Starting phenix.real_space_refine on Tue Feb 13 09:45:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/02_2024/8ade_15361.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/02_2024/8ade_15361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/02_2024/8ade_15361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/02_2024/8ade_15361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/02_2024/8ade_15361.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ade_15361/02_2024/8ade_15361.pdb" } resolution = 2.78 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= 0.002 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 7 5.16 5 C 3255 2.51 5 N 826 2.21 5 O 938 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 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 103": "NH1" <-> "NH2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 103": "NH1" <-> "NH2" Residue "G TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5026 Number of models: 1 Model: "" Number of chains: 7 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 Chain: "G" 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: 2.98, per 1000 atoms: 0.59 Number of scatterers: 5026 At special positions: 0 Unit cell: (68.64, 85.28, 50.96, 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 7 16.00 O 938 8.00 N 826 7.00 C 3255 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: 2.01 Conformation dependent library (CDL) restraints added in 910.1 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 6.253A pdb=" N LEU A 12 " --> pdb=" O MET B 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS B 15 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL A 14 " --> pdb=" O LYS B 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 12 " --> pdb=" O MET C 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS C 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL B 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 12 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS D 15 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 14 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU D 12 " --> pdb=" O MET E 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS E 15 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL D 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU E 12 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N LYS F 15 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL E 14 " --> pdb=" O LYS F 15 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU F 12 " --> pdb=" O MET G 13 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LYS G 15 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL F 14 " --> pdb=" O LYS G 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 removed outlier: 6.802A pdb=" N VAL A 20 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 20 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL C 20 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 20 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL E 20 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL F 20 " --> pdb=" O ARG G 21 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 62 removed outlier: 6.403A pdb=" N THR A 59 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU B 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU A 61 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 59 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU C 62 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU B 61 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 59 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU D 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU C 61 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR D 59 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU E 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU D 61 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR E 59 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU F 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU E 61 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR F 59 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLU G 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU F 61 " --> pdb=" O GLU G 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.474A pdb=" N GLU A 72 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU B 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU C 72 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU D 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU E 72 " --> pdb=" O ILE F 73 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU F 72 " --> pdb=" O ILE G 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80 removed outlier: 