Starting phenix.real_space_refine on Sun Mar 10 19:19:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/03_2024/8pkf_17737.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/03_2024/8pkf_17737.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3673 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/03_2024/8pkf_17737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/03_2024/8pkf_17737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/03_2024/8pkf_17737.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/03_2024/8pkf_17737.pdb" } resolution = 2.3673 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2790 2.51 5 N 708 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 63": "OE1" <-> "OE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 63": "OE1" <-> "OE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 63": "OE1" <-> "OE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 34": "NH1" <-> "NH2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 104": "NH1" <-> "NH2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 116": "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: 4308 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 2.64, per 1000 atoms: 0.61 Number of scatterers: 4308 At special positions: 0 Unit cell: (69.116, 86.862, 46.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 804 8.00 N 708 7.00 C 2790 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: 1.68 Conformation dependent library (CDL) restraints added in 781.0 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.478A pdb=" N LEU A 12 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS B 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 12 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LYS C 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 12 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LYS D 15 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL C 14 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 12 " --> pdb=" O MET E 13 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS E 15 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 12 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS F 15 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL E 14 " --> pdb=" O LYS F 15 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 34 removed outlier: 6.480A pdb=" N VAL A 30 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE B 33 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 32 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL B 30 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE C 33 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 32 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 30 " --> pdb=" O HIS D 31 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE D 33 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 32 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D 30 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE E 33 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL D 32 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL E 30 " --> pdb=" O HIS F 31 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE F 33 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 32 " --> pdb=" O PHE F 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.391A pdb=" N THR A 59 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N GLU B 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU A 61 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR B 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLU C 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU B 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR C 59 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLU D 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU C 61 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR D 59 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLU E 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU D 61 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR E 59 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLU F 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU E 61 " --> pdb=" O GLU F 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 80 removed outlier: 6.280A pdb=" N GLU A 72 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR B 75 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ASP A 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N SER B 77 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N LYS A 76 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N TRP B 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A 78 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU B 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR C 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASP B 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N SER C 77 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N LYS B 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N TRP C 79 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR B 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C 72 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR D 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP C 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N SER D 77 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N LYS C 76 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N TRP D 79 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR C 78 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU D 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR E 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP D 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N SER E 77 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N LYS D 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N TRP E 79 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR D 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU E 72 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR F 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP E 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N SER F 77 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N LYS E 76 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 9.644A pdb=" N TRP F 79 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR E 78 " --> pdb=" O TRP F 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 92 through 99 Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 107 removed outlier: 6.345A pdb=" N ARG A 104 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE B 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR A 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG B 104 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE C 107 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR B 106 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG C 104 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE D 107 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR C 106 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG D 104 " --> pdb=" O TYR E 105 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE E 107 " --> pdb=" O ARG D 104 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR D 106 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG E 104 " --> pdb=" O TYR F 105 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE F 107 " --> pdb=" O ARG E 104 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR E 106 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 114 through 115 removed outlier: 7.033A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR B 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR C 114 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N TYR D 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR E 114 " --> pdb=" O SER F 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 118 through 122 70 hydrogen bonds defined for protein. 210 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: 1.18 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 708 1.32 - 1.44: 1194 1.44 - 1.56: 2496 1.56 - 1.68: 0 1.68 - 1.81: 12 Bond restraints: 4410 Sorted by residual: bond pdb=" N SER A 85 " pdb=" CA SER A 85 " ideal model delta sigma weight residual 1.457 1.491 -0.035 9.10e-03 1.21e+04 1.47e+01 bond pdb=" N SER B 85 " pdb=" CA SER B 85 " ideal model delta sigma weight residual 1.457 1.491 -0.035 9.10e-03 1.21e+04 1.46e+01 bond pdb=" N SER E 85 " pdb=" CA SER E 85 " ideal model delta sigma weight residual 1.457 1.491 -0.034 9.10e-03 1.21e+04 1.39e+01 bond pdb=" N SER D 85 " pdb=" CA SER D 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.38e+01 bond pdb=" N SER F 85 " pdb=" CA SER F 85 " ideal model delta sigma weight residual 1.457 1.490 -0.034 9.10e-03 1.21e+04 1.38e+01 ... (remaining 4405 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.20: 259 107.20 - 113.95: 2373 113.95 - 120.70: 2076 120.70 - 127.45: 1244 127.45 - 134.20: 48 Bond angle restraints: 6000 Sorted by residual: angle pdb=" C THR B 106 " pdb=" N ILE B 107 " pdb=" CA ILE B 107 " ideal model delta sigma weight residual 123.19 115.57 7.62 1.24e+00 6.50e-01 3.78e+01 angle pdb=" C THR F 106 " pdb=" N ILE F 107 " pdb=" CA ILE F 107 " ideal model delta sigma weight residual 123.19 115.57 7.62 1.24e+00 6.50e-01 3.77e+01 angle pdb=" C THR D 106 " pdb=" N ILE D 107 " pdb=" CA ILE D 107 " ideal model delta sigma weight residual 123.19 115.59 7.60 1.24e+00 6.50e-01 3.76e+01 angle pdb=" C THR E 106 " pdb=" N ILE E 107 " pdb=" CA ILE E 107 " ideal model delta sigma weight residual 123.19 115.60 7.59 1.24e+00 6.50e-01 3.74e+01 angle pdb=" C THR A 106 " pdb=" N ILE A 107 " pdb=" CA ILE A 107 " ideal model delta sigma weight residual 123.19 115.64 7.55 1.24e+00 6.50e-01 3.71e+01 ... (remaining 5995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.55: 2238 9.55 - 19.10: 203 19.10 - 28.65: 97 28.65 - 38.21: 36 38.21 - 47.76: 24 Dihedral angle restraints: 2598 sinusoidal: 984 harmonic: 1614 Sorted by residual: dihedral pdb=" N ALA A 25 " pdb=" C ALA A 25 " pdb=" CA ALA A 25 " pdb=" CB ALA A 25 " ideal model delta harmonic sigma weight residual 122.90 115.19 7.71 0 2.50e+00 1.60e-01 9.50e+00 dihedral pdb=" N ALA C 25 " pdb=" C ALA C 25 " pdb=" CA ALA C 25 " pdb=" CB ALA C 25 " ideal model delta harmonic sigma weight residual 122.90 115.20 7.70 0 2.50e+00 1.60e-01 9.48e+00 dihedral pdb=" N ALA E 25 " pdb=" C ALA E 25 " pdb=" CA ALA E 25 " pdb=" CB ALA E 25 " ideal model delta harmonic sigma weight residual 122.90 115.22 7.68 0 2.50e+00 1.60e-01 9.44e+00 ... (remaining 2595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 268 0.069 - 0.138: 288 0.138 - 0.208: 98 0.208 - 0.277: 48 0.277 - 0.346: 6 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA ASN C 27 " pdb=" N ASN C 27 " pdb=" C ASN C 27 " pdb=" CB ASN C 27 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ASN E 27 " pdb=" N ASN E 27 " pdb=" C ASN E 27 " pdb=" CB ASN E 27 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA ASN B 27 " pdb=" N ASN B 27 " pdb=" C ASN B 27 " pdb=" CB ASN B 27 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 705 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 98 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C ASN B 98 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN B 98 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP B 99 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 98 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C ASN F 98 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN F 98 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP F 99 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 98 " -0.017 2.00e-02 2.50e+03 3.56e-02 1.26e+01 pdb=" C ASN C 98 " 0.061 2.00e-02 2.50e+03 pdb=" O ASN C 98 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP C 99 " -0.021 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 1487 2.86 - 3.37: 3574 3.37 - 3.88: 7650 3.88 - 4.39: 8655 4.39 - 4.90: 16497 Nonbonded interactions: 37863 Sorted by model distance: nonbonded pdb=" O ALA D 109 " pdb=" OG SER E 112 " model vdw 2.355 2.440 nonbonded pdb=" O ALA C 109 " pdb=" OG SER D 112 " model vdw 2.356 2.440 nonbonded pdb=" O ALA E 109 " pdb=" OG SER F 112 " model vdw 2.356 2.440 nonbonded pdb=" O ALA A 109 " pdb=" OG SER B 112 " model vdw 2.356 2.440 nonbonded pdb=" O ALA B 109 " pdb=" OG SER C 112 " model vdw 2.356 2.440 ... (remaining 37858 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' } 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: 0.800 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: 3.530 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.040 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 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 : 0.013 0.042 4410 Z= 0.849 Angle : 1.726 7.623 6000 Z= 1.275 Chirality : 0.117 0.346 708 Planarity : 0.008 0.052 738 Dihedral : 11.302 47.757 1554 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 0.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % 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: -2.77 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS D 31 PHE 0.012 0.003 PHE B 95 TYR 0.014 0.003 TYR B 114 ARG 0.001 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.568 Fit side-chains REVERT: A 62 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 66 GLU cc_start: 0.7230 (tt0) cc_final: 0.6943 (tt0) REVERT: A 80 LYS cc_start: 0.7325 (tttt) cc_final: 0.6926 (ttpt) REVERT: A 104 ARG cc_start: 0.7339 (mtt180) cc_final: 0.6702 (mtm-85) REVERT: B 13 MET cc_start: 0.7373 (ttm) cc_final: 0.6492 (mtp) REVERT: B 15 LYS cc_start: 0.6999 (mtpt) cc_final: 0.6647 (mtpt) REVERT: B 34 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.7200 (ttt180) REVERT: B 104 ARG cc_start: 0.6828 (mtt180) cc_final: 0.6226 (mtp180) REVERT: C 13 MET cc_start: 0.7289 (ttm) cc_final: 0.6985 (ttm) REVERT: C 15 LYS cc_start: 0.7078 (mtpt) cc_final: 0.6705 (mtpt) REVERT: C 62 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6918 (mt-10) REVERT: C 66 GLU cc_start: 0.7328 (tt0) cc_final: 0.6585 (tm-30) REVERT: C 80 LYS cc_start: 0.7283 (tttt) cc_final: 0.6814 (ttmt) REVERT: C 89 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6828 (mt-10) REVERT: C 104 ARG cc_start: 0.7051 (mtt180) cc_final: 0.6245 (mtp180) REVERT: C 123 THR cc_start: 0.6169 (m) cc_final: 0.5878 (p) REVERT: D 13 MET cc_start: 0.7190 (ttm) cc_final: 0.6795 (ttm) REVERT: D 15 LYS cc_start: 0.7082 (mtpt) cc_final: 0.6710 (mtpt) REVERT: D 59 THR cc_start: 0.7247 (m) cc_final: 0.6981 (p) REVERT: D 62 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7281 (mt-10) REVERT: D 66 GLU cc_start: 0.7243 (tt0) cc_final: 0.6857 (tt0) REVERT: D 80 LYS cc_start: 0.7394 (tttt) cc_final: 0.6781 (tttm) REVERT: D 89 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7157 (mt-10) REVERT: D 104 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6296 (mtm-85) REVERT: E 13 MET cc_start: 0.7352 (ttm) cc_final: 0.6871 (ttm) REVERT: E 15 LYS cc_start: 0.7254 (mtpt) cc_final: 0.6946 (mtpp) REVERT: E 21 ARG cc_start: 0.6974 (ttt180) cc_final: 0.6701 (ttm-80) REVERT: E 34 ARG cc_start: 0.7071 (ttt-90) cc_final: 0.6855 (tpt-90) REVERT: E 35 LYS cc_start: 0.7262 (tttt) cc_final: 0.6924 (tttm) REVERT: E 62 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7077 (mt-10) REVERT: E 80 LYS cc_start: 0.7433 (tttt) cc_final: 0.7088 (ttpp) REVERT: E 92 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7543 (mt-10) REVERT: E 104 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6361 (mtp180) REVERT: F 13 MET cc_start: 0.7362 (ttm) cc_final: 0.6373 (mtm) REVERT: F 26 ILE cc_start: 0.8510 (mt) cc_final: 0.8273 (mp) REVERT: F 62 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6803 (mt-10) REVERT: F 70 LYS cc_start: 0.7822 (tttt) cc_final: 0.7620 (tttm) REVERT: F 80 LYS cc_start: 0.7870 (tttt) cc_final: 0.7614 (ttpp) REVERT: F 89 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7319 (tt0) REVERT: F 104 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7262 (ttp-110) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 1.4156 time to fit residues: 208.1066 Evaluate side-chains 106 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS B 98 ASN C 98 ASN D 98 ASN E 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4410 Z= 0.183 Angle : 0.569 5.223 6000 Z= 0.320 Chirality : 0.048 0.127 708 Planarity : 0.005 0.042 738 Dihedral : 5.049 14.488 594 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.28 % Allowed : 14.96 % Favored : 83.76 % 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: -2.17 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 79 HIS 0.009 0.001 HIS D 31 PHE 0.016 0.003 PHE D 64 TYR 0.011 0.001 TYR D 114 ARG 0.002 0.000 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 0.551 Fit side-chains REVERT: A 21 ARG cc_start: 0.7701 (ttt90) cc_final: 0.7208 (ttt90) REVERT: A 66 GLU cc_start: 0.7299 (tt0) cc_final: 0.6944 (tt0) REVERT: A 70 LYS