Starting phenix.real_space_refine on Thu Jan 18 18:54:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/01_2024/7z23_14456.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/01_2024/7z23_14456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/01_2024/7z23_14456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/01_2024/7z23_14456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/01_2024/7z23_14456.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/01_2024/7z23_14456.pdb" } resolution = 3.98 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= 0.001 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 48 5.16 5 C 6198 2.51 5 N 1446 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 42": "OE1" <-> "OE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9246 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Time building chain proxies: 6.47, per 1000 atoms: 0.70 Number of scatterers: 9246 At special positions: 0 Unit cell: (101.37, 105.294, 86.328, 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 48 16.00 O 1554 8.00 N 1446 7.00 C 6198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 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: 3.92 Conformation dependent library (CDL) restraints added in 1.8 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 77.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'E' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 103 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 178 Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'A' and resid 3 through 15 removed outlier: 4.298A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 103 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 178 Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 15 removed outlier: 4.298A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 178 Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 103 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 178 Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 103 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 178 Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 103 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 178 Processing helix chain 'F' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'E' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE E 199 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 199 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 199 " --> pdb=" O ARG B 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 199 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 199 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE F 199 " --> pdb=" O ARG F 53 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 2034 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: 2.50 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2676 1.34 - 1.46: 2079 1.46 - 1.58: 4689 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 9504 Sorted by residual: bond pdb=" C VAL D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 bond pdb=" C VAL E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.68e+00 bond pdb=" C ASP C 190 " pdb=" N PRO C 191 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.19e-02 7.06e+03 3.58e+00 bond pdb=" C VAL C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.54e+00 bond pdb=" C VAL F 87 " pdb=" N PRO F 88 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.50e+00 ... (remaining 9499 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.74: 204 106.74 - 113.56: 5156 113.56 - 120.39: 3823 120.39 - 127.21: 3602 127.21 - 134.04: 115 Bond angle restraints: 12900 Sorted by residual: angle pdb=" N ARG D 76 " pdb=" CA ARG D 76 " pdb=" C ARG D 76 " ideal model delta sigma weight residual 111.36 107.02 4.34 1.09e+00 8.42e-01 1.59e+01 angle pdb=" N ARG B 76 " pdb=" CA ARG B 76 " pdb=" C ARG B 76 " ideal model delta sigma weight residual 111.36 107.05 4.31 1.09e+00 8.42e-01 1.56e+01 angle pdb=" N ARG A 76 " pdb=" CA ARG A 76 " pdb=" C ARG A 76 " ideal model delta sigma weight residual 111.36 107.06 4.30 1.09e+00 8.42e-01 1.56e+01 angle pdb=" N ARG E 76 " pdb=" CA ARG E 76 " pdb=" C ARG E 76 " ideal model delta sigma weight residual 111.36 107.06 4.30 1.09e+00 8.42e-01 1.55e+01 angle pdb=" N ARG C 76 " pdb=" CA ARG C 76 " pdb=" C ARG C 76 " ideal model delta sigma weight residual 111.36 107.07 4.29 1.09e+00 8.42e-01 1.55e+01 ... (remaining 12895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4824 15.94 - 31.87: 564 31.87 - 47.81: 114 47.81 - 63.75: 18 63.75 - 79.68: 12 Dihedral angle restraints: 5532 sinusoidal: 2196 harmonic: 3336 Sorted by residual: dihedral pdb=" CB CYS A 61 " pdb=" SG CYS A 61 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 35.11 57.89 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS D 61 " pdb=" SG CYS D 61 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual 93.00 35.13 57.87 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CB CYS B 61 " pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual 93.00 35.13 57.87 1 1.00e+01 1.00e-02 4.49e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1168 0.049 - 0.097: 236 0.097 - 0.146: 57 0.146 - 0.194: 4 0.194 - 0.243: 11 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA TRP C 78 " pdb=" N TRP C 78 " pdb=" C TRP C 78 " pdb=" CB TRP C 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TRP F 78 " pdb=" N TRP F 78 " pdb=" C TRP F 78 " pdb=" CB TRP F 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TRP D 78 " pdb=" N TRP D 78 " pdb=" C TRP D 78 " pdb=" CB TRP D 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1473 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 212 " 0.020 2.00e-02 2.50e+03 1.93e-02 6.51e+00 pdb=" CG PHE C 212 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 212 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 212 