7.031A pdb=" N TRP A 79 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS B 80 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TRP B 79 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS C 80 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP C 79 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS D 80 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP D 79 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS E 80 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP E 79 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS F 80 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TRP F 79 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS G 80 " --> pdb=" O TRP F 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 93 through 98 Processing sheet with id=AA9, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AB1, first strand: chain 'A' and resid 109 through 110 removed outlier: 6.486A pdb=" N ALA A 109 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA B 109 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA C 109 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA D 109 " --> pdb=" O LEU E 110 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA E 109 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA F 109 " --> pdb=" O LEU G 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 114 through 115 removed outlier: 6.857A pdb=" N TYR A 114 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR B 114 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR C 114 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR D 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR E 114 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N TYR F 114 " --> pdb=" O SER G 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 122 114 hydrogen bonds defined for protein. 342 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: 1.38 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 902 1.33 - 1.45: 1317 1.45 - 1.57: 2912 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 5145 Sorted by residual: bond pdb=" N ILE A 26 " pdb=" CA ILE A 26 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.40e+01 bond pdb=" N ILE C 26 " pdb=" CA ILE C 26 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.11e-02 8.12e+03 1.40e+01 bond pdb=" N ILE E 26 " pdb=" CA ILE E 26 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.11e-02 8.12e+03 1.37e+01 bond pdb=" N ILE D 26 " pdb=" CA ILE D 26 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.11e-02 8.12e+03 1.36e+01 bond pdb=" N ILE G 26 " pdb=" CA ILE G 26 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.11e-02 8.12e+03 1.36e+01 ... (remaining 5140 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.23: 245 107.23 - 113.99: 2909 113.99 - 120.75: 2320 120.75 - 127.51: 1491 127.51 - 134.26: 35 Bond angle restraints: 7000 Sorted by residual: angle pdb=" C PRO B 24 " pdb=" CA PRO B 24 " pdb=" CB PRO B 24 " ideal model delta sigma weight residual 110.95 104.89 6.06 1.31e+00 5.83e-01 2.14e+01 angle pdb=" C PRO C 24 " pdb=" CA PRO C 24 " pdb=" CB PRO C 24 " ideal model delta sigma weight residual 110.95 104.91 6.04 1.31e+00 5.83e-01 2.13e+01 angle pdb=" C PRO E 24 " pdb=" CA PRO E 24 " pdb=" CB PRO E 24 " ideal model delta sigma weight residual 110.95 104.91 6.04 1.31e+00 5.83e-01 2.13e+01 angle pdb=" C PRO A 24 " pdb=" CA PRO A 24 " pdb=" CB PRO A 24 " ideal model delta sigma weight residual 110.95 104.92 6.03 1.31e+00 5.83e-01 2.12e+01 angle pdb=" C PRO D 24 " pdb=" CA PRO D 24 " pdb=" CB PRO D 24 " ideal model delta sigma weight residual 110.95 104.93 6.02 1.31e+00 5.83e-01 2.11e+01 ... (remaining 6995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.52: 2737 11.52 - 23.03: 238 23.03 - 34.55: 42 34.55 - 46.07: 0 46.07 - 57.58: 14 Dihedral angle restraints: 3031 sinusoidal: 1148 harmonic: 1883 Sorted by residual: dihedral pdb=" C PRO C 24 " pdb=" N PRO C 24 " pdb=" CA PRO C 24 " pdb=" CB PRO C 24 " ideal model delta harmonic sigma weight residual -120.70 -112.66 -8.04 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" C PRO B 24 " pdb=" N PRO B 24 " pdb=" CA PRO B 24 " pdb=" CB PRO B 24 " ideal model delta harmonic sigma weight residual -120.70 -112.66 -8.04 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" C PRO E 24 " pdb=" N PRO E 24 " pdb=" CA PRO E 24 " pdb=" CB PRO E 24 " ideal model delta harmonic sigma weight residual -120.70 -112.67 -8.03 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 3028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 209 0.047 - 0.094: 249 0.094 - 0.141: 203 0.141 - 0.189: 116 0.189 - 0.236: 49 Chirality restraints: 826 Sorted by residual: chirality pdb=" CA ILE F 68 " pdb=" N ILE F 68 " pdb=" C ILE F 68 " pdb=" CB ILE F 68 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA ILE E 68 " pdb=" N ILE E 68 " pdb=" C ILE E 68 " pdb=" CB ILE E 68 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 823 not shown) Planarity restraints: 861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 114 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C TYR C 114 " -0.045 2.00e-02 2.50e+03 pdb=" O TYR C 114 " 0.017 2.00e-02 2.50e+03 pdb=" N SER C 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 114 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C TYR A 114 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR A 114 " 0.017 2.00e-02 2.50e+03 pdb=" N SER A 115 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR E 114 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C TYR E 114 " -0.044 2.00e-02 2.50e+03 pdb=" O TYR E 114 " 0.017 2.00e-02 2.50e+03 pdb=" N SER E 115 " 0.015 2.00e-02 2.50e+03 ... (remaining 858 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 406 2.75 - 3.29: 5005 3.29 - 3.82: 8088 3.82 - 4.36: 11472 4.36 - 4.90: 20635 Nonbonded interactions: 45606 Sorted by model distance: nonbonded pdb=" O SER A 117 " pdb=" OG SER B 117 " model vdw 2.213 2.440 nonbonded pdb=" O SER D 117 " pdb=" OG SER E 117 " model vdw 2.213 2.440 nonbonded pdb=" O SER C 117 " pdb=" OG SER D 117 " model vdw 2.213 2.440 nonbonded pdb=" O SER B 117 " pdb=" OG SER C 117 " model vdw 2.213 2.440 nonbonded pdb=" O SER F 117 " pdb=" OG SER G 117 " model vdw 2.213 2.440 ... (remaining 45601 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' } 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: 5.250 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: 0.010 Extract box with map and model: 5.480 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.930 Find NCS groups from input model: 0.330 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: 0.010 Load rotamer database and sin/cos tables:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 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 : 0.012 0.042 5145 Z= 0.832 Angle : 1.581 7.283 7000 Z= 1.154 Chirality : 0.107 0.236 826 Planarity : 0.005 0.026 861 Dihedral : 9.637 57.583 1813 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -4.12 (0.23), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.18), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP E 79 HIS 0.003 0.001 HIS B 90 PHE 0.004 0.001 PHE G 33 TYR 0.006 0.001 TYR C 116 ARG 0.002 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 THR cc_start: 0.8874 (m) cc_final: 0.8558 (p) REVERT: C 123 THR cc_start: 0.7245 (t) cc_final: 0.6610 (p) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 1.1401 time to fit residues: 213.2977 Evaluate side-chains 132 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 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 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5145 Z= 0.357 Angle : 0.685 6.644 7000 Z= 0.359 Chirality : 0.051 0.157 826 Planarity : 0.005 0.044 861 Dihedral : 5.258 16.794 693 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.66 % Allowed : 17.22 % Favored : 79.12 % 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: -3.16 (0.25), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.19), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 79 HIS 0.002 0.001 HIS B 31 PHE 0.014 0.002 PHE B 33 TYR 0.017 0.002 TYR E 114 ARG 0.009 0.001 ARG D 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8182 (p) REVERT: B 92 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7376 (tm-30) REVERT: B 99 ASP cc_start: 0.6818 (t0) cc_final: 0.6529 (t0) REVERT: B 104 ARG cc_start: 0.7795 (ttp-110) cc_final: 0.7110 (ttm110) REVERT: C 92 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: D 34 ARG cc_start: 0.8188 (tpt-90) cc_final: 0.7942 (ttt90) REVERT: D 92 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7393 (tm-30) REVERT: E 21 ARG cc_start: 0.8307 (mmm160) cc_final: 0.7913 (tpp80) REVERT: E 35 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8268 (ttmm) REVERT: F 13 MET cc_start: 0.7565 (tmt) cc_final: 0.7347 (tmt) REVERT: F 34 ARG cc_start: 0.8042 (tpt-90) cc_final: 0.7679 (ttt90) REVERT: G 13 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7219 (tmt) outliers start: 20 outliers final: 3 residues processed: 141 average time/residue: 1.5298 time to fit residues: 222.1527 Evaluate side-chains 117 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 5145 Z= 0.368 Angle : 0.653 7.150 7000 Z= 0.343 Chirality : 0.049 0.167 826 Planarity : 0.005 0.044 861 Dihedral : 5.245 16.360 693 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.48 % Allowed : 19.60 