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6817 (mt-10) REVERT: C 35 GLU cc_start: 0.6795 (mp0) cc_final: 0.6263 (mp0) REVERT: D 24 GLN cc_start: 0.7005 (mp10) cc_final: 0.6571 (mp10) outliers start: 16 outliers final: 15 residues processed: 100 average time/residue: 0.2211 time to fit residues: 27.3740 Evaluate side-chains 95 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 5180 Z= 0.396 Angle : 0.546 5.193 6980 Z= 0.303 Chirality : 0.054 0.134 920 Planarity : 0.002 0.015 860 Dihedral : 4.749 14.372 740 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.27 % Allowed : 9.81 % Favored : 86.92 % 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 (0.24), 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 0.005 0.002 HIS A 50 PHE 0.004 0.001 PHE J 94 TYR 0.014 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 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 104 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.571 Fit side-chains REVERT: A 35 GLU cc_start: 0.7106 (mp0) cc_final: 0.6646 (mp0) REVERT: A 57 GLU cc_start: 0.7610 (tm-30) cc_final: 0.6812 (tm-30) REVERT: B 58 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8287 (mtpt) REVERT: C 35 GLU cc_start: 0.6856 (mp0) cc_final: 0.6420 (mp0) REVERT: C 57 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6977 (tm-30) REVERT: D 24 GLN cc_start: 0.7174 (mp10) cc_final: 0.6752 (mp10) REVERT: J 58 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7977 (mtpp) REVERT: J 80 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8759 (mtpt) outliers start: 17 outliers final: 17 residues processed: 94 average time/residue: 0.2193 time to fit residues: 25.3361 Evaluate side-chains 100 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL 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 33 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 I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 5180 Z= 0.473 Angle : 0.588 5.167 6980 Z= 0.327 Chirality : 0.055 0.137 920 Planarity : 0.003 0.016 860 Dihedral : 4.904 14.970 740 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.62 % Allowed : 9.81 % Favored : 85.58 % 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: -3.50 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 50 PHE 0.004 0.001 PHE J 94 TYR 0.015 0.003 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 115 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.569 Fit side-chains REVERT: A 35 GLU cc_start: 0.7134 (mp0) cc_final: 0.6751 (mp0) REVERT: B 35 GLU cc_start: 0.7055 (mp0) cc_final: 0.6513 (mp0) REVERT: C 35 GLU cc_start: 0.6963 (mp0) cc_final: 0.6214 (mp0) REVERT: C 57 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6960 (tm-30) REVERT: D 24 GLN cc_start: 0.7328 (mp10) cc_final: 0.6944 (mp10) REVERT: E 35 GLU cc_start: 0.7417 (mp0) cc_final: 0.6553 (mp0) REVERT: J 58 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7937 (mtpp) REVERT: J 80 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8775 (mtpt) outliers start: 24 outliers final: 23 residues processed: 104 average time/residue: 0.2152 time to fit residues: 27.8418 Evaluate side-chains 110 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 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 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 33 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 33 THR 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 33 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 ** 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** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5180 Z= 0.335 Angle : 0.523 4.705 6980 Z= 0.289 Chirality : 0.053 0.133 920 Planarity : 0.002 0.013 860 Dihedral : 4.657 15.347 740 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.00 % Allowed : 9.23 % Favored : 85.77 % 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 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 50 PHE 0.004 0.001 PHE J 94 TYR 0.012 0.003 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 35 GLU cc_start: 0.7148 (mp0) cc_final: 0.6744 (mp0) REVERT: B 35 GLU cc_start: 0.6986 (mp0) cc_final: 0.6404 (mp0) REVERT: C 35 GLU cc_start: 0.6946 (mp0) cc_final: 0.6083 (mp0) REVERT: C 57 GLU cc_start: 0.7433 (tm-30) cc_final: 0.6932 (tm-30) REVERT: D 24 GLN cc_start: 0.7355 (mp10) cc_final: 0.6952 (mp10) REVERT: D 35 GLU cc_start: 0.6888 (mp0) cc_final: 0.6278 (mp0) REVERT: E 35 GLU cc_start: 0.7369 (mp0) cc_final: 0.6467 (mp0) REVERT: J 58 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7989 (mtpp) REVERT: J 87 SER cc_start: 0.8480 (m) cc_final: 0.8063 (p) outliers start: 26 outliers final: 25 residues processed: 107 average time/residue: 0.1934 time to fit residues: 25.9671 Evaluate side-chains 112 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 87 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 33 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 33 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 20.0000 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5180 Z= 0.252 Angle : 0.486 4.408 6980 Z= 0.269 Chirality : 0.052 0.128 920 Planarity : 0.002 0.014 860 Dihedral : 4.470 17.126 740 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 5.00 % Allowed : 9.42 % Favored : 85.58 % 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: -3.37 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.004 0.001 PHE J 94 TYR 0.010 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 0.625 Fit side-chains REVERT: A 80 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8393 (mtpp) REVERT: B 35 GLU cc_start: 0.6929 (mp0) cc_final: 0.6315 (mp0) REVERT: C 35 GLU cc_start: 0.6887 (mp0) cc_final: 0.6104 (mp0) REVERT: C 57 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6876 (tm-30) REVERT: C 72 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8181 (m) REVERT: D 24 GLN cc_start: 0.7410 (mp10) cc_final: 0.7010 (mp10) REVERT: D 35 GLU cc_start: 0.6831 (mp0) cc_final: 0.6125 (mp0) REVERT: E 35 GLU cc_start: 0.7331 (mp0) cc_final: 0.6462 (mp0) REVERT: E 80 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8520 (mtpp) REVERT: H 80 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8035 (mttm) REVERT: H 83 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7403 (mm-30) REVERT: J 58 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7981 (mtpp) REVERT: J 87 SER cc_start: 0.8426 (m) cc_final: 0.8073 (p) outliers