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 212 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 212 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 212 " 0.021 2.00e-02 2.50e+03 1.93e-02 6.49e+00 pdb=" CG PHE B 212 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 212 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 212 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 212 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 212 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 212 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 212 " -0.021 2.00e-02 2.50e+03 1.92e-02 6.44e+00 pdb=" CG PHE D 212 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE D 212 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 212 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 212 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 212 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 212 " -0.002 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2502 2.80 - 3.33: 10130 3.33 - 3.85: 15635 3.85 - 4.38: 16709 4.38 - 4.90: 27744 Nonbonded interactions: 72720 Sorted by model distance: nonbonded pdb=" NH1 ARG B 76 " pdb=" O ALA C 40 " model vdw 2.280 2.520 nonbonded pdb=" NH1 ARG E 76 " pdb=" O ALA A 40 " model vdw 2.283 2.520 nonbonded pdb=" O SER B 86 " pdb=" OG1 THR B 89 " model vdw 2.283 2.440 nonbonded pdb=" O SER F 86 " pdb=" OG1 THR F 89 " model vdw 2.284 2.440 nonbonded pdb=" O SER D 86 " pdb=" OG1 THR D 89 " model vdw 2.284 2.440 ... (remaining 72715 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.580 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: 12.150 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 29.400 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 0.033 9504 Z= 0.224 Angle : 0.922 7.456 12900 Z= 0.559 Chirality : 0.047 0.243 1476 Planarity : 0.006 0.055 1548 Dihedral : 14.001 79.684 3318 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1110 helix: 0.28 (0.18), residues: 864 sheet: 0.15 (0.69), residues: 60 loop : -2.31 (0.36), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 174 HIS 0.009 0.002 HIS B 74 PHE 0.045 0.003 PHE C 212 TYR 0.009 0.001 TYR E 66 ARG 0.004 0.001 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 MET cc_start: 0.9292 (mpp) cc_final: 0.9054 (mpp) REVERT: E 224 ASN cc_start: 0.9358 (p0) cc_final: 0.8822 (p0) REVERT: A 100 MET cc_start: 0.9243 (mpp) cc_final: 0.8991 (mpp) REVERT: A 166 GLU cc_start: 0.9379 (mt-10) cc_final: 0.9157 (pt0) REVERT: A 224 ASN cc_start: 0.9365 (p0) cc_final: 0.8832 (p0) REVERT: B 100 MET cc_start: 0.9155 (mpp) cc_final: 0.8934 (mpp) REVERT: B 224 ASN cc_start: 0.9298 (p0) cc_final: 0.8725 (p0) REVERT: C 100 MET cc_start: 0.9306 (mpp) cc_final: 0.9042 (mpp) REVERT: C 224 ASN cc_start: 0.9348 (p0) cc_final: 0.8789 (p0) REVERT: D 66 TYR cc_start: 0.8846 (t80) cc_final: 0.8616 (t80) REVERT: D 100 MET cc_start: 0.9146 (mpp) cc_final: 0.8936 (mpp) REVERT: D 224 ASN cc_start: 0.9307 (p0) cc_final: 0.8771 (p0) REVERT: F 100 MET cc_start: 0.9263 (mpp) cc_final: 0.8983 (mpp) REVERT: F 166 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9161 (pt0) REVERT: F 224 ASN cc_start: 0.9358 (p0) cc_final: 0.8805 (p0) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2669 time to fit residues: 116.1693 Evaluate side-chains 251 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 0.0770 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9504 Z= 0.218 Angle : 0.809 9.618 12900 Z= 0.409 Chirality : 0.045 0.197 1476 Planarity : 0.005 0.044 1548 Dihedral : 4.517 14.664 1218 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.88 % Allowed : 13.53 % Favored : 85.59 % 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: 0.05 (0.24), residues: 1110 helix: 0.53 (0.17), residues: 870 sheet: 0.81 (0.62), residues: 60 loop : -2.31 (0.36), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 78 HIS 0.003 0.001 HIS B 74 PHE 0.045 0.002 PHE E 212 TYR 0.018 0.002 TYR A 66 ARG 0.004 0.001 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 297 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 HIS cc_start: 0.9289 (m-70) cc_final: 0.8874 (m-70) REVERT: E 102 LYS cc_start: 0.9412 (pttm) cc_final: 0.8702 (pttm) REVERT: E 173 GLN cc_start: 0.9579 (tp-100) cc_final: 0.9371 (tp-100) REVERT: E 202 ARG cc_start: 0.8235 (tpt170) cc_final: 0.7976 (mtm180) REVERT: A 74 HIS cc_start: 0.9220 (m-70) cc_final: 0.8803 (m-70) REVERT: A 102 LYS cc_start: 0.9367 (pttm) cc_final: 0.8626 (pttm) REVERT: A 105 LYS cc_start: 0.6530 (mmmt) cc_final: 0.5675 (mmmt) REVERT: A 166 GLU cc_start: 0.9340 (mt-10) cc_final: 0.9093 (pt0) REVERT: A 202 ARG cc_start: 0.8382 (mmp-170) cc_final: 0.7950 (mtm180) REVERT: A 206 LYS cc_start: 0.9291 (ptpt) cc_final: 0.8641 (mttm) REVERT: A 209 PHE cc_start: 0.9650 (m-10) cc_final: 0.9386 (m-80) REVERT: A 224 ASN cc_start: 0.9325 (p0) cc_final: 0.8958 (p0) REVERT: B 74 HIS cc_start: 0.9257 (m-70) cc_final: 0.9030 (m-70) REVERT: B 102 LYS cc_start: 0.9308 (pttm) cc_final: 0.8604 (pttm) REVERT: B 166 GLU cc_start: 0.8870 (pt0) cc_final: 0.8618 (pt0) REVERT: B 173 GLN cc_start: 0.9492 (tp-100) cc_final: 0.9231 (tp-100) REVERT: B 206 LYS cc_start: 0.9277 (ptpp) cc_final: 0.9029 (mttp) REVERT: B 209 PHE cc_start: 0.9717 (m-10) cc_final: 0.9427 (m-80) REVERT: C 74 HIS cc_start: 0.9225 (m-70) cc_final: 0.8824 (m-70) REVERT: C 102 LYS cc_start: 0.9399 (pttm) cc_final: 0.8722 (pttm) REVERT: C 104 GLU cc_start: 0.8211 (tp30) cc_final: 0.7931 (tm-30) REVERT: C 105 LYS cc_start: 0.6575 (mmmt) cc_final: 0.5798 (mmmt) REVERT: C 166 GLU cc_start: 0.8771 (pt0) cc_final: 0.8540 (pt0) REVERT: C 173 GLN cc_start: 0.9563 (tp-100) cc_final: 0.9348 (tp-100) REVERT: C 202 ARG cc_start: 0.8284 (mmp-170) cc_final: 0.7838 (mtm180) REVERT: C 206 LYS cc_start: 0.9325 (ptpp) cc_final: 0.9008 (mttp) REVERT: C 209 PHE cc_start: 0.9704 (m-10) cc_final: 0.9415 (m-80) REVERT: D 74 HIS cc_start: 0.9257 (m-70) cc_final: 0.9038 (m-70) REVERT: D 102 LYS cc_start: 0.9292 (pttm) cc_final: 0.8566 (pttm) REVERT: D 166 GLU cc_start: 0.8873 (pt0) cc_final: 0.8620 (pt0) REVERT: D 173 GLN cc_start: 0.9527 (tp-100) cc_final: 0.9321 (tp-100) REVERT: D 202 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8118 (mtm180) REVERT: D 206 LYS cc_start: 0.9382 (ptpp) cc_final: 0.9039 (mttp) REVERT: D 209 PHE cc_start: 0.9733 (m-10) cc_final: 0.9434 (m-80) REVERT: F 74 HIS cc_start: 0.9248 (m-70) cc_final: 0.8836 (m-70) REVERT: F 102 LYS cc_start: 0.9399 (pttm) cc_final: 0.8698 (pttm) REVERT: F 104 GLU cc_start: 0.8059 (tp30) cc_final: 0.7806 (tm-30) REVERT: F 105 LYS cc_start: 0.6503 (mmmt) cc_final: 0.5652 (mmmt) REVERT: F 166 GLU cc_start: 0.9331 (mt-10) cc_final: 0.9096 (pt0) REVERT: F 202 ARG cc_start: 0.8459 (mmp-170) cc_final: 0.8085 (mtp-110) REVERT: F 206 LYS cc_start: 0.9258 (ptpt) cc_final: 0.8568 (mttm) REVERT: F 209 PHE cc_start: 0.9608 (m-10) cc_final: 0.9368 (m-80) REVERT: F 224 ASN cc_start: 0.9307 (p0) cc_final: 0.8924 (p0) outliers start: 9 outliers final: 6 residues processed: 299 average time/residue: 0.2726 time to fit residues: 104.5065 Evaluate side-chains 270 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 263 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN A 63 ASN A 95 HIS B 63 ASN B 95 HIS ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 95 HIS C 173 GLN D 63 ASN D 95 HIS D 173 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9504 Z= 0.213 Angle : 0.767 10.993 12900 Z= 0.389 Chirality : 0.045 0.285 1476 Planarity : 0.005 0.046 1548 Dihedral : 4.244 15.506 1218 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.76 % Allowed : 16.67 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1110 helix: 0.86 (0.17), residues: 870 sheet: 0.88 (0.61), residues: 60 loop : -2.19 (0.36), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 78 HIS 0.002 0.001 HIS C 74 PHE 0.044 0.002 PHE E 212 TYR 0.017 0.002 TYR F 155 ARG 0.007 0.001 ARG E 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 74 HIS cc_start: 0.9255 (m-70) cc_final: 0.8821 (m-70) REVERT: E 173 GLN cc_start: 0.9599 (tp40) cc_final: 0.9392 (tp-100) REVERT: A 23 LYS cc_start: 0.9015 (tptp) cc_final: 0.8754 (tptp) REVERT: A 74 HIS cc_start: 0.9228 (m-70) cc_final: 0.8783 (m-70) REVERT: A 78 TRP cc_start: 0.8647 (m-90) cc_final: 0.8119 (m-90) REVERT: A 92 TYR cc_start: 0.8406 (t80) cc_final: 0.8120 (t80) REVERT: A 162 LYS cc_start: 0.9676 (ttmm) cc_final: 0.9369 (ptpp) REVERT: A 206 LYS cc_start: 0.9284 (ptpt) cc_final: 0.8897 (mttp) REVERT: A 209 PHE cc_start: 0.9630 (m-10) cc_final: 0.9336 (m-80) REVERT: B 13 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9256 (mmmt) REVERT: B 74 HIS cc_start: 0.9281 (m-70) cc_final: 0.8997 (m-70) REVERT: B 173 GLN cc_start: 0.9502 (tp-100) cc_final: 0.9244 (tp-100) REVERT: B 206 LYS cc_start: 0.9313 (ptpp) cc_final: 0.9004 (mttp) REVERT: B 209 PHE cc_start: 0.9647 (m-10) cc_final: 0.9346 (m-80) REVERT: C 74 HIS cc_start: 0.9199 (m-70) cc_final: 0.8802 (m-70) REVERT: C 173 GLN cc_start: 0.9587 (tp40) cc_final: 0.9379 (tp-100) REVERT: C 206 LYS cc_start: 0.9321 (ptpp) cc_final: 0.8998 (mttp) REVERT: C 209 PHE cc_start: 0.9699 (m-10) cc_final: 0.9415 (m-80) REVERT: D 13 LYS cc_start: 0.9480 (mmmt) cc_final: 0.9250 (mmmt) REVERT: D 74 HIS cc_start: 0.9300 (m-70) cc_final: 0.9022 (m-70) REVERT: D 173 GLN cc_start: 0.9553 (tp40) cc_final: 0.9297 (tp-100) REVERT: D 202 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7715 (mtp-110) REVERT: D 206 LYS cc_start: 0.9348 (ptpp) cc_final: 0.9039 (mttp) REVERT: D 209 PHE cc_start: 0.9668 (m-10) cc_final: 0.9343 (m-80) REVERT: F 23 LYS cc_start: 0.9022 (tptp) cc_final: 0.8776 (tptp) REVERT: F 74 HIS cc_start: 0.9276 (m-70) cc_final: 0.8843 (m-70) REVERT: F 78 TRP cc_start: 0.8670 (m-90) cc_final: 0.8157 (m-90) REVERT: F 92 TYR cc_start: 0.8391 (t80) cc_final: 0.8112 (t80) REVERT: F 166 GLU cc_start: 0.9324 (mt-10) cc_final: 0.9034 (mt-10) REVERT: F 202 ARG cc_start: 0.8377 (mmp-170) cc_final: 0.7921 (mtp-110) REVERT: F 206 LYS cc_start: 0.9253 (ptpt) cc_final: 0.8873 (mttp) REVERT: F 209 PHE cc_start: 0.9582 (m-10) cc_final: 0.9301 (m-80) REVERT: F 224 ASN cc_start: 0.9297 (p0) cc_final: 0.9068 (p0) outliers start: 18 outliers final: 11 residues processed: 272 average time/residue: 0.2453 time to fit residues: 87.7246 Evaluate side-chains 264 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 252 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 103 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 ASN E 95 HIS ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9504 Z= 0.302 Angle : 0.761 11.650 12900 Z= 0.410 Chirality : 0.043 0.191 1476 Planarity : 0.005 0.045 1548 Dihedral : 4.388 15.689 1218 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.25 % Allowed : 18.04 % Favored : 79.71 % 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: 0.73 (0.24), residues: 1110 helix: 0.98 (0.16), residues: 870 sheet: 1.33 (0.66), residues: 60 loop : -2.05 (0.37), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP C 78 HIS 0.004 0.001 HIS C 74 PHE 0.039 0.002 PHE A 212 TYR 0.022 0.002 TYR D 155 ARG 0.006 0.001 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 283 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8416 (m-80) cc_final: 0.7756 (m-10) REVERT: E 42 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8380 (mt-10) REVERT: E 63 ASN cc_start: 0.9387 (OUTLIER) cc_final: 0.8953 (t0) REVERT: E 173 GLN cc_start: 0.9607 (tp40) cc_final: 0.9398 (tp-100) REVERT: E 200 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9078 (tp) REVERT: E 227 GLU cc_start: 0.9753 (mm-30) cc_final: 0.9472 (mm-30) REVERT: A 17 TYR cc_start: 0.8422 (m-80) cc_final: 0.7793 (m-10) REVERT: A 23 LYS cc_start: 0.9156 (tptp) cc_final: 0.8874 (tptp) REVERT: A 37 LEU cc_start: 0.9557 (pp) cc_final: 0.9145 (pp) REVERT: A 42 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8426 (mt-10) REVERT: A 74 HIS cc_start: 0.9322 (m-70) cc_final: 0.8966 (m90) REVERT: A 92 TYR cc_start: 0.8634 (t80) cc_final: 0.8412 (t80) REVERT: A 190 ASP cc_start: 0.9163 (t0) cc_final: 0.8866 (p0) REVERT: A 202 ARG cc_start: 0.8875 (mtp-110) cc_final: 0.8478 (mmp-170) REVERT: A 206 LYS cc_start: 0.9378 (ptpt) cc_final: 0.9027 (mttp) REVERT: A 209 PHE cc_start: 0.9564 (m-10) cc_final: 0.9299 (m-80) REVERT: A 227 GLU cc_start: 0.9711 (mm-30) cc_final: 0.9396 (mm-30) REVERT: B 17 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7170 (t80) REVERT: B 42 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8429 (mt-10) REVERT: B 74 HIS cc_start: 0.9321 (m-70) cc_final: 0.8981 (m-70) REVERT: B 173 GLN cc_start: 0.9545 (tp-100) cc_final: 0.9259 (tp-100) REVERT: B 202 ARG cc_start: 0.8728 (mtm180) cc_final: 0.8511 (mmp-170) REVERT: B 205 GLU cc_start: 0.8181 (mp0) cc_final: 0.7956 (mp0) REVERT: B 206 LYS cc_start: 0.9409 (ptpp) cc_final: 0.9089 (mttp) REVERT: B 209 PHE cc_start: 0.9635 (m-10) cc_final: 0.9329 (m-80) REVERT: B 227 GLU cc_start: 0.9654 (mm-30) cc_final: 0.9347 (mm-30) REVERT: C 17 TYR cc_start: 0.8382 (m-80) cc_final: 0.7735 (m-10) REVERT: C 42 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8411 (mt-10) REVERT: C 173 GLN cc_start: 0.9581 (tp40) cc_final: 0.9360 (tp-100) REVERT: C 200 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9144 (tp) REVERT: C 202 ARG cc_start: 0.8870 (mtp-110) cc_final: 0.8476 (mtm-85) REVERT: C 206 LYS cc_start: 0.9410 (ptpp) cc_final: 0.9090 (mttp) REVERT: C 209 PHE cc_start: 0.9625 (m-10) cc_final: 0.9340 (m-80) REVERT: C 227 GLU cc_start: 0.9769 (mm-30) cc_final: 0.9485 (mm-30) REVERT: D 74 HIS cc_start: 0.9327 (m-70) cc_final: 0.8997 (m-70) REVERT: D 173 GLN cc_start: 0.9563 (tp40) cc_final: 0.9288 (tp-100) REVERT: D 190 ASP cc_start: 0.9062 (t0) cc_final: 0.8779 (p0) REVERT: D 202 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7836 (mtp180) REVERT: D 206 LYS cc_start: 0.9441 (ptpp) cc_final: 0.9105 (mttp) REVERT: D 209 PHE cc_start: 0.9659 (m-10) cc_final: 0.9308 (m-80) REVERT: D 227 GLU cc_start: 0.9656 (mm-30) cc_final: 0.9348 (mm-30) REVERT: F 17 TYR cc_start: 0.8331 (m-10) cc_final: 0.7896 (m-10) REVERT: F 37 LEU cc_start: 0.9563 (pp) cc_final: 0.9156 (pp) REVERT: F 42 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8437 (mt-10) REVERT: F 74 HIS cc_start: 0.9341 (m-70) cc_final: 0.8984 (m90) REVERT: F 78 TRP cc_start: 0.8664 (m-10) cc_final: 0.8260 (m-90) REVERT: F 162 LYS cc_start: 0.9654 (ttmm) cc_final: 0.9394 (ptpp) REVERT: F 190 ASP cc_start: 0.9121 (t0) cc_final: 0.8836 (p0) REVERT: F 202 ARG cc_start: 0.8583 (mmp-170) cc_final: 0.7983 (mtp180) REVERT: F 206 LYS cc_start: 0.9364 (ptpt) cc_final: 0.8818 (mttp) REVERT: F 209 PHE cc_start: 0.9534 (m-10) cc_final: 0.9270 (m-80) REVERT: F 227 GLU cc_start: 0.9726 (mm-30) cc_final: 0.9429 (mm-30) outliers start: 23 outliers final: 8 residues processed: 296 average time/residue: 0.2420 time to fit residues: 94.1736 Evaluate side-chains 271 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 258 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN F 15 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9504 Z= 0.231 Angle : 0.802 12.468 12900 Z= 0.416 Chirality : 0.045 0.331 1476 Planarity : 0.004 0.046 1548 Dihedral : 4.316 17.347 1218 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.35 % Allowed : 24.41 % Favored : 73.24 % 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: 0.88 (0.24), residues: 1110 helix: 1.12 (0.17), residues: 864 sheet: 1.12 (0.65), residues: 60 loop : -1.98 (0.36), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 78 HIS 0.005 0.001 HIS A 74 PHE 0.045 0.002 PHE C 212 TYR 0.020 0.002 TYR D 155 ARG 0.004 0.001 ARG F 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 288 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8453 (m-80) cc_final: 0.7810 (m-10) REVERT: E 42 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8396 (mt-10) REVERT: E 221 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9543 (mm) REVERT: E 227 GLU cc_start: 0.9759 (mm-30) cc_final: 0.9466 (mm-30) REVERT: A 17 TYR cc_start: 0.8378 (m-80) cc_final: 0.7782 (m-10) REVERT: A 37 LEU cc_start: 0.9540 (pp) cc_final: 0.9108 (pp) REVERT: A 42 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8397 (mt-10) REVERT: A 74 HIS cc_start: 0.9300 (m-70) cc_final: 0.9000 (m90) REVERT: A 78 TRP cc_start: 0.8488 (m-90) cc_final: 0.8116 (m-90) REVERT: A 202 ARG cc_start: 0.8842 (mtp-110) cc_final: 0.8369 (mtm180) REVERT: A 206 LYS cc_start: 0.9326 (ptpt) cc_final: 0.8960 (mttp) REVERT: A 209 PHE cc_start: 0.9511 (m-10) cc_final: 0.9241 (m-80) REVERT: A 227 GLU cc_start: 0.9714 (mm-30) cc_final: 0.9440 (mm-30) REVERT: B 42 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8428 (mt-10) REVERT: B 74 HIS cc_start: 0.9295 (m-70) cc_final: 0.8955 (m-70) REVERT: B 173 GLN cc_start: 0.9540 (tp-100) cc_final: 0.9274 (tp-100) REVERT: B 200 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.8966 (tp) REVERT: B 206 LYS cc_start: 0.9424 (ptpp) cc_final: 0.9162 (mttp) REVERT: B 209 PHE cc_start: 0.9584 (m-10) cc_final: 0.9210 (m-80) REVERT: B 227 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9330 (mm-30) REVERT: C 17 TYR cc_start: 0.8385 (m-80) cc_final: 0.7751 (m-10) REVERT: C 81 GLN cc_start: 0.9236 (mt0) cc_final: 0.8968 (pt0) REVERT: C 162 LYS cc_start: 0.9548 (ptpp) cc_final: 0.9256 (ptpp) REVERT: C 173 GLN cc_start: 0.9582 (tp40) cc_final: 0.9358 (tp-100) REVERT: C 202 ARG cc_start: 0.8854 (mtp-110) cc_final: 0.8504 (mtm-85) REVERT: C 206 LYS cc_start: 0.9358 (ptpp) cc_final: 0.9084 (mttp) REVERT: C 209 PHE cc_start: 0.9626 (m-10) cc_final: 0.9299 (m-80) REVERT: C 227 GLU cc_start: 0.9777 (mm-30) cc_final: 0.9476 (mm-30) REVERT: D 74 HIS cc_start: 0.9295 (m-70) cc_final: 0.8944 (m-70) REVERT: D 173 GLN cc_start: 0.9566 (tp40) cc_final: 0.9299 (tp-100) REVERT: D 200 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9139 (tp) REVERT: D 202 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7893 (mtp180) REVERT: D 206 LYS cc_start: 0.9419 (ptpp) cc_final: 0.9094 (mttp) REVERT: D 209 PHE cc_start: 0.9615 (m-10) cc_final: 0.9216 (m-80) REVERT: D 227 GLU cc_start: 0.9652 (mm-30) cc_final: 0.9333 (mm-30) REVERT: F 17 TYR cc_start: 0.8324 (m-10) cc_final: 0.7923 (m-10) REVERT: F 74 HIS cc_start: 0.9326 (m-70) cc_final: 0.8920 (m90) REVERT: F 78 TRP cc_start: 0.8858 (m-10) cc_final: 0.8206 (m-90) REVERT: F 92 TYR cc_start: 0.8241 (t80) cc_final: 0.8023 (t80) REVERT: F 206 LYS cc_start: 0.9323 (ptpt) cc_final: 0.8883 (mttp) REVERT: F 209 PHE cc_start: 0.9428 (m-10) cc_final: 0.9221 (m-80) REVERT: F 227 GLU cc_start: 0.9722 (mm-30) cc_final: 0.9388 (mm-30) outliers start: 24 outliers final: 11 residues processed: 303 average time/residue: 0.2437 time to fit residues: 97.0241 Evaluate side-chains 281 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 266 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain F residue 91 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 63 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9504 Z= 0.242 Angle : 0.847 13.445 12900 Z= 0.441 Chirality : 0.045 0.255 1476 Planarity : 0.004 0.038 1548 Dihedral : 4.336 19.447 1218 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 26.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.86 % Allowed : 28.14 % Favored : 70.00 % 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: 0.90 (0.24), residues: 1110 helix: 1.12 (0.17), residues: 864 sheet: 1.32 (0.64), residues: 60 loop : -1.95 (0.37), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP C 78 HIS 0.003 0.001 HIS C 74 PHE 0.042 0.002 PHE E 212 TYR 0.016 0.001 TYR D 155 ARG 0.009 0.001 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 282 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8452 (m-80) cc_final: 0.7823 (m-10) REVERT: E 42 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8407 (mt-10) REVERT: E 227 GLU cc_start: 0.9769 (mm-30) cc_final: 0.9466 (mm-30) REVERT: A 17 TYR cc_start: 0.8374 (m-80) cc_final: 0.7813 (m-80) REVERT: A 37 LEU cc_start: 0.9569 (pp) cc_final: 0.9169 (pp) REVERT: A 42 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8453 (mt-10) REVERT: A 202 ARG cc_start: 0.8895 (mtp-110) cc_final: 0.8404 (mtm180) REVERT: A 206 LYS cc_start: 0.9325 (ptpt) cc_final: 0.8978 (mttp) REVERT: A 209 PHE cc_start: 0.9465 (m-10) cc_final: 0.9187 (m-80) REVERT: A 214 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9376 (mm) REVERT: A 227 GLU cc_start: 0.9725 (mm-30) cc_final: 0.9443 (mm-30) REVERT: B 42 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8406 (mt-10) REVERT: B 74 HIS cc_start: 0.9254 (m-70) cc_final: 0.9009 (m90) REVERT: B 173 GLN cc_start: 0.9543 (tp-100) cc_final: 0.9303 (tp-100) REVERT: B 190 ASP cc_start: 0.9038 (t0) cc_final: 0.8789 (p0) REVERT: B 200 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9205 (tp) REVERT: B 206 LYS cc_start: 0.9443 (ptpp) cc_final: 0.9183 (mttp) REVERT: B 209 PHE cc_start: 0.9581 (m-10) cc_final: 0.9222 (m-80) REVERT: B 227 GLU cc_start: 0.9660 (mm-30) cc_final: 0.9336 (mm-30) REVERT: C 17 TYR cc_start: 0.8394 (m-80) cc_final: 0.7779 (m-10) REVERT: C 42 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8481 (mt-10) REVERT: C 81 GLN cc_start: 0.9295 (mt0) cc_final: 0.9069 (pt0) REVERT: C 162 LYS cc_start: 0.9568 (ptpp) cc_final: 0.9309 (ptpp) REVERT: C 202 ARG cc_start: 0.8862 (mtp-110) cc_final: 0.8546 (mtm-85) REVERT: C 206 LYS cc_start: 0.9354 (ptpp) cc_final: 0.9106 (mttp) REVERT: C 209 PHE cc_start: 0.9615 (m-10) cc_final: 0.9278 (m-80) REVERT: C 227 GLU cc_start: 0.9786 (mm-30) cc_final: 0.9482 (mm-30) REVERT: D 13 LYS cc_start: 0.9581 (mmmt) cc_final: 0.9371 (mmtm) REVERT: D 42 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8575 (mt-10) REVERT: D 74 HIS cc_start: 0.9248 (m-70) cc_final: 0.9020 (m90) REVERT: D 81 GLN cc_start: 0.9816 (tt0) cc_final: 0.9434 (mt0) REVERT: D 98 TYR cc_start: 0.9457 (m-10) cc_final: 0.9128 (m-10) REVERT: D 166 GLU cc_start: 0.8712 (pt0) cc_final: 0.8442 (pt0) REVERT: D 173 GLN cc_start: 0.9563 (tp40) cc_final: 0.9334 (tp-100) REVERT: D 190 ASP cc_start: 0.9030 (t0) cc_final: 0.8768 (p0) REVERT: D 202 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7719 (mtp-110) REVERT: D 206 LYS cc_start: 0.9412 (ptpp) cc_final: 0.9133 (mttp) REVERT: D 209 PHE cc_start: 0.9612 (m-10) cc_final: 0.9194 (m-80) REVERT: D 227 GLU cc_start: 0.9658 (mm-30) cc_final: 0.9340 (mm-30) REVERT: F 17 TYR cc_start: 0.8353 (m-10) cc_final: 0.7991 (m-10) REVERT: F 74 HIS cc_start: 0.9344 (m-70) cc_final: 0.9094 (m90) REVERT: F 190 ASP cc_start: 0.9125 (t0) cc_final: 0.8867 (p0) REVERT: F 202 ARG cc_start: 0.8550 (mmp-170) cc_final: 0.8037 (mtp180) REVERT: F 206 LYS cc_start: 0.9346 (ptpt) cc_final: 0.8924 (ptpt) REVERT: F 209 PHE cc_start: 0.9448 (m-10) cc_final: 0.9180 (m-80) REVERT: F 214 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9363 (mm) REVERT: F 227 GLU cc_start: 0.9735 (mm-30) cc_final: 0.9452 (mm-30) outliers start: 19 outliers final: 10 residues processed: 291 average time/residue: 0.2436 time to fit residues: 93.2866 Evaluate side-chains 280 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 266 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 TRP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 78 TRP Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 15 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9504 Z= 0.277 Angle : 0.886 12.832 12900 Z= 0.461 Chirality : 0.046 0.227 1476 Planarity : 0.005 0.029 1548 Dihedral : 4.492 19.688 1218 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 30.