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.26), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 79 HIS 0.002 0.001 HIS D 88 PHE 0.010 0.002 PHE B 33 TYR 0.015 0.002 TYR F 114 ARG 0.008 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: B 92 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: B 99 ASP cc_start: 0.6745 (t0) cc_final: 0.5725 (t0) REVERT: B 104 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7299 (ttm110) REVERT: C 92 GLU cc_start: 0.8065 (pt0) cc_final: 0.7724 (tm-30) REVERT: C 99 ASP cc_start: 0.6971 (t70) cc_final: 0.6661 (p0) REVERT: D 92 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 13 MET cc_start: 0.7599 (tmt) cc_final: 0.6766 (tmt) REVERT: E 26 ILE cc_start: 0.8624 (pt) cc_final: 0.8415 (mt) REVERT: E 35 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8217 (ttmm) REVERT: F 13 MET cc_start: 0.7557 (tmt) cc_final: 0.7330 (tmt) REVERT: F 21 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7822 (tpp80) REVERT: F 35 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7955 (ttmt) REVERT: G 13 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.7251 (tmt) REVERT: G 80 LYS cc_start: 0.8179 (tttt) cc_final: 0.7883 (tttm) outliers start: 19 outliers final: 9 residues processed: 125 average time/residue: 1.6217 time to fit residues: 208.5599 Evaluate side-chains 120 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5145 Z= 0.343 Angle : 0.623 6.477 7000 Z= 0.326 Chirality : 0.049 0.138 826 Planarity : 0.005 0.051 861 Dihedral : 5.197 16.686 693 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.03 % Allowed : 20.70 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.26), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.20), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 79 HIS 0.002 0.001 HIS A 88 PHE 0.007 0.002 PHE B 33 TYR 0.013 0.002 TYR C 114 ARG 0.007 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: B 92 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: B 104 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7359 (ttm110) REVERT: C 92 GLU cc_start: 0.8073 (pt0) cc_final: 0.7773 (tm-30) REVERT: D 13 MET cc_start: 0.7229 (tmt) cc_final: 0.7019 (tpt) REVERT: D 92 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7512 (tm-30) REVERT: E 13 MET cc_start: 0.7520 (tmt) cc_final: 0.6770 (tmt) REVERT: E 35 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8280 (tttt) REVERT: F 13 MET cc_start: 0.7558 (tmt) cc_final: 0.7201 (tpt) REVERT: F 21 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7837 (tpp80) REVERT: F 35 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8102 (ttmt) REVERT: F 76 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7722 (mptt) REVERT: G 13 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7268 (tmt) REVERT: G 80 LYS cc_start: 0.8181 (tttt) cc_final: 0.7861 (tttm) outliers start: 22 outliers final: 9 residues processed: 122 average time/residue: 1.5998 time to fit residues: 200.7732 Evaluate side-chains 122 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 MET Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5145 Z= 0.289 Angle : 0.598 5.867 7000 Z= 0.313 Chirality : 0.048 0.150 826 Planarity : 0.004 0.052 861 Dihedral : 5.094 16.732 693 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.30 % Allowed : 21.61 % Favored : 75.09 % 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: -2.78 (0.27), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 79 HIS 0.002 0.001 HIS D 88 PHE 0.007 0.002 PHE E 64 TYR 0.014 0.002 TYR C 114 ARG 0.008 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: B 92 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: B 104 ARG cc_start: 0.7826 (ttp-110) cc_final: 0.7368 (ttm110) REVERT: C 92 GLU cc_start: 0.8030 (pt0) cc_final: 0.7754 (tm-30) REVERT: D 13 MET cc_start: 0.7299 (tmt) cc_final: 0.7052 (tpt) REVERT: D 58 LEU cc_start: 0.8670 (mt) cc_final: 0.8412 (mt) REVERT: D 92 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7529 (tm-30) REVERT: E 13 MET cc_start: 0.7473 (tmt) cc_final: 0.6751 (tmt) REVERT: E 35 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8277 (tttt) REVERT: F 13 MET cc_start: 0.7600 (tmt) cc_final: 0.7236 (tpt) REVERT: F 21 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7813 (tpp80) REVERT: G 13 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7177 (tmt) REVERT: G 34 ARG cc_start: 0.8171 (tpt-90) cc_final: 0.7906 (tpt-90) REVERT: G 80 LYS cc_start: 0.8129 (tttt) cc_final: 0.7829 (tttm) outliers start: 18 outliers final: 7 residues processed: 120 average time/residue: 1.7261 time to fit residues: 212.9817 Evaluate side-chains 118 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 76 LYS Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5145 