cc_start: 0.8000 (tttt) cc_final: 0.7576 (tttp) REVERT: A 80 LYS cc_start: 0.7365 (tttt) cc_final: 0.6833 (ttpt) REVERT: A 104 ARG cc_start: 0.7325 (mtt180) cc_final: 0.6735 (mtm-85) REVERT: B 13 MET cc_start: 0.7487 (ttm) cc_final: 0.7248 (ttm) REVERT: B 15 LYS cc_start: 0.7051 (mtpt) cc_final: 0.6645 (mtpt) REVERT: B 70 LYS cc_start: 0.8040 (tttt) cc_final: 0.7627 (tttp) REVERT: B 104 ARG cc_start: 0.6961 (mtt180) cc_final: 0.6287 (mtm-85) REVERT: C 13 MET cc_start: 0.7207 (ttm) cc_final: 0.6492 (mtp) REVERT: C 15 LYS cc_start: 0.6987 (mtpt) cc_final: 0.6569 (mtmt) REVERT: C 62 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6713 (mt-10) REVERT: C 66 GLU cc_start: 0.7316 (tt0) cc_final: 0.6528 (tm-30) REVERT: C 72 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7690 (mt-10) REVERT: C 92 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7351 (mt-10) REVERT: C 104 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6228 (mtp180) REVERT: D 13 MET cc_start: 0.7178 (ttm) cc_final: 0.6316 (mtm) REVERT: D 15 LYS cc_start: 0.6998 (mtpt) cc_final: 0.6615 (mtpt) REVERT: D 62 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6950 (mt-10) REVERT: D 80 LYS cc_start: 0.7368 (tttt) cc_final: 0.6881 (tttm) REVERT: D 104 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6341 (mtp-110) REVERT: E 15 LYS cc_start: 0.7148 (mtpt) cc_final: 0.6792 (mtpp) REVERT: E 34 ARG cc_start: 0.7139 (ttt-90) cc_final: 0.6244 (tmt-80) REVERT: E 62 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6838 (mt-10) REVERT: E 80 LYS cc_start: 0.7395 (tttt) cc_final: 0.6907 (tttm) REVERT: E 92 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7534 (mt-10) REVERT: E 104 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6462 (mtm110) REVERT: F 13 MET cc_start: 0.7284 (ttm) cc_final: 0.6476 (mtm) REVERT: F 26 ILE cc_start: 0.8479 (mt) cc_final: 0.8258 (mt) REVERT: F 62 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6632 (mt-10) REVERT: F 70 LYS cc_start: 0.8029 (tttt) cc_final: 0.7766 (tttm) REVERT: F 80 LYS cc_start: 0.7789 (tttt) cc_final: 0.7451 (tttp) REVERT: F 89 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7184 (tt0) REVERT: F 104 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7136 (mtm110) REVERT: F 118 THR cc_start: 0.7929 (m) cc_final: 0.7470 (p) outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 1.6888 time to fit residues: 192.0982 Evaluate side-chains 107 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain E residue 12 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4410 Z= 0.293 Angle : 0.597 5.303 6000 Z= 0.336 Chirality : 0.050 0.137 708 Planarity : 0.005 0.034 738 Dihedral : 5.070 15.175 594 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.21 % Allowed : 14.74 % Favored : 82.05 % 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: -2.32 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.007 0.002 HIS D 31 PHE 0.010 0.002 PHE C 33 TYR 0.013 0.002 TYR D 114 ARG 0.003 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.533 Fit side-chains REVERT: A 15 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7744 (mtpt) REVERT: A 21 ARG cc_start: 0.7825 (ttt90) cc_final: 0.7399 (ttt90) REVERT: A 66 GLU cc_start: 0.7558 (tt0) cc_final: 0.7098 (tt0) REVERT: A 70 LYS cc_start: 0.7995 (tttt) cc_final: 0.7639 (tttp) REVERT: A 80 LYS cc_start: 0.7375 (tttt) cc_final: 0.6915 (ttpt) REVERT: A 104 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6576 (mtm-85) REVERT: B 15 LYS cc_start: 0.7083 (mtpt) cc_final: 0.6702 (mtpt) REVERT: B 34 ARG cc_start: 0.7598 (ttt-90) cc_final: 0.7168 (ttt180) REVERT: B 70 LYS cc_start: 0.7982 (tttt) cc_final: 0.7611 (tttp) REVERT: B 104 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6298 (mtp180) REVERT: C 13 MET cc_start: 0.7263 (ttm) cc_final: 0.6616 (mtp) REVERT: C 15 LYS cc_start: 0.7321 (mtpt) cc_final: 0.6838 (mtmt) REVERT: C 62 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7036 (mt-10) REVERT: C 66 GLU cc_start: 0.7554 (tt0) cc_final: 0.6407 (tm-30) REVERT: C 72 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7704 (mt-10) REVERT: C 104 ARG cc_start: 0.7046 (mtt180) cc_final: 0.6197 (mtp180) REVERT: D 13 MET cc_start: 0.7193 (ttm) cc_final: 0.6477 (mtm) REVERT: D 15 LYS cc_start: 0.7244 (mtpt) cc_final: 0.6922 (mtpt) REVERT: D 62 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6552 (tt0) REVERT: D 66 GLU cc_start: 0.7734 (tt0) cc_final: 0.6464 (tm-30) REVERT: D 80 LYS cc_start: 0.7368 (tttt) cc_final: 0.6811 (tttm) REVERT: D 104 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6459 (mtp180) REVERT: E 15 LYS cc_start: 0.7172 (mtpt) cc_final: 0.6785 (mtmt) REVERT: E 62 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6985 (mt-10) REVERT: E 66 GLU cc_start: 0.7495 (tt0) cc_final: 0.6440 (tm-30) REVERT: E 80 LYS cc_start: 0.7335 (tttt) cc_final: 0.6856 (tttm) REVERT: E 92 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7168 (mt-10) REVERT: E 104 ARG cc_start: 0.7083 (mtt180) cc_final: 0.6285 (mtp180) REVERT: F 13 MET cc_start: 0.7101 (ttm) cc_final: 0.6267 (mtm) REVERT: F 15 LYS cc_start: 0.7340 (mtpt) cc_final: 0.6791 (mtpt) REVERT: F 62 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6792 (mt-10) REVERT: F 66 GLU cc_start: 0.7895 (tt0) cc_final: 0.7119 (tm-30) REVERT: F 70 LYS cc_start: 0.8235 (tttt) cc_final: 0.7904 (tttm) REVERT: F 80 LYS cc_start: 0.7716 (tttt) cc_final: 0.7436 (ttpp) REVERT: F 92 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7552 (mt-10) REVERT: F 104 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7161 (mtm-85) outliers start: 15 outliers final: 7 residues processed: 107 average time/residue: 1.8165 