start: 26 outliers final: 24 residues processed: 105 average time/residue: 0.2738 time to fit residues: 36.4049 Evaluate side-chains 107 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 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 33 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 15 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 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** ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.054 5180 Z= 0.607 Angle : 0.671 5.394 6980 Z= 0.376 Chirality : 0.058 0.155 920 Planarity : 0.003 0.018 860 Dihedral : 5.129 16.029 740 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.42 % Allowed : 10.19 % 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: -3.60 (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 0.007 0.002 HIS A 50 PHE 0.007 0.001 PHE F 94 TYR 0.017 0.004 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 94 time to evaluate : 0.576 Fit side-chains REVERT: A 57 GLU cc_start: 0.7656 (tm-30) cc_final: 0.6674 (tm-30) REVERT: B 35 GLU cc_start: 0.7078 (mp0) cc_final: 0.6608 (mp0) REVERT: C 57 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6945 (tm-30) REVERT: D 24 GLN cc_start: 0.7499 (mp10) cc_final: 0.7065 (mp10) REVERT: D 35 GLU cc_start: 0.6894 (mp0) cc_final: 0.6477 (mp0) REVERT: H 35 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6536 (mt-10) REVERT: J 58 LYS cc_start: 0.8270 (mtpp) cc_final: 0.8063 (mtpp) outliers start: 23 outliers final: 22 residues processed: 108 average time/residue: 0.2180 time to fit residues: 29.0788 Evaluate side-chains 113 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 33 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 33 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 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5180 Z= 0.282 Angle : 0.525 4.182 6980 Z= 0.291 Chirality : 0.053 0.133 920 Planarity : 0.002 0.018 860 Dihedral : 4.635 17.640 740 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 5.19 % Allowed : 9.81 % Favored : 85.00 % 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: -3.55 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.004 0.001 PHE J 94 TYR 0.010 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 0.541 Fit side-chains REVERT: A 35 GLU cc_start: 0.7439 (mp0) cc_final: 0.7208 (mp0) REVERT: A 80 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8460 (mtpp) REVERT: B 35 GLU cc_start: 0.7065 (mp0) cc_final: 0.6578 (mp0) REVERT: C 24 GLN cc_start: 0.7581 (mp10) cc_final: 0.7320 (mp10) REVERT: C 57 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6900 (tm-30) REVERT: C 72 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8130 (m) REVERT: D 24 GLN cc_start: 0.7548 (mp10) cc_final: 0.7152 (mp10) REVERT: D 35 GLU cc_start: 0.6819 (mp0) cc_final: 0.6073 (mp0) REVERT: E 35 GLU cc_start: 0.7352 (mp0) cc_final: 0.6388 (mp0) REVERT: E 80 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8727 (mtpp) REVERT: H 35 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6429 (mt-10) REVERT: H 80 LYS cc_start: 0.8805 (mttt) cc_final: 0.8564 (mttm) REVERT: J 87 SER cc_start: 0.8360 (m) cc_final: 0.8047 (p) outliers start: 27 outliers final: 22 residues processed: 104 average time/residue: 0.2114 time to fit residues: 28.1909 Evaluate side-chains 110 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 33 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 33 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 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 34 optimal weight: 0.0770 chunk 44 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 overall best weight: 4.4146 ------------------------------------------------------------------------------- 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 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 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 5180 Z= 0.392 Angle : 0.579 5.132 6980 Z= 0.321 Chirality : 0.054 0.134 920 Planarity : 0.002 0.019 860 Dihedral : 4.817 17.438 740 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.42 % Allowed : 10.77 % 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: -3.57 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 50 PHE 0.005 0.001 PHE G 94 TYR 0.013 0.003 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 111 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.583 Fit side-chains REVERT: A 35 GLU cc_start: 0.7492 (mp0) cc_final: 0.7260 (mp0) REVERT: A 80 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8418 (mtpp) REVERT: B 35 GLU cc_start: 0.7078 (mp0) cc_final: 0.6621 (mp0) REVERT: C 24 GLN cc_start: 0.7548 (mp10) cc_final: 0.7298 (mp10) REVERT: C 57 GLU cc_start: 0.7435 (tm-30) cc_final: 0.6909 (tm-30) REVERT: D 24 GLN cc_start: 0.7574 (mp10) cc_final: 0.7173 (mp10) REVERT: D 35 GLU cc_start: 0.6809 (mp0) cc_final: 0.6052 (mp0) REVERT: E 35 GLU cc_start: 0.7370 (mp0) cc_final: 0.6380 (mp0) REVERT: E 80 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8724 (mtpp) REVERT: H 35 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6478 (mt-10) REVERT: H 80 LYS cc_start: 0.8821 (mttt) cc_final: 0.8198 (mttm) REVERT: J 87 SER cc_start: 0.8395 (m) cc_final: 0.8039 (p) outliers start: 23 outliers final: 22 residues processed: 101 average time/residue: 0.1940 time to fit residues: 24.6593 Evaluate side-chains 110 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 33 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 33 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 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 = 0.3799 r_free = 0.3799 target = 0.107290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.094907 restraints weight = 7225.406| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.20 r_work: 0.3493 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5180 Z= 0.356 Angle : 0.558 4.588 6980 Z= 0.310 Chirality : 0.054 0.134 920 Planarity : 0.002 0.019 860 Dihedral : 4.737 17.276 740 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.62 % Allowed : 10.58 % 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: -3.55 (0.24), residues: 710 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.18), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.004 0.001 PHE G 94 TYR 0.012 0.003 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1348.73 seconds wall clock time: 25 minutes 33.69 seconds (1533.69 seconds total)