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.06 % Allowed : 29.80 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1110 helix: 1.08 (0.17), residues: 864 sheet: 1.33 (0.65), residues: 60 loop : -2.08 (0.37), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP C 78 HIS 0.003 0.001 HIS B 74 PHE 0.026 0.002 PHE D 212 TYR 0.011 0.001 TYR A 155 ARG 0.007 0.001 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 291 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8510 (m-80) cc_final: 0.7894 (m-10) REVERT: E 37 LEU cc_start: 0.9568 (pp) cc_final: 0.9095 (pp) REVERT: E 42 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8464 (mt-10) REVERT: E 78 TRP cc_start: 0.8625 (m-90) cc_final: 0.8170 (m-90) REVERT: E 179 PHE cc_start: 0.8486 (m-80) cc_final: 0.8145 (m-80) REVERT: E 190 ASP cc_start: 0.9056 (t0) cc_final: 0.8682 (p0) REVERT: E 209 PHE cc_start: 0.9445 (m-10) cc_final: 0.9190 (m-80) REVERT: E 227 GLU cc_start: 0.9785 (mm-30) cc_final: 0.9496 (mm-30) REVERT: A 17 TYR cc_start: 0.8505 (m-80) cc_final: 0.7950 (m-10) REVERT: A 42 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8535 (mt-10) REVERT: A 190 ASP cc_start: 0.9190 (t0) cc_final: 0.8921 (p0) REVERT: A 206 LYS cc_start: 0.9373 (ptpt) cc_final: 0.9086 (mttp) REVERT: A 209 PHE cc_start: 0.9500 (m-10) cc_final: 0.9220 (m-80) REVERT: A 214 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9441 (mt) REVERT: A 227 GLU cc_start: 0.9746 (mm-30) cc_final: 0.9464 (mm-30) REVERT: B 17 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7127 (t80) REVERT: B 42 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8512 (mt-10) REVERT: B 162 LYS cc_start: 0.9503 (ptpp) cc_final: 0.9281 (ptpp) REVERT: B 173 GLN cc_start: 0.9552 (tp-100) cc_final: 0.9330 (tp-100) REVERT: B 206 LYS cc_start: 0.9488 (ptpp) cc_final: 0.9135 (mttp) REVERT: B 209 PHE cc_start: 0.9616 (m-10) cc_final: 0.9254 (m-80) REVERT: B 227 GLU cc_start: 0.9675 (mm-30) cc_final: 0.9359 (mm-30) REVERT: C 17 TYR cc_start: 0.8475 (m-80) cc_final: 0.7875 (m-10) REVERT: C 37 LEU cc_start: 0.9588 (pp) cc_final: 0.9123 (pp) REVERT: C 42 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8560 (mt-10) REVERT: C 162 LYS cc_start: 0.9590 (ptpp) cc_final: 0.9341 (ptpp) REVERT: C 179 PHE cc_start: 0.8621 (m-80) cc_final: 0.8414 (m-80) REVERT: C 190 ASP cc_start: 0.9052 (t0) cc_final: 0.8691 (p0) REVERT: C 202 ARG cc_start: 0.8883 (mtp-110) cc_final: 0.8561 (mtm-85) REVERT: C 206 LYS cc_start: 0.9373 (ptpp) cc_final: 0.9161 (mttp) REVERT: C 209 PHE cc_start: 0.9621 (m-10) cc_final: 0.9252 (m-80) REVERT: C 227 GLU cc_start: 0.9802 (mm-30) cc_final: 0.9508 (mm-30) REVERT: D 13 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9399 (mmtm) REVERT: D 37 LEU cc_start: 0.9593 (pp) cc_final: 0.9245 (pp) REVERT: D 42 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8643 (mt-10) REVERT: D 81 GLN cc_start: 0.9810 (tt0) cc_final: 0.9534 (tt0) REVERT: D 162 LYS cc_start: 0.9519 (ptpp) cc_final: 0.9297 (ptpp) REVERT: D 173 GLN cc_start: 0.9555 (tp40) cc_final: 0.9302 (tp-100) REVERT: D 200 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9160 (tp) REVERT: D 202 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.7944 (mtp180) REVERT: D 206 LYS cc_start: 0.9450 (ptpp) cc_final: 0.9161 (mttp) REVERT: D 209 PHE cc_start: 0.9635 (m-10) cc_final: 0.9270 (m-80) REVERT: D 227 GLU cc_start: 0.9672 (mm-30) cc_final: 0.9356 (mm-30) REVERT: F 17 TYR cc_start: 0.8409 (m-10) cc_final: 0.8047 (m-10) REVERT: F 37 LEU cc_start: 0.9677 (pp) cc_final: 0.9367 (pp) REVERT: F 42 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8596 (mt-10) REVERT: F 74 HIS cc_start: 0.9345 (m-70) cc_final: 0.9144 (m90) REVERT: F 202 ARG cc_start: 0.8545 (mmp-170) cc_final: 0.8200 (mtp180) REVERT: F 206 LYS cc_start: 0.9364 (ptpt) cc_final: 0.8921 (ptpt) REVERT: F 209 PHE cc_start: 0.9476 (m-10) cc_final: 0.9218 (m-80) REVERT: F 214 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9422 (mm) REVERT: F 227 GLU cc_start: 0.9758 (mm-30) cc_final: 0.9477 (mm-30) outliers start: 21 outliers final: 10 residues processed: 301 average time/residue: 0.2436 time to fit residues: 96.2890 Evaluate side-chains 291 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 276 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN B 74 HIS D 74 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9504 Z= 0.248 Angle : 0.966 16.467 12900 Z= 0.498 Chirality : 0.048 0.355 1476 Planarity : 0.004 0.038 1548 Dihedral : 4.460 22.347 1218 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 27.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.16 % Allowed : 31.37 % Favored : 66.47 % 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: 0.72 (0.24), residues: 1110 helix: 0.98 (0.17), residues: 864 sheet: 1.27 (0.61), residues: 60 loop : -1.95 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP C 78 HIS 0.002 0.001 HIS E 74 PHE 0.025 0.002 PHE F 212 TYR 0.009 0.001 TYR A 155 ARG 0.016 0.001 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 302 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8474 (m-80) cc_final: 0.7846 (m-10) REVERT: E 33 ARG cc_start: 0.9547 (mmm-85) cc_final: 0.9311 (mtm110) REVERT: E 42 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8473 (mt-10) REVERT: E 179 PHE cc_start: 0.8580 (m-80) cc_final: 0.8146 (m-80) REVERT: E 209 PHE cc_start: 0.9424 (m-10) cc_final: 0.9109 (m-80) REVERT: E 227 GLU cc_start: 0.9792 (mm-30) cc_final: 0.9508 (mm-30) REVERT: A 17 TYR cc_start: 0.8502 (m-80) cc_final: 0.7944 (m-10) REVERT: A 37 LEU cc_start: 0.9612 (pp) cc_final: 0.9199 (pp) REVERT: A 42 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8531 (mt-10) REVERT: A 63 ASN cc_start: 0.9344 (OUTLIER) cc_final: 0.9027 (t0) REVERT: A 202 ARG cc_start: 0.8888 (mtp-110) cc_final: 0.8424 (mtm180) REVERT: A 206 LYS