time to fit residues: 198.8700 Evaluate side-chains 105 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 90 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN C 98 ASN F 88 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4410 Z= 0.193 Angle : 0.513 6.190 6000 Z= 0.282 Chirality : 0.048 0.124 708 Planarity : 0.004 0.032 738 Dihedral : 4.826 14.168 594 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.99 % Allowed : 15.81 % Favored : 81.20 % 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: -2.32 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.005 0.001 HIS D 31 PHE 0.009 0.002 PHE B 64 TYR 0.014 0.001 TYR B 114 ARG 0.002 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.484 Fit side-chains REVERT: A 15 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7791 (mtpt) REVERT: A 21 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7346 (ttt90) REVERT: A 66 GLU cc_start: 0.7583 (tt0) cc_final: 0.7132 (tt0) REVERT: A 70 LYS cc_start: 0.7974 (tttt) cc_final: 0.7730 (tttp) REVERT: A 80 LYS cc_start: 0.7435 (tttt) cc_final: 0.6947 (ttpt) REVERT: A 104 ARG cc_start: 0.7278 (mtt180) cc_final: 0.6588 (mtm-85) REVERT: B 15 LYS cc_start: 0.7003 (mtpt) cc_final: 0.6549 (mtpt) REVERT: B 34 ARG cc_start: 0.7664 (ttt-90) cc_final: 0.7232 (ttt180) REVERT: B 104 ARG cc_start: 0.7220 (mtt180) cc_final: 0.6328 (mtp180) REVERT: C 13 MET cc_start: 0.7237 (ttm) cc_final: 0.6780 (mtp) REVERT: C 15 LYS cc_start: 0.7258 (mtpt) cc_final: 0.6737 (mtmt) REVERT: C 62 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6936 (mt-10) REVERT: C 66 GLU cc_start: 0.7570 (tt0) cc_final: 0.6382 (tm-30) REVERT: C 72 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7626 (mt-10) REVERT: C 104 ARG cc_start: 0.7036 (mtt180) cc_final: 0.6163 (mtp180) REVERT: D 13 MET cc_start: 0.7155 (ttm) cc_final: 0.6693 (mtp) REVERT: D 15 LYS cc_start: 0.7246 (mtpt) cc_final: 0.6787 (mtpt) REVERT: D 62 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6542 (tt0) REVERT: D 66 GLU cc_start: 0.7718 (tt0) cc_final: 0.6403 (tm-30) REVERT: D 80 LYS cc_start: 0.7380 (tttt) cc_final: 0.6804 (tttm) REVERT: E 15 LYS cc_start: 0.7233 (mtpt) cc_final: 0.6760 (mtmt) REVERT: E 62 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7046 (mt-10) REVERT: E 66 GLU cc_start: 0.7466 (tt0) cc_final: 0.6367 (tm-30) REVERT: E 80 LYS cc_start: 0.7295 (tttt) cc_final: 0.6942 (ttpp) REVERT: E 92 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7304 (mt-10) REVERT: E 104 ARG cc_start: 0.7154 (mtt180) cc_final: 0.6796 (mtm-85) REVERT: F 13 MET cc_start: 0.7055 (ttm) cc_final: 0.6231 (mtm) REVERT: F 15 LYS cc_start: 0.7401 (mtpt) cc_final: 0.6892 (mtpt) REVERT: F 62 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7095 (mt-10) REVERT: F 66 GLU cc_start: 0.7954 (tt0) cc_final: 0.7190 (tm-30) REVERT: F 70 LYS cc_start: 0.8264 (tttt) cc_final: 0.7940 (tttm) REVERT: F 80 LYS cc_start: 0.7612 (tttt) cc_final: 0.7363 (ttpp) REVERT: F 92 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7443 (mt-10) REVERT: F 104 ARG cc_start: 0.7773 (mtt180) cc_final: 0.7193 (mtm110) outliers start: 14 outliers final: 5 residues processed: 107 average time/residue: 1.9258 time to fit residues: 210.5513 Evaluate side-chains 103 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4410 Z= 0.322 Angle : 0.585 6.232 6000 Z= 0.327 Chirality : 0.050 0.128 708 Planarity : 0.004 0.033 738 Dihedral : 5.034 15.506 594 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.06 % Allowed : 15.17 % Favored : 80.77 % 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: -2.36 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 79 HIS 0.005 0.001 HIS D 31 PHE 0.010 0.002 PHE C 33 TYR 0.013 0.002 TYR A 114 ARG 0.004 0.000 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.484 Fit side-chains REVERT: A 15 LYS cc_start: 0.8143 (mtpt) cc_final: 0.6021 (pptt) REVERT: A 21 ARG cc_start: 0.7851 (ttt90) cc_final: 0.7306 (ttt90) REVERT: A 66 GLU cc_start: 0.7717 (tt0) cc_final: 0.7515 (tt0) REVERT: A 70 LYS cc_start: 0.7946 (tttt) cc_final: 0.7569 (tttp) REVERT: A 80 LYS cc_start: 0.7448 (tttt) cc_final: 0.7000 (ttpt) REVERT: A 104 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6429 (mtm-85) REVERT: B 15 LYS cc_start: 0.7018 (mtpt) cc_final: 0.6657 (mtpt) REVERT: B 34 ARG cc_start: 0.7640 (ttt-90) cc_final: 0.7273 (ttt180) REVERT: B 70 LYS cc_start: 0.7928 (tttt) cc_final: 0.7569 (tttp) REVERT: B 104 ARG cc_start: 0.7333 (mtt180) cc_final: 0.6320 (mtp180) REVERT: C 15 LYS cc_start: 0.7218 (mtpt) cc_final: 0.6781 (mtpt) REVERT: C 62 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7094 (mt-10) REVERT: C 72 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7654 (mt-10) REVERT: C 104 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6168 (mtp180) REVERT: D 13 MET cc_start: 0.7136 (ttm) cc_final: 0.6841 (mtp) REVERT: D 15 LYS cc_start: 0.7412 (mtpt) cc_final: 0.6975 (mtpt) REVERT: D 21 ARG cc_start: 0.7082 (ttt90) cc_final: 0.6645 (ttt180) REVERT: D 62 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6581 (tt0) REVERT: D 66 GLU cc_start: 0.7706 (tt0) cc_final: 0.6271 (tm-30) REVERT: D 80 LYS cc_start: 0.7303 (tttt) cc_final: 0.6704 (tttm) REVERT: E 15 LYS cc_start: 0.7272 (mtpt) cc_final: 0.6830 (mtmt) REVERT: E 62 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7012 (mt-10) REVERT: E 66 GLU cc_start: 0.7402 (tt0) cc_final: 0.6382 (tm-30) REVERT: E 80 LYS cc_start: 0.7312 (tttt) cc_final: 0.6845 (tttm) REVERT: E 92 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7246 (mt-10) REVERT: E 104 ARG cc_start: 0.7294 (mtt180) cc_final: 0.6563 (mtm110) REVERT: F 13 MET cc_start: 0.6934 (ttm) cc_final: 