Z= 0.337 Angle : 0.606 5.490 7000 Z= 0.319 Chirality : 0.048 0.128 826 Planarity : 0.004 0.054 861 Dihedral : 5.153 17.772 693 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.85 % Allowed : 22.16 % Favored : 73.99 % 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: -2.63 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 79 HIS 0.004 0.001 HIS F 90 PHE 0.007 0.002 PHE E 64 TYR 0.013 0.002 TYR C 114 ARG 0.010 0.001 ARG F 104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 92 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: B 104 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7361 (ttm110) REVERT: C 92 GLU cc_start: 0.7939 (pt0) cc_final: 0.7730 (tm-30) REVERT: D 13 MET cc_start: 0.7317 (tmt) cc_final: 0.7047 (tpt) REVERT: D 92 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7682 (tm-30) REVERT: E 13 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6756 (tmt) REVERT: E 35 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8244 (tttt) REVERT: F 13 MET cc_start: 0.7594 (tmt) cc_final: 0.7175 (tpt) REVERT: F 21 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.7824 (tpp80) REVERT: G 13 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7191 (tmt) REVERT: G 34 ARG cc_start: 0.8190 (tpt-90) cc_final: 0.7930 (tpt-90) REVERT: G 80 LYS cc_start: 0.8137 (tttt) cc_final: 0.7843 (tttm) outliers start: 21 outliers final: 8 residues processed: 123 average time/residue: 1.7572 time to fit residues: 222.1631 Evaluate side-chains 120 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5145 Z= 0.359 Angle : 0.623 6.105 7000 Z= 0.328 Chirality : 0.049 0.134 826 Planarity : 0.004 0.039 861 Dihedral : 5.205 18.168 693 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.03 % Allowed : 22.34 % Favored : 73.63 % 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: -2.56 (0.28), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 79 HIS 0.002 0.001 HIS D 88 PHE 0.007 0.001 PHE E 64 TYR 0.012 0.002 TYR C 114 ARG 0.010 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: B 92 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: B 104 ARG cc_start: 0.7844 (ttp-110) cc_final: 0.7348 (ttm110) REVERT: C 92 GLU cc_start: 0.8075 (pt0) cc_final: 0.7764 (tm-30) REVERT: D 13 MET cc_start: 0.7336 (tmt) cc_final: 0.7059 (tpt) REVERT: D 92 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7691 (tm-30) REVERT: E 13 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6782 (tmt) REVERT: E 35 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8083 (ttmm) REVERT: F 13 MET cc_start: 0.7596 (tmt) cc_final: 0.7192 (tpt) REVERT: F 21 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7800 (tpp80) REVERT: F 35 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7902 (ttmt) REVERT: G 13 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7289 (tmt) REVERT: G 34 ARG cc_start: 0.8201 (tpt-90) cc_final: 0.7943 (tpt-90) REVERT: G 80 LYS cc_start: 0.8150 (tttt) cc_final: 0.7863 (tttm) outliers start: 22 outliers final: 10 residues processed: 126 average time/residue: 1.6425 time to fit residues: 212.8721 Evaluate side-chains 126 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5145 Z= 0.352 Angle : 0.622 6.514 7000 Z= 0.327 Chirality : 0.050 0.156 826 Planarity : 0.004 0.039 861 Dihedral : 5.219 17.972 693 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.03 % Allowed : 22.34 % Favored : 73.63 % 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: -2.51 (0.29), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 79 HIS 0.002 0.001 HIS C 88 PHE 0.007 0.001 PHE E 64 TYR 0.013 0.002 TYR C 114 ARG 0.009 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7819 (tm-30) REVERT: B 92 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: B 104 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7349 (ttm110) REVERT: C 92 GLU cc_start: 0.7952 (pt0) cc_final: 0.7741 (tm-30) REVERT: D 13 MET cc_start: 0.7381 (tmt) cc_final: 0.7077 (tpt) REVERT: D 21 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.6602 (tmm-80) REVERT: D 92 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7661 (tm-30) REVERT: E 13 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.6820 (tmt) REVERT: E 35 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8068 (ttmm) REVERT: F 13 MET cc_start: 0.7599 (tmt) cc_final: 0.7129 (tpt) REVERT: F 21 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7786 (tpp80) REVERT: G 13 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7205 (tmt) REVERT: G 80 LYS cc_start: 0.8163 (tttt) cc_final: 0.7876 (tttm) outliers start: 22 outliers final: 9 residues processed: 120 average time/residue: 1.7308 time to fit residues: 213.4200 Evaluate side-chains 121 