cc_start: 0.9350 (ptpt) cc_final: 0.9049 (mttp) REVERT: A 209 PHE cc_start: 0.9460 (m-10) cc_final: 0.9177 (m-80) REVERT: A 214 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9453 (mm) REVERT: A 227 GLU cc_start: 0.9754 (mm-30) cc_final: 0.9477 (mm-30) REVERT: B 42 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8471 (mt-10) REVERT: B 74 HIS cc_start: 0.9366 (m-70) cc_final: 0.9101 (m90) REVERT: B 81 GLN cc_start: 0.9791 (tt0) cc_final: 0.9291 (mm-40) REVERT: B 162 LYS cc_start: 0.9496 (ptpp) cc_final: 0.9256 (ptpp) REVERT: B 166 GLU cc_start: 0.8620 (pt0) cc_final: 0.8415 (pt0) REVERT: B 173 GLN cc_start: 0.9546 (tp-100) cc_final: 0.9332 (tp-100) REVERT: B 190 ASP cc_start: 0.9057 (t0) cc_final: 0.8838 (p0) REVERT: B 209 PHE cc_start: 0.9519 (m-10) cc_final: 0.9254 (m-80) REVERT: B 227 GLU cc_start: 0.9681 (mm-30) cc_final: 0.9368 (mm-30) REVERT: C 17 TYR cc_start: 0.8443 (m-80) cc_final: 0.7864 (m-10) REVERT: C 33 ARG cc_start: 0.9532 (mmm-85) cc_final: 0.9309 (mtm110) REVERT: C 37 LEU cc_start: 0.9583 (pp) cc_final: 0.9071 (pp) REVERT: C 42 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8515 (mt-10) REVERT: C 162 LYS cc_start: 0.9579 (ptpp) cc_final: 0.9323 (ptpp) REVERT: C 179 PHE cc_start: 0.8656 (m-80) cc_final: 0.8364 (m-80) REVERT: C 200 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9234 (mm) REVERT: C 202 ARG cc_start: 0.8884 (mtp-110) cc_final: 0.8530 (mtm-85) REVERT: C 206 LYS cc_start: 0.9343 (ptpp) cc_final: 0.9083 (mttp) REVERT: C 209 PHE cc_start: 0.9583 (m-10) cc_final: 0.9232 (m-80) REVERT: C 227 GLU cc_start: 0.9806 (mm-30) cc_final: 0.9503 (mm-30) REVERT: D 17 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7163 (t80) REVERT: D 42 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8615 (mt-10) REVERT: D 74 HIS cc_start: 0.9365 (m-70) cc_final: 0.9104 (m90) REVERT: D 81 GLN cc_start: 0.9768 (tt0) cc_final: 0.9502 (tt0) REVERT: D 162 LYS cc_start: 0.9511 (ptpp) cc_final: 0.9284 (ptpp) REVERT: D 173 GLN cc_start: 0.9558 (tp40) cc_final: 0.9263 (tp-100) REVERT: D 190 ASP cc_start: 0.9069 (t0) cc_final: 0.8830 (p0) REVERT: D 200 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9179 (tp) REVERT: D 209 PHE cc_start: 0.9568 (m-10) cc_final: 0.9228 (m-80) REVERT: D 227 GLU cc_start: 0.9681 (mm-30) cc_final: 0.9374 (mm-30) REVERT: F 17 TYR cc_start: 0.8388 (m-10) cc_final: 0.8059 (m-10) REVERT: F 37 LEU cc_start: 0.9650 (pp) cc_final: 0.9340 (pp) REVERT: F 42 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8576 (mt-10) REVERT: F 74 HIS cc_start: 0.9331 (m-70) cc_final: 0.9113 (m90) REVERT: F 190 ASP cc_start: 0.9107 (t0) cc_final: 0.8873 (p0) REVERT: F 206 LYS cc_start: 0.9350 (ptpt) cc_final: 0.9008 (pttt) REVERT: F 209 PHE cc_start: 0.9425 (m-10) cc_final: 0.9177 (m-80) REVERT: F 214 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9449 (mm) REVERT: F 227 GLU cc_start: 0.9770 (mm-30) cc_final: 0.9489 (mm-30) outliers start: 22 outliers final: 9 residues processed: 311 average time/residue: 0.2405 time to fit residues: 98.8225 Evaluate side-chains 292 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 277 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 63 ASN C 63 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.6497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9504 Z= 0.312 Angle : 0.989 14.560 12900 Z= 0.529 Chirality : 0.049 0.298 1476 Planarity : 0.006 0.054 1548 Dihedral : 4.797 24.917 1218 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 35.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.67 % Allowed : 33.43 % Favored : 64.90 % 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: 0.66 (0.24), residues: 1110 helix: 0.96 (0.17), residues: 870 sheet: 0.84 (0.61), residues: 60 loop : -2.04 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.003 TRP C 78 HIS 0.003 0.001 HIS D 194 PHE 0.026 0.002 PHE C 212 TYR 0.013 0.002 TYR E 155 ARG 0.016 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 291 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8575 (m-80) cc_final: 0.7993 (m-10) REVERT: E 42 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8603 (mt-10) REVERT: E 179 PHE cc_start: 0.8507 (m-80) cc_final: 0.8128 (m-80) REVERT: E 206 LYS cc_start: 0.9492 (mttp) cc_final: 0.9163 (mttt) REVERT: E 209 PHE cc_start: 0.9494 (m-10) cc_final: 0.9165 (m-80) REVERT: E 227 GLU cc_start: 0.9809 (mm-30) cc_final: 0.9542 (mm-30) REVERT: A 17 TYR cc_start: 0.8547 (m-80) cc_final: 0.8050 (m-10) REVERT: A 33 ARG cc_start: 0.9216 (mtm110) cc_final: 0.8958 (mtm110) REVERT: A 42 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8666 (mt-10) REVERT: A 190 ASP cc_start: 0.9205 (t0) cc_final: 0.8959 (p0) REVERT: A 206 LYS cc_start: 0.9405 (ptpt) cc_final: 0.9111 (mttp) REVERT: A 209 PHE cc_start: 0.9488 (m-10) cc_final: 0.9182 (m-80) REVERT: A 227 GLU cc_start: 0.9777 (mm-30) cc_final: 0.9494 (mm-30) REVERT: B 17 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7118 (t80) REVERT: B 33 ARG cc_start: 0.9217 (mtm110) cc_final: 0.8970 (mtm110) REVERT: B 42 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8607 (mt-10) REVERT: B 47 ASP cc_start: 0.9370 (p0) cc_final: 0.8995 (p0) REVERT: B 162 LYS cc_start: 0.9492 (ptpp) cc_final: 0.9267 (ptpp) REVERT: B 173 GLN cc_start: 0.9574 (tp-100) cc_final: 0.9340 (tp-100) REVERT: B 190 ASP cc_start: 0.9103 (t0) cc_final: 0.8885 (p0) REVERT: B 202 ARG cc_start: 0.8377 (mmp-170) cc_final: 0.8064 (mmm160) REVERT: B 209 PHE cc_start: 0.9595 (m-10) cc_final: 0.9245 (m-80) REVERT: B 227 GLU cc_start: 0.9697 (mm-30) cc_final: 0.9425 (mm-30) REVERT: C 17 TYR cc_start: 0.8513 (m-80) cc_final: 0.7930 (m-10) REVERT: C 33 ARG cc_start: 0.9552 (mmm-85) cc_final: 0.9343 (mtm110) REVERT: C 42 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8651 (mt-10) REVERT: C 162 LYS cc_start: 0.9591 (ptpp) cc_final: 0.9359 (ptpp) REVERT: C 179 PHE