0.6075 (mtm) REVERT: F 15 LYS cc_start: 0.7480 (mtpt) cc_final: 0.7024 (mtpt) REVERT: F 34 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7518 (ttt180) REVERT: F 62 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6903 (mt-10) REVERT: F 66 GLU cc_start: 0.8027 (tt0) cc_final: 0.7294 (tm-30) REVERT: F 70 LYS cc_start: 0.8290 (tttt) cc_final: 0.7973 (tttm) REVERT: F 80 LYS cc_start: 0.7716 (tttt) cc_final: 0.7373 (tttp) REVERT: F 92 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7476 (mt-10) REVERT: F 104 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7187 (mtm110) outliers start: 19 outliers final: 9 residues processed: 108 average time/residue: 1.7946 time to fit residues: 198.2416 Evaluate side-chains 107 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 5 optimal weight: 0.0060 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4410 Z= 0.220 Angle : 0.523 6.392 6000 Z= 0.290 Chirality : 0.048 0.126 708 Planarity : 0.004 0.030 738 Dihedral : 4.899 14.302 594 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.78 % Allowed : 16.67 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.34 (0.34), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.004 0.001 HIS D 31 PHE 0.010 0.002 PHE C 33 TYR 0.014 0.002 TYR C 114 ARG 0.003 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.505 Fit side-chains REVERT: A 15 LYS cc_start: 0.8182 (mtpt) cc_final: 0.5990 (pptt) REVERT: A 21 ARG cc_start: 0.7802 (ttt90) cc_final: 0.7368 (ttt90) REVERT: A 70 LYS cc_start: 0.7964 (tttt) cc_final: 0.7573 (tttp) REVERT: A 80 LYS cc_start: 0.7445 (tttt) cc_final: 0.6931 (ttpt) REVERT: A 104 ARG cc_start: 0.7287 (mtt180) cc_final: 0.6483 (mtm-85) REVERT: B 15 LYS cc_start: 0.7090 (mtpt) cc_final: 0.6713 (mtpt) REVERT: B 34 ARG cc_start: 0.7568 (ttt-90) cc_final: 0.7184 (ttt180) REVERT: B 70 LYS cc_start: 0.7924 (tttt) cc_final: 0.7573 (tttp) REVERT: B 104 ARG cc_start: 0.7281 (mtt180) cc_final: 0.6313 (mtp180) REVERT: C 15 LYS cc_start: 0.7280 (mtpt) cc_final: 0.6837 (mtmt) REVERT: C 62 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7035 (mt-10) REVERT: C 72 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7630 (mt-10) REVERT: C 104 ARG cc_start: 0.7066 (mtt180) cc_final: 0.6173 (mtp180) REVERT: D 13 MET cc_start: 0.7057 (ttm) cc_final: 0.6804 (mtp) REVERT: D 15 LYS cc_start: 0.7288 (mtpt) cc_final: 0.6861 (mtpt) REVERT: D 21 ARG cc_start: 0.7140 (ttt90) cc_final: 0.6821 (ttt90) REVERT: D 34 ARG cc_start: 0.7496 (ttt-90) cc_final: 0.7291 (tmt90) REVERT: D 62 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6567 (tt0) REVERT: D 66 GLU cc_start: 0.7661 (tt0) cc_final: 0.6432 (tm-30) REVERT: D 80 LYS cc_start: 0.7257 (tttt) cc_final: 0.6689 (tttm) REVERT: E 15 LYS cc_start: 0.7285 (mtpt) cc_final: 0.6851 (mtmt) REVERT: E 62 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7022 (mt-10) REVERT: E 66 GLU cc_start: 0.7363 (tt0) cc_final: 0.6339 (tm-30) REVERT: E 80 LYS cc_start: 0.7263 (tttt) cc_final: 0.6885 (ttpp) REVERT: E 92 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7279 (mt-10) REVERT: E 104 ARG cc_start: 0.7295 (mtt180) cc_final: 0.6571 (mtm110) REVERT: F 13 MET cc_start: 0.6860 (ttm) cc_final: 0.6103 (mtm) REVERT: F 15 LYS cc_start: 0.7481 (mtpt) cc_final: 0.7035 (mtpt) REVERT: F 34 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7557 (ttt180) REVERT: F 62 GLU cc_start: 0.7522 (mt-10) cc_final: 0.6868 (mp0) REVERT: F 66 GLU cc_start: 0.8018 (tt0) cc_final: 0.7229 (tm-30) REVERT: F 70 LYS cc_start: 0.8298 (tttt) cc_final: 0.7999 (tttm) REVERT: F 80 LYS cc_start: 0.7685 (tttt) cc_final: 0.7356 (tttp) REVERT: F 92 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7478 (mt-10) REVERT: F 104 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7195 (mtm110) outliers start: 13 outliers final: 7 residues processed: 105 average time/residue: 1.9810 time to fit residues: 212.8890 Evaluate side-chains 107 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4410 Z= 0.308 Angle : 0.580 6.421 6000 Z= 0.324 Chirality : 0.049 0.132 708 Planarity : 0.004 0.030 738 Dihedral : 5.141 16.451 594 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.85 % Allowed : 16.03 % Favored : 80.13 % 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: -2.39 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.004 0.001 HIS D 31 PHE 0.010 0.002 PHE E 87 TYR 0.014 0.002 TYR A 114 ARG 0.003 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.518 Fit side-chains REVERT: A 15 LYS cc_start: 0.8189 (mtpt) cc_final: 0.6018 (pptt) REVERT: A 21 ARG cc_start: 0.7864 (ttt90) cc_final: 0.7314 (ttt90) REVERT: A 70 LYS cc_start: 0.7914 (tttt) cc_final: 0.7527 (tttp) REVERT: A 80 LYS cc_start: 0.7493 (tttt) cc_final: 0.6932 (ttpt) REVERT: A 104 ARG cc_start: 0.7345 (mtt180) cc_final: 0.6568 (mtm-85) REVERT: B 15 LYS cc_start: 0.7083 (mtpt) cc_final: 0.6787 (mtpt) REVERT: B 34 ARG cc_start: 0.7647 (ttt-90) cc_final: 0.7265 (ttt180) REVERT: B 70 LYS cc_start: 0.7895 (tttt) cc_final: 0.7552 (tttp) REVERT: B 104 ARG cc_start: 0.7289 (mtt180) cc_final: 0.6346 (mtp180) REVERT: C 15 LYS cc_start: 0.7277 (mtpt) cc_final: 0.6841 (mtmt) REVERT: C 62 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7048 (mt-10) REVERT: C 70 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7918 (tttt) REVERT: C 72 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7632 (mt-10) REVERT: D 15 LYS cc_start: 0.7252 (mtpt) cc_final: 0.6845 (mtpt) REVERT: D 21 ARG cc_start: 0.7192 (ttt90) cc_final: 0.6894 (ttt90) REVERT: D 34 ARG cc_start: 0.7506 (ttt-90) cc_final: 0.7301 (tmt90) REVERT: D 62 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6594 (tt0) REVERT: D 