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5145 Z= 0.317 Angle : 0.625 7.044 7000 Z= 0.327 Chirality : 0.049 0.170 826 Planarity : 0.004 0.047 861 Dihedral : 5.174 17.112 693 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.66 % Allowed : 23.26 % 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: -2.50 (0.29), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 79 HIS 0.001 0.000 HIS A 31 PHE 0.007 0.001 PHE E 64 TYR 0.013 0.002 TYR C 114 ARG 0.014 0.001 ARG E 104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 92 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: B 104 ARG cc_start: 0.7853 (ttp-110) cc_final: 0.7366 (ttm110) REVERT: C 84 ILE cc_start: 0.8472 (mm) cc_final: 0.8266 (mm) REVERT: C 92 GLU cc_start: 0.7946 (pt0) cc_final: 0.7737 (tm-30) REVERT: D 13 MET cc_start: 0.7433 (tmt) cc_final: 0.7140 (tpt) REVERT: D 21 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.6633 (tmm-80) REVERT: D 26 ILE cc_start: 0.8689 (pt) cc_final: 0.8474 (mt) REVERT: D 92 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7738 (tm-30) REVERT: E 13 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6793 (tmt) REVERT: E 35 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8085 (ttmm) REVERT: F 13 MET cc_start: 0.7590 (tmt) cc_final: 0.7207 (tpt) REVERT: F 21 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7784 (tpp80) REVERT: F 35 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7919 (ttmt) REVERT: F 92 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7537 (tm-30) REVERT: G 13 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7225 (tmt) REVERT: G 80 LYS cc_start: 0.8115 (tttt) cc_final: 0.7840 (tttm) outliers start: 20 outliers final: 10 residues processed: 118 average time/residue: 1.7160 time to fit residues: 208.1823 Evaluate side-chains 123 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5145 Z= 0.324 Angle : 0.628 7.438 7000 Z= 0.327 Chirality : 0.049 0.185 826 Planarity : 0.004 0.044 861 Dihedral : 5.182 17.795 693 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.48 % Allowed : 23.44 % 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: -2.47 (0.29), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 79 HIS 0.002 0.001 HIS A 88 PHE 0.007 0.001 PHE E 64 TYR 0.013 0.002 TYR C 114 ARG 0.014 0.001 ARG E 104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7624 (tm-30) REVERT: B 92 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: B 104 ARG cc_start: 0.7889 (ttp-110) cc_final: 0.7307 (ttm110) REVERT: C 84 ILE cc_start: 0.8462 (mm) cc_final: 0.8254 (mm) REVERT: C 92 GLU cc_start: 0.7946 (pt0) cc_final: 0.7742 (tm-30) REVERT: D 13 MET cc_start: 0.7437 (tmt) cc_final: 0.7144 (tpt) REVERT: D 21 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.6651 (tmm-80) REVERT: D 92 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7746 (tm-30) REVERT: E 13 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6796 (tmt) REVERT: E 35 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8036 (ttmm) REVERT: F 13 MET cc_start: 0.7588 (tmt) cc_final: 0.7201 (tpt) REVERT: F 21 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7787 (tpp80) REVERT: F 35 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7843 (ttmt) REVERT: F 104 ARG cc_start: 0.7949 (ttp-110) cc_final: 0.7635 (ttm110) REVERT: G 13 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7265 (tmt) REVERT: G 80 LYS cc_start: 0.8120 (tttt) cc_final: 0.7845 (tttm) outliers start: 19 outliers final: 10 residues processed: 118 average time/residue: 1.6166 time to fit residues: 196.3038 Evaluate side-chains 123 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 13 MET Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain C residue 104 ARG Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain G residue 13 MET Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.0670 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.149000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.124290 restraints weight = 5681.667| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.51 r_work: 0.3866 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5145 Z= 0.360 Angle : 0.641 8.041 7000 Z= 0.335 Chirality : 0.050 0.147 826 Planarity : 0.004 0.040 861 Dihedral : 5.262 19.867 693 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.66 % Allowed : 23.26 % 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: -2.46 (0.29), residues: 616 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 79 HIS 0.002 0.001 HIS A 88 PHE 0.007 0.001 PHE E 64 TYR 0.012 0.002 TYR C 114 ARG 0.014 0.001 ARG E 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3484.79 seconds wall clock time: 61 minutes 50.60 seconds (3710.60 seconds total)