Starting phenix.real_space_refine on Thu Dec 7 20:17:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/12_2023/8pkf_17737.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/12_2023/8pkf_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_17737/12_2023/8pkf_17737.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/12_2023/8pkf_17737.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/12_2023/8pkf_17737.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pkf_17737/12_2023/8pkf_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-1.21rc1-5172/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: 2.63, 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: 1.63 Conformation dependent library (CDL) restraints added in 754.5 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: 0.59 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: 1.04 Time building geometry restraints manager: 1.77 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: 0.010 Normalize map: mean=0, sd=1: 0.720 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: 3.550 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.740 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- 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 : 0.478 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 1.4237 time to fit residues: 209.1557 Evaluate side-chains 101 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6819 ------------------------------------------------------------------------------- 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: 2.9990 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 F 88 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4410 Z= 0.186 Angle : 0.578 5.147 6000 Z= 0.323 Chirality : 0.049 0.132 708 Planarity : 0.005 0.041 738 Dihedral : 5.087 14.886 594 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.14 % Allowed : 19.66 % Favored : 78.21 % 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: -2.16 (0.32), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.008 0.001 HIS D 31 PHE 0.017 0.002 PHE D 64 TYR 0.012 0.002 TYR D 114 ARG 0.004 0.000 ARG C 104 *********************** 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 113 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.532 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 107 average time/residue: 1.7243 time to fit residues: 188.9982 Evaluate side-chains 102 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.490 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.0610 time to fit residues: 0.9725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7411 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4410 Z= 0.223 Angle : 0.548 5.675 6000 Z= 0.305 Chirality : 0.049 0.125 708 Planarity : 0.005 0.054 738 Dihedral : 4.911 14.301 594 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.13 % Allowed : 17.74 % Favored : 77.14 % 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: -2.28 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 79 HIS 0.007 0.001 HIS D 31 PHE 0.010 0.002 PHE D 64 TYR 0.013 0.002 TYR D 114 ARG 0.007 0.001 ARG C 104 *********************** 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 121 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 0.545 Fit side-chains outliers start: 24 outliers final: 10 residues processed: 105 average time/residue: 1.8125 time to fit residues: 194.8450 Evaluate side-chains 104 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.491 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 2 residues processed: 8 average time/residue: 0.0512 time to fit residues: 1.3657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** C 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4410 Z= 0.243 Angle : 0.552 6.138 6000 Z= 0.306 Chirality : 0.049 0.129 708 Planarity : 0.004 0.039 738 Dihedral : 4.915 14.801 594 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.91 % Allowed : 18.59 % Favored : 76.50 % 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: -2.33 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.006 0.001 HIS D 31 PHE 0.009 0.002 PHE C 95 TYR 0.013 0.002 TYR D 114 ARG 0.008 0.001 ARG E 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: 23 poor density : 91 time to evaluate : 0.507 Fit side-chains outliers start: 23 outliers final: 11 residues processed: 105 average time/residue: 1.7503 time to fit residues: 188.2198 Evaluate side-chains 102 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 5 residues processed: 6 average time/residue: 0.0550 time to fit residues: 1.2221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.7429 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4410 Z= 0.393 Angle : 0.642 6.202 6000 Z= 0.360 Chirality : 0.051 0.128 708 Planarity : 0.005 0.042 738 Dihedral : 5.285 17.737 594 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.98 % Allowed : 19.02 % Favored : 75.00 % 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: -2.48 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 79 HIS 0.005 0.001 HIS D 31 PHE 0.011 0.003 PHE C 33 TYR 0.013 0.003 TYR A 114 ARG 0.006 0.001 ARG E 34 *********************** 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 123 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.507 Fit side-chains outliers start: 28 outliers final: 16 residues processed: 110 average time/residue: 1.7732 time to fit residues: 199.6185 Evaluate side-chains 109 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.497 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 0.6981 time to fit residues: 7.2276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7402 moved from start: 0.4044 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= 0.215 Angle : 0.535 6.595 6000 Z= 0.296 Chirality : 0.049 0.129 708 Planarity : 0.004 0.037 738 Dihedral : 5.041 15.248 594 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.06 % Allowed : 20.30 % Favored : 75.64 % 