66 GLU cc_start: 0.7536 (tt0) cc_final: 0.6290 (tm-30) REVERT: D 80 LYS cc_start: 0.7314 (tttt) cc_final: 0.6776 (tttm) REVERT: E 15 LYS cc_start: 0.7292 (mtpt) cc_final: 0.7018 (mtmt) REVERT: E 62 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7096 (mt-10) REVERT: E 66 GLU cc_start: 0.7387 (tt0) cc_final: 0.6344 (tm-30) REVERT: E 80 LYS cc_start: 0.7340 (tttt) cc_final: 0.6957 (ttpp) REVERT: E 92 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7224 (mt-10) REVERT: E 104 ARG cc_start: 0.7272 (mtt180) cc_final: 0.6521 (mtm110) REVERT: F 13 MET cc_start: 0.6881 (ttm) cc_final: 0.6169 (mtm) REVERT: F 15 LYS cc_start: 0.7512 (mtpt) cc_final: 0.7166 (mtpm) REVERT: F 34 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7520 (ttt180) REVERT: F 62 GLU cc_start: 0.7557 (mt-10) cc_final: 0.6828 (mp0) REVERT: F 70 LYS cc_start: 0.8255 (tttt) cc_final: 0.7894 (tttm) REVERT: F 80 LYS cc_start: 0.7700 (tttt) cc_final: 0.7401 (tttp) REVERT: F 92 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7453 (mt-10) REVERT: F 104 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7161 (mtm110) outliers start: 18 outliers final: 10 residues processed: 106 average time/residue: 1.9956 time to fit residues: 215.9649 Evaluate side-chains 109 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4410 Z= 0.238 Angle : 0.534 7.006 6000 Z= 0.296 Chirality : 0.048 0.128 708 Planarity : 0.004 0.029 738 Dihedral : 5.023 15.180 594 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.99 % Allowed : 16.24 % Favored : 80.77 % 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: -2.37 (0.34), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.004 0.001 HIS D 31 PHE 0.009 0.002 PHE B 64 TYR 0.014 0.002 TYR D 114 ARG 0.002 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.620 Fit side-chains REVERT: A 15 LYS cc_start: 0.8184 (mtpt) cc_final: 0.6014 (pptt) REVERT: A 21 ARG cc_start: 0.7836 (ttt90) cc_final: 0.7375 (ttt90) REVERT: A 34 ARG cc_start: 0.7211 (ttt-90) cc_final: 0.6827 (ttt-90) REVERT: A 70 LYS cc_start: 0.7898 (tttt) cc_final: 0.7505 (tttp) REVERT: A 80 LYS cc_start: 0.7542 (tttt) cc_final: 0.7030 (ttpt) REVERT: A 104 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6708 (mtm-85) REVERT: B 15 LYS cc_start: 0.7049 (mtpt) cc_final: 0.6647 (mtpt) REVERT: B 34 ARG cc_start: 0.7606 (ttt-90) cc_final: 0.7248 (ttt180) REVERT: B 70 LYS cc_start: 0.7889 (tttt) cc_final: 0.7560 (tttp) REVERT: B 104 ARG cc_start: 0.7280 (mtt180) cc_final: 0.6386 (mtp180) REVERT: C 15 LYS cc_start: 0.7278 (mtpt) cc_final: 0.6883 (mtmt) REVERT: C 62 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6910 (mt-10) REVERT: C 72 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7642 (mt-10) REVERT: C 92 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6581 (mt-10) REVERT: D 15 LYS cc_start: 0.7223 (mtpt) cc_final: 0.6851 (mtpt) REVERT: D 21 ARG cc_start: 0.7105 (ttt90) cc_final: 0.6844 (ttt90) REVERT: D 34 ARG cc_start: 0.7509 (ttt-90) cc_final: 0.7300 (tmt90) REVERT: D 62 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7112 (mt-10) REVERT: D 66 GLU cc_start: 0.7482 (tt0) cc_final: 0.6172 (tm-30) REVERT: D 80 LYS cc_start: 0.7308 (tttt) cc_final: 0.6769 (tttm) REVERT: E 15 LYS cc_start: 0.7285 (mtpt) cc_final: 0.7008 (mtmt) REVERT: E 62 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7071 (mt-10) REVERT: E 66 GLU cc_start: 0.7411 (tt0) cc_final: 0.6374 (tm-30) REVERT: E 80 LYS cc_start: 0.7334 (tttt) cc_final: 0.6887 (tttm) REVERT: E 92 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7216 (mt-10) REVERT: E 104 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6567 (mtm110) REVERT: F 13 MET cc_start: 0.6906 (ttm) cc_final: 0.6167 (mtm) REVERT: F 15 LYS cc_start: 0.7517 (mtpt) cc_final: 0.7012 (mtpt) REVERT: F 34 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7511 (ttt180) REVERT: F 62 GLU cc_start: 0.7571 (mt-10) cc_final: 0.6846 (mp0) REVERT: F 70 LYS cc_start: 0.8251 (tttt) cc_final: 0.7889 (tttm) REVERT: F 80 LYS cc_start: 0.7704 (tttt) cc_final: 0.7372 (tttp) REVERT: F 92 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7452 (mt-10) REVERT: F 104 ARG cc_start: 0.7831 (mtt180) cc_final: 0.7195 (mtm110) outliers start: 14 outliers final: 10 residues processed: 103 average time/residue: 2.0083 time to fit residues: 211.2661 Evaluate side-chains 109 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 48 optimal weight: 0.0030 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4410 Z= 0.223 Angle : 0.523 7.233 6000 Z= 0.289 Chirality : 0.048 0.128 708 Planarity : 0.004 0.027 738 Dihedral : 4.948 15.518 594 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.99 % Allowed : 16.24 % Favored : 80.77 % 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: -2.39 (0.34), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.004 0.001 HIS D 31 PHE 0.008 0.002 PHE C 95 TYR 0.014 0.002 TYR D 114 ARG 0.001 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.558 Fit side-chains REVERT: A 15 LYS cc_start: 0.8179 (mtpt) cc_final: 0.5997 (pptt) REVERT: A 21 ARG cc_start: 0.7885 (ttt90) cc_final: 0.7431 (ttt90) REVERT: A 34 ARG cc_start: 0.7288 (ttt-90) cc_final: 0.6862 (ttt-90) REVERT: A 70 LYS cc_start: 0.7903 (tttt) cc_final: 0.7511 (tttp) REVERT: A 80 LYS cc_start: 0.7568 (tttt) cc_final: 0.7060 (ttpt) REVERT: A 104 ARG cc_start: 0.7439 (mtt180) cc_final: 0.6618 (mtm-85) REVERT: B 15 LYS cc_start: 0.7061 (mtpt) cc_final: 0.6681 (mtpt) REVERT: B 34 ARG cc_start: 0.7443 (ttt-90) cc_final: 0.7065 (ttt180) REVERT: B 70 LYS cc_start: 0.7895 (tttt) cc_final: 0.7560 (tttp) REVERT: B 104 ARG cc_start: 0.7353 (mtt180) cc_final: 0.6443 (mtp180) REVERT: C 