Starting phenix.real_space_refine on Fri Dec 8 08:11:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/12_2023/8a4l_15148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/12_2023/8a4l_15148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/12_2023/8a4l_15148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/12_2023/8a4l_15148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/12_2023/8a4l_15148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/12_2023/8a4l_15148.pdb" } resolution = 2.68 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= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4845 2.51 5 N 1350 2.21 5 O 1560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7755 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "B" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "C" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "D" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "E" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "F" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "G" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "H" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "I" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "J" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "K" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "L" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "M" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "O" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Chain: "P" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Time building chain proxies: 4.50, per 1000 atoms: 0.58 Number of scatterers: 7755 At special positions: 0 Unit cell: (145.95, 141.75, 43.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1560 8.00 N 1350 7.00 C 4845 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: 3.01 Conformation dependent library (CDL) restraints added in 1.5 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 21 sheets defined 0.0% alpha, 61.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.083A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS B 34 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS C 34 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS D 34 " --> pdb=" O GLU E 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 49 removed outlier: 6.808A pdb=" N TYR B 39 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A 40 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY B 41 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER A 42 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS B 43 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 44 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR C 39 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 40 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY C 41 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER B 42 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS C 43 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B 44 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR D 39 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 40 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY D 41 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER C 42 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS D 43 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS D 45 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR E 39 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 40 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY E 41 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER D 42 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS E 43 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR D 44 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS E 45 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA7, first strand: chain 'A' and resid 85 through 92 Processing sheet with id=AA8, first strand: chain 'F' and resid 15 through 23 Processing sheet with id=AA9, first strand: chain 'F' and resid 34 through 35 removed outlier: 6.083A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS I 34 " --> pdb=" O GLU J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 38 through 49 removed outlier: 6.808A pdb=" N TYR G 39 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL F 40 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY G 41 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER F 42 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS G 43 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR F 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS G 45 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR H 39 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G 40 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY H 41 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER G 42 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS H 43 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR G 44 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS H 45 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR I 39 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL H 40 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY I 41 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER H 42 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS I 43 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR H 44 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS I 45 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR J 39 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL I 40 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY J 41 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER I 42 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS J 43 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR I 44 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS J 45 " --> pdb=" O THR I 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 57 Processing sheet with id=AB3, first strand: chain 'F' and resid 61 through 72 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 79 Processing sheet with id=AB5, first strand: chain 'F' and resid 85 through 92 Processing sheet with id=AB6, first strand: chain 'K' and resid 15 through 23 Processing sheet with id=AB7, first strand: chain 'K' and resid 34 through 35 removed outlier: 6.082A pdb=" N LYS K 34 " --> pdb=" O GLU L 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS L 34 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS M 34 " --> pdb=" O GLU O 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS O 34 " --> pdb=" O GLU P 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 38 through 49 removed outlier: 6.808A pdb=" N TYR L 39 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL K 40 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY L 41 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER K 42 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS L 43 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR K 44 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS L 45 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR M 39 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL L 40 " --> pdb=" O TYR M 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY M 41 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER L 42 " --> pdb=" O GLY M 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS M 43 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR L 44 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS M 45 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR O 39 " --> pdb=" O LEU M 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL M 40 " --> pdb=" O TYR O 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY O 41 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER M 42 " --> pdb=" O GLY O 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS O 43 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR M 44 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS O 45 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR P 39 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL O 40 " --> pdb=" O TYR P 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY P 41 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER O 42 " --> pdb=" O GLY P 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS P 43 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR O 44 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS P 45 " --> pdb=" O THR O 44 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 53 through 57 Processing sheet with id=AC1, first strand: chain 'K' and resid 61 through 72 Processing sheet with id=AC2, first strand: chain 'K' and resid 75 through 79 Processing sheet with id=AC3, first strand: chain 'K' and resid 85 through 92 456 hydrogen bonds defined for protein. 1368 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: 2.37 Time building geometry restraints manager: 3.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1365 1.29 - 1.35: 1199 1.35 - 1.42: 256 1.42 - 1.48: 1281 1.48 - 1.54: 3669 Bond restraints: 7770 Sorted by residual: bond pdb=" CB THR H 72 " pdb=" CG2 THR H 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CB THR A 72 " pdb=" CG2 THR A 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.49e+00 bond pdb=" CB THR E 72 " pdb=" CG2 THR E 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CB THR C 72 " pdb=" CG2 THR C 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CB THR F 72 " pdb=" CG2 THR F 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 ... (remaining 7765 not shown) Histogram of bond angle deviations from ideal: 105.94 - 111.00: 3156 111.00 - 116.06: 2395 116.06 - 121.11: 2509 121.11 - 126.17: 2395 126.17 - 131.23: 15 Bond angle restraints: 10470 Sorted by residual: angle pdb=" CA GLU H 61 " pdb=" CB GLU H 61 " pdb=" CG GLU H 61 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.87e+00 angle pdb=" CA GLU O 61 " pdb=" CB GLU O 61 " pdb=" CG GLU O 61 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.87e+00 angle pdb=" CA GLU D 61 " pdb=" CB GLU D 61 " pdb=" CG GLU D 61 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.83e+00 angle pdb=" CA GLU M 61 " pdb=" CB GLU M 61 " pdb=" CG GLU M 61 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.80e+00 angle pdb=" CA GLU A 61 " pdb=" CB GLU A 61 " pdb=" CG GLU A 61 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.78e+00 ... (remaining 10465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 4260 15.30 - 30.60: 180 30.60 - 45.91: 90 45.91 - 61.21: 30 61.21 - 76.51: 15 Dihedral angle restraints: 4575 sinusoidal: 1545 harmonic: 3030 Sorted by residual: dihedral pdb=" CA LYS E 60 " pdb=" C LYS E 60 " pdb=" N GLU E 61 " pdb=" CA GLU E 61 " ideal model delta harmonic sigma weight residual -180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LYS I 60 " pdb=" C LYS I 60 " pdb=" N GLU I 61 " pdb=" CA GLU I 61 " ideal model delta harmonic sigma weight residual 180.00 -155.23 -24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LYS C 60 " pdb=" C LYS C 60 " pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta harmonic sigma weight residual -180.00 -155.24 -24.76 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 4572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 718 0.032 - 0.065: 358 0.065 - 0.097: 139 0.097 - 0.130: 150 0.130 - 0.162: 15 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB THR A 72 " pdb=" CA THR A 72 " pdb=" OG1 THR A 72 " pdb=" CG2 THR A 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CB THR H 72 " pdb=" CA THR H 72 " pdb=" OG1 THR H 72 " pdb=" CG2 THR H 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB THR B 72 " pdb=" CA THR B 72 " pdb=" OG1 THR B 72 " pdb=" CG2 THR B 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1377 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 73 " 0.003 2.00e-02 2.50e+03 6.21e-03 3.85e-01 pdb=" C GLY B 73 " -0.011 2.00e-02 2.50e+03 pdb=" O GLY B 73 " 0.004 2.00e-02 2.50e+03 pdb=" N VAL B 74 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 73 " -0.003 2.00e-02 2.50e+03 6.18e-03 3.82e-01 pdb=" C GLY O 73 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY O 73 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL O 74 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 73 " -0.003 2.00e-02 2.50e+03 6.18e-03 3.81e-01 pdb=" C GLY G 73 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY G 73 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL G 74 " -0.004 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 2667 2.89 - 3.39: 6455 3.39 - 3.89: 13223 3.89 - 4.40: 15272 4.40 - 4.90: 28140 Nonbonded interactions: 65757 Sorted by model distance: nonbonded pdb=" OE2 GLU D 35 " pdb=" NZ LYS D 80 " model vdw 2.385 2.520 nonbonded pdb=" OE2 GLU P 35 " pdb=" NZ LYS P 80 " model vdw 2.385 2.520 nonbonded pdb=" OE2 GLU O 35 " pdb=" NZ LYS O 80 " model vdw 2.385 2.520 nonbonded pdb=" OE2 GLU G 35 " pdb=" NZ LYS G 80 " model vdw 2.385 2.520 nonbonded pdb=" OE2 GLU F 35 " pdb=" NZ LYS F 80 " model vdw 2.385 2.520 ... (remaining 65752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 3.620 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.030 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7770 Z= 0.255 Angle : 0.646 5.957 10470 Z= 0.369 Chirality : 0.053 0.162 1380 Planarity : 0.001 0.006 1290 Dihedral : 13.435 76.508 2655 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.22), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS J 50 PHE 0.007 0.003 PHE O 94 TYR 0.009 0.002 TYR O 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.937 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 1.5922 time to fit residues: 295.4297 Evaluate side-chains 141 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN F 65 ASN H 65 ASN I 65 ASN K 65 ASN L 65 ASN M 65 ASN O 65 ASN P 65 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.068 7770 Z= 0.633 Angle : 0.731 7.864 10470 Z= 0.399 Chirality : 0.059 0.189 1380 Planarity : 0.003 0.010 1290 Dihedral : 5.821 28.584 1110 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.18 % Allowed : 13.85 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS J 50 PHE 0.015 0.003 PHE O 94 TYR 0.009 0.002 TYR P 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 188 time to evaluate : 0.968 Fit side-chains outliers start: 17 outliers final: 6 residues processed: 193 average time/residue: 1.5288 time to fit residues: 307.9108 Evaluate side-chains 189 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 183 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 1.5701 time to fit residues: 4.3264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN D 65 ASN G 65 ASN I 65 ASN L 65 ASN M 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7770 Z= 0.168 Angle : 0.474 6.180 10470 Z= 0.257 Chirality : 0.052 0.123 1380 Planarity : 0.002 0.007 1290 Dihedral : 4.733 21.838 1110 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.95 % Allowed : 17.82 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS P 50 PHE 0.008 0.002 PHE G 94 TYR 0.009 0.001 TYR P 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 0.915 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 182 average time/residue: 1.5747 time to fit residues: 299.9032 Evaluate side-chains 162 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 0.956 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.0858 time to fit residues: 3.9253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 90 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN D 65 ASN I 65 ASN L 65 ASN M 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7770 Z= 0.273 Angle : 0.508 7.548 10470 Z= 0.276 Chirality : 0.052 0.121 1380 Planarity : 0.002 0.007 1290 Dihedral : 4.769 20.263 1110 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.59 % Allowed : 21.03 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS J 50 PHE 0.010 0.002 PHE G 94 TYR 0.009 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 0.838 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 174 average time/residue: 1.4312 time to fit residues: 260.8358 Evaluate side-chains 171 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 0.813 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 0.4464 time to fit residues: 3.0536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 20.0000 chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 overall best weight: 6.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN M 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 7770 Z= 0.478 Angle : 0.613 9.368 10470 Z= 0.336 Chirality : 0.055 0.160 1380 Planarity : 0.002 0.008 1290 Dihedral : 5.181 21.483 1110 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.62 % Allowed : 19.74 % 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: -3.64 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS A 50 PHE 0.013 0.003 PHE G 94 TYR 0.011 0.002 TYR O 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 0.917 Fit side-chains outliers start: 36 outliers final: 16 residues processed: 195 average time/residue: 1.4433 time to fit residues: 294.7446 Evaluate side-chains 182 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 10 residues processed: 6 average time/residue: 0.5792 time to fit residues: 5.0114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN D 65 ASN I 65 ASN L 65 ASN M 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7770 Z= 0.337 Angle : 0.544 9.619 10470 Z= 0.296 Chirality : 0.053 0.128 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.871 17.822 1110 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.23 % Allowed : 20.64 % Favored : 75.13 % 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: -3.63 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS J 50 PHE 0.011 0.002 PHE G 94 TYR 0.008 0.002 TYR O 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 0.936 Fit side-chains outliers start: 33 outliers final: 16 residues processed: 179 average time/residue: 1.3874 time to fit residues: 260.2563 Evaluate side-chains 173 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.4395 time to fit residues: 3.1965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN M 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 7770 Z= 0.445 Angle : 0.600 9.827 10470 Z= 0.329 Chirality : 0.055 0.151 1380 Planarity : 0.002 0.008 1290 Dihedral : 5.070 16.390 1110 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.72 % Allowed : 21.15 % Favored : 75.13 % 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: -3.64 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS A 50 PHE 0.013 0.003 PHE G 94 TYR 0.010 0.002 TYR P 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 0.847 Fit side-chains outliers start: 29 outliers final: 17 residues processed: 188 average time/residue: 1.4238 time to fit residues: 280.2878 Evaluate side-chains 185 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.4443 time to fit residues: 3.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN G 65 ASN H 65 ASN I 65 ASN L 65 ASN M 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 7770 Z= 0.248 Angle : 0.511 9.063 10470 Z= 0.278 Chirality : 0.052 0.120 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.677 13.422 1110 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.33 % Allowed : 22.44 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.010 0.002 PHE H 94 TYR 0.010 0.002 TYR L 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 0.957 Fit side-chains outliers start: 26 outliers final: 18 residues processed: 178 average time/residue: 1.4237 time to fit residues: 265.4361 Evaluate side-chains 174 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 156 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 4 average time/residue: 0.8649 time to fit residues: 4.8528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN F 65 ASN G 65 ASN I 65 ASN L 65 ASN M 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.036 7770 Z= 0.584 Angle : 0.667 10.153 10470 Z= 0.369 Chirality : 0.057 0.174 1380 Planarity : 0.003 0.010 1290 Dihedral : 5.278 16.513 1110 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.08 % Allowed : 22.56 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS A 50 PHE 0.014 0.004 PHE O 94 TYR 0.015 0.002 TYR O 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 0.879 Fit side-chains outliers start: 24 outliers final: 15 residues processed: 195 average time/residue: 1.4096 time to fit residues: 287.8923 Evaluate side-chains 194 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 0.834 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.0694 time to fit residues: 1.5950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN M 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7770 Z= 0.145 Angle : 0.489 8.565 10470 Z= 0.266 Chirality : 0.052 0.122 1380 Planarity : 0.002 0.011 1290 Dihedral : 4.394 13.023 1110 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.95 % Allowed : 23.97 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS P 50 PHE 0.008 0.002 PHE G 94 TYR 0.009 0.001 TYR L 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.934 Fit side-chains outliers start: 23 outliers final: 13 residues processed: 168 average time/residue: 1.4571 time to fit residues: 256.5683 Evaluate side-chains 159 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.0741 time to fit residues: 1.2823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN M 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.105156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087071 restraints weight = 9585.139| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.16 r_work: 0.3246 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.031 7770 Z= 0.506 Angle : 0.642 9.824 10470 Z= 0.352 Chirality : 0.055 0.163 1380 Planarity : 0.003 0.011 1290 Dihedral : 5.109 15.629 1110 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.95 % Allowed : 23.46 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS J 50 PHE 0.014 0.003 PHE O 94 TYR 0.018 0.002 TYR O 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.37 seconds wall clock time: 74 minutes 45.28 seconds (4485.28 seconds total)