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: -2.42 (0.33), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.25), 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 C 64 TYR 0.015 0.002 TYR D 114 ARG 0.007 0.001 ARG E 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 110 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.483 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 1.8305 time to fit residues: 190.8852 Evaluate side-chains 102 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.507 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.8960 time to fit residues: 7.1682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 33 optimal weight: 0.9980 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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: 0.7389 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4410 Z= 0.173 Angle : 0.503 6.649 6000 Z= 0.276 Chirality : 0.048 0.128 708 Planarity : 0.004 0.039 738 Dihedral : 4.819 14.455 594 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.78 % Allowed : 22.01 % Favored : 75.21 % 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: -2.42 (0.34), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 79 HIS 0.004 0.001 HIS D 31 PHE 0.009 0.002 PHE B 64 TYR 0.015 0.001 TYR C 114 ARG 0.009 0.001 ARG E 34 *********************** 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 105 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.498 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 101 average time/residue: 1.8281 time to fit residues: 189.0122 Evaluate side-chains 99 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.465 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.9834 time to fit residues: 2.6551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7394 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4410 Z= 0.203 Angle : 0.519 6.842 6000 Z= 0.286 Chirality : 0.048 0.129 708 Planarity : 0.004 0.030 738 Dihedral : 4.802 14.447 594 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.99 % Allowed : 21.58 % Favored : 75.43 % 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: -2.41 (0.34), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS D 31 PHE 0.008 0.002 PHE D 95 TYR 0.014 0.002 TYR D 114 ARG 0.005 0.001 ARG E 104 *********************** 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 104 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.512 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 101 average time/residue: 1.8506 time to fit residues: 191.2774 Evaluate side-chains 98 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.7270 time to fit residues: 2.8876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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: 0.7405 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4410 Z= 0.294 Angle : 0.576 6.786 6000 Z= 0.320 Chirality : 0.049 0.130 708 Planarity : 0.004 0.038 738 Dihedral : 5.047 15.861 594 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.99 % Allowed : 21.79 % Favored : 75.21 % 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: -2.43 (0.34), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.26), 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 0.008 0.002 PHE E 87 TYR 0.013 0.002 TYR D 114 ARG 0.007 0.001 ARG E 104 *********************** 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 104 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.482 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 99 average time/residue: 1.8923 time to fit residues: 191.5837 Evaluate side-chains 100 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 90 time to evaluate : 0.496 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.4859 time to fit residues: 3.2551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7386 moved from start: 0.4221 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= 0.183 Angle : 0.519 7.391 6000 Z= 0.284 Chirality : 0.048 0.130 708 Planarity : 0.004 0.033 738 Dihedral : 4.824 14.674 594 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.71 % Allowed : 22.86 % Favored : 75.43 % 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: -2.41 (0.34), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (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 D 95 TYR 0.015 0.001 TYR D 114 ARG 0.007 0.001 ARG E 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 97 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 89 time to evaluate : 0.523 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 96 average time/residue: 1.8602 time to fit residues: 182.7290 Evaluate side-chains 94 residues out of total 468 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 88 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.1823 time to fit residues: 0.8065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 0.0020 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 49 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.9528 ------------------------------------------------------------------------------- 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 = 0.4024 r_free = 0.4024 target = 0.124087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.104075 restraints weight = 5003.556| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 2.02 r_work: 0.3592 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4410 Z= 0.202 Angle : 0.525 7.660 6000 Z= 0.287 Chirality : 0.048 0.126 708 Planarity : 0.004 0.036 738 Dihedral : 4.816 14.595 594 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.35 % Allowed : 23.08 % Favored : 74.57 % 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 : -1.82 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS D 31 PHE 0.008 0.002 PHE E 95 TYR 0.014 0.002 TYR D 114 ARG 0.007 0.001 ARG E 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3168.25 seconds wall clock time: 56 minutes 19.98 seconds (3379.98 seconds total)