15 LYS cc_start: 0.7249 (mtpt) cc_final: 0.6845 (mtmt) REVERT: C 62 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6916 (mt-10) REVERT: C 72 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7687 (mt-10) REVERT: C 92 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6574 (mt-10) REVERT: D 15 LYS cc_start: 0.7176 (mtpt) cc_final: 0.6834 (mtpt) REVERT: D 21 ARG cc_start: 0.7030 (ttt90) cc_final: 0.6778 (ttt90) REVERT: D 34 ARG cc_start: 0.7512 (ttt-90) cc_final: 0.7302 (tmt90) REVERT: D 62 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7160 (mt-10) REVERT: D 66 GLU cc_start: 0.7539 (tt0) cc_final: 0.6225 (tm-30) REVERT: D 80 LYS cc_start: 0.7296 (tttt) cc_final: 0.6935 (ttpp) REVERT: E 62 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6996 (mt-10) REVERT: E 66 GLU cc_start: 0.7409 (tt0) cc_final: 0.6421 (tm-30) REVERT: E 80 LYS cc_start: 0.7283 (tttt) cc_final: 0.6804 (tttm) REVERT: E 104 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6476 (mtm110) REVERT: F 13 MET cc_start: 0.6915 (ttm) cc_final: 0.6136 (mtm) REVERT: F 15 LYS cc_start: 0.7525 (mtpt) cc_final: 0.7016 (mtpt) REVERT: F 34 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7516 (ttt180) REVERT: F 62 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6845 (mp0) REVERT: F 70 LYS cc_start: 0.8319 (tttt) cc_final: 0.7968 (tttm) REVERT: F 80 LYS cc_start: 0.7694 (tttt) cc_final: 0.7386 (tttp) REVERT: F 92 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7590 (mt-10) REVERT: F 104 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7140 (mtm110) outliers start: 14 outliers final: 9 residues processed: 105 average time/residue: 1.8642 time to fit residues: 200.0862 Evaluate side-chains 107 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 18 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4410 Z= 0.246 Angle : 0.536 7.569 6000 Z= 0.296 Chirality : 0.048 0.129 708 Planarity : 0.004 0.028 738 Dihedral : 5.002 15.651 594 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.35 % Allowed : 17.09 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.38 (0.34), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.004 0.001 HIS D 31 PHE 0.008 0.002 PHE C 95 TYR 0.014 0.002 TYR D 114 ARG 0.002 0.000 ARG B 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.509 Fit side-chains REVERT: A 15 LYS cc_start: 0.8202 (mtpt) cc_final: 0.6040 (pptt) REVERT: A 21 ARG cc_start: 0.7914 (ttt90) cc_final: 0.7447 (ttt90) REVERT: A 34 ARG cc_start: 0.7332 (ttt-90) cc_final: 0.6913 (ttt-90) REVERT: A 70 LYS cc_start: 0.7893 (tttt) cc_final: 0.7498 (tttp) REVERT: A 80 LYS cc_start: 0.7583 (tttt) cc_final: 0.7083 (ttpt) REVERT: A 104 ARG cc_start: 0.7447 (mtt180) cc_final: 0.6643 (mtm-85) REVERT: B 15 LYS cc_start: 0.7055 (mtpt) cc_final: 0.6673 (mtpt) REVERT: B 34 ARG cc_start: 0.7614 (ttt-90) cc_final: 0.7230 (ttt180) REVERT: B 70 LYS cc_start: 0.7871 (tttt) cc_final: 0.7536 (tttp) REVERT: B 104 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6443 (mtp180) REVERT: C 15 LYS cc_start: 0.7302 (mtpt) cc_final: 0.6885 (mtmt) REVERT: C 62 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6903 (mt-10) REVERT: C 72 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 92 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6603 (mt-10) REVERT: D 15 LYS cc_start: 0.7108 (mtpt) cc_final: 0.6785 (mtpt) REVERT: D 21 ARG cc_start: 0.7141 (ttt90) cc_final: 0.6871 (ttt90) REVERT: D 34 ARG cc_start: 0.7507 (ttt-90) cc_final: 0.7302 (tmt90) REVERT: D 62 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7177 (mt-10) REVERT: D 66 GLU cc_start: 0.7518 (tt0) cc_final: 0.6240 (tm-30) REVERT: D 80 LYS cc_start: 0.7284 (tttt) cc_final: 0.6947 (ttpp) REVERT: E 62 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6944 (mt-10) REVERT: E 66 GLU cc_start: 0.7391 (tt0) cc_final: 0.6419 (tm-30) REVERT: E 80 LYS cc_start: 0.7295 (tttt) cc_final: 0.6789 (tttm) REVERT: E 104 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6517 (mtm110) REVERT: F 13 MET cc_start: 0.6917 (ttm) cc_final: 0.6162 (mtm) REVERT: F 15 LYS cc_start: 0.7519 (mtpt) cc_final: 0.7025 (mtpt) REVERT: F 34 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7517 (ttt180) REVERT: F 62 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6855 (mp0) REVERT: F 70 LYS cc_start: 0.8257 (tttt) cc_final: 0.7893 (tttm) REVERT: F 80 LYS cc_start: 0.7675 (tttt) cc_final: 0.7382 (tttp) REVERT: F 92 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7588 (mt-10) REVERT: F 104 ARG cc_start: 0.7820 (mtt180) cc_final: 0.7143 (mtm110) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 1.9661 time to fit residues: 206.8481 Evaluate side-chains 107 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain F residue 34 ARG Chi-restraints excluded: chain F residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.0170 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.121566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.101705 restraints weight = 5053.577| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.06 r_work: 0.3518 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4410 Z= 0.249 Angle : 0.539 7.583 6000 Z= 0.297 Chirality : 0.049 0.129 708 Planarity : 0.004 0.028 738 Dihedral : 5.023 15.895 594 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.56 % Allowed : 16.88 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.40 (0.34), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.004 0.001 HIS D 31 PHE 0.008 0.002 PHE C 95 TYR 0.014 0.002 TYR D 114 ARG 0.003 0.000 ARG B 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3325.95 seconds wall clock time: 59 minutes 6.43 seconds (3546.43 seconds total)