cc_start: 0.8599 (m-80) cc_final: 0.8349 (m-80) REVERT: C 206 LYS cc_start: 0.9374 (ptpp) cc_final: 0.9157 (mttp) REVERT: C 209 PHE cc_start: 0.9622 (m-10) cc_final: 0.9276 (m-80) REVERT: C 227 GLU cc_start: 0.9821 (mm-30) cc_final: 0.9551 (mm-30) REVERT: D 17 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7482 (t80) REVERT: D 33 ARG cc_start: 0.9182 (mtm110) cc_final: 0.8924 (mtm110) REVERT: D 47 ASP cc_start: 0.9332 (p0) cc_final: 0.8981 (p0) REVERT: D 81 GLN cc_start: 0.9666 (tt0) cc_final: 0.9428 (tt0) REVERT: D 162 LYS cc_start: 0.9519 (ptpp) cc_final: 0.9297 (ptpp) REVERT: D 173 GLN cc_start: 0.9539 (tp40) cc_final: 0.9259 (tp-100) REVERT: D 190 ASP cc_start: 0.9117 (t0) cc_final: 0.8876 (p0) REVERT: D 206 LYS cc_start: 0.9416 (mttp) cc_final: 0.8968 (pttt) REVERT: D 209 PHE cc_start: 0.9551 (m-10) cc_final: 0.9238 (m-80) REVERT: D 227 GLU cc_start: 0.9700 (mm-30) cc_final: 0.9436 (mm-30) REVERT: F 17 TYR cc_start: 0.8469 (m-10) cc_final: 0.8123 (m-10) REVERT: F 33 ARG cc_start: 0.9182 (mtm110) cc_final: 0.8907 (mtm110) REVERT: F 42 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8682 (mt-10) REVERT: F 47 ASP cc_start: 0.9326 (p0) cc_final: 0.9109 (p0) REVERT: F 74 HIS cc_start: 0.9349 (m-70) cc_final: 0.9052 (m90) REVERT: F 78 TRP cc_start: 0.9200 (m-10) cc_final: 0.8236 (m-90) REVERT: F 202 ARG cc_start: 0.9046 (mtp180) cc_final: 0.8388 (ptt90) REVERT: F 206 LYS cc_start: 0.9238 (ptpt) cc_final: 0.9025 (ptpt) REVERT: F 209 PHE cc_start: 0.9466 (m-10) cc_final: 0.9187 (m-80) REVERT: F 227 GLU cc_start: 0.9787 (mm-30) cc_final: 0.9492 (mm-30) outliers start: 17 outliers final: 10 residues processed: 299 average time/residue: 0.2480 time to fit residues: 98.7718 Evaluate side-chains 288 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 276 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 8 optimal weight: 0.0570 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 68 optimal weight: 0.0370 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 63 ASN C 63 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9504 Z= 0.254 Angle : 1.069 17.348 12900 Z= 0.551 Chirality : 0.050 0.327 1476 Planarity : 0.005 0.049 1548 Dihedral : 4.596 22.536 1218 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 29.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.27 % Allowed : 34.71 % Favored : 64.02 % 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: 0.77 (0.24), residues: 1110 helix: 1.02 (0.17), residues: 870 sheet: 0.77 (0.58), residues: 60 loop : -1.87 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP E 78 HIS 0.008 0.001 HIS E 74 PHE 0.031 0.002 PHE E 212 TYR 0.010 0.001 TYR B 177 ARG 0.015 0.001 ARG B 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 306 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 TYR cc_start: 0.8546 (m-80) cc_final: 0.7980 (m-10) REVERT: E 33 ARG cc_start: 0.9578 (mmm-85) cc_final: 0.9329 (mtm110) REVERT: E 37 LEU cc_start: 0.9601 (pp) cc_final: 0.9088 (pp) REVERT: E 42 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8543 (mt-10) REVERT: E 161 PHE cc_start: 0.9527 (m-80) cc_final: 0.9036 (m-80) REVERT: E 179 PHE cc_start: 0.8568 (m-80) cc_final: 0.8246 (m-80) REVERT: E 190 ASP cc_start: 0.9060 (t0) cc_final: 0.8766 (p0) REVERT: E 206 LYS cc_start: 0.9454 (mttp) cc_final: 0.9147 (mttt) REVERT: E 209 PHE cc_start: 0.9472 (m-10) cc_final: 0.9102 (m-80) REVERT: E 214 LEU cc_start: 0.9773 (OUTLIER) cc_final: 0.9440 (mm) REVERT: E 227 GLU cc_start: 0.9807 (mm-30) cc_final: 0.9524 (mm-30) REVERT: A 17 TYR cc_start: 0.8550 (m-80) cc_final: 0.8029 (m-10) REVERT: A 42 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8627 (mt-10) REVERT: A 162 LYS cc_start: 0.9688 (ptmt) cc_final: 0.9468 (ptpp) REVERT: A 166 GLU cc_start: 0.9324 (pm20) cc_final: 0.9117 (pm20) REVERT: A 202 ARG cc_start: 0.8976 (mtp-110) cc_final: 0.8529 (mtm180) REVERT: A 209 PHE cc_start: 0.9454 (m-10) cc_final: 0.9140 (m-80) REVERT: A 227 GLU cc_start: 0.9773 (mm-30) cc_final: 0.9487 (mm-30) REVERT: B 17 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7388 (t80) REVERT: B 33 ARG cc_start: 0.9227 (mtm110) cc_final: 0.8966 (mtm110) REVERT: B 42 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8611 (mt-10) REVERT: B 173 GLN cc_start: 0.9510 (tp-100) cc_final: 0.9267 (tp-100) REVERT: B 209 PHE cc_start: 0.9557 (m-10) cc_final: 0.9186 (m-80) REVERT: B 227 GLU cc_start: 0.9691 (mm-30) cc_final: 0.9380 (mm-30) REVERT: C 17 TYR cc_start: 0.8476 (m-80) cc_final: 0.7918 (m-10) REVERT: C 33 ARG cc_start: 0.9542 (mmm-85) cc_final: 0.9328 (mtm110) REVERT: C 42 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8577 (mt-10) REVERT: C 162 LYS cc_start: 0.9590 (ptpp) cc_final: 0.9359 (ptpp) REVERT: C 179 PHE cc_start: 0.8580 (m-80) cc_final: 0.8236 (m-80) REVERT: C 190 ASP cc_start: 0.9050 (t0) cc_final: 0.8763 (p0) REVERT: C 209 PHE cc_start: 0.9522 (m-10) cc_final: 0.9225 (m-80) REVERT: C 227 GLU cc_start: 0.9817 (mm-30) cc_final: 0.9534 (mm-30) REVERT: D 17 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7443 (t80) REVERT: D 33 ARG cc_start: 0.9155 (mtm110) cc_final: 0.8900 (mtm110) REVERT: D 173 GLN cc_start: 0.9506 (tp40) cc_final: 0.9232 (tp-100) REVERT: D 206 LYS cc_start: 0.9416 (mttp) cc_final: 0.9002 (pttt) REVERT: D 209 PHE cc_start: 0.9560 (m-10) cc_final: 0.9252 (m-80) REVERT: D 227 GLU cc_start: 0.9696 (mm-30) cc_final: 0.9398 (mm-30) REVERT: F 17 TYR cc_start: 0.8419 (m-10) cc_final: 0.8121 (m-10) REVERT: F 33 ARG cc_start: 0.9193 (mtm110) cc_final: 0.8949 (mtm110) REVERT: F 37 LEU cc_start: 0.9674 (pp) cc_final: 0.9330 (pp) REVERT: F 42 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8635 (mt-10) REVERT: F 47 ASP cc_start: 0.9281 (p0) cc_final: 0.9034 (p0) REVERT: F 101 ARG cc_start: 0.8938 (ttp80) cc_final: 0.8731 (ttp80) REVERT: F 190 ASP cc_start: 0.9126 (t0) cc_final: 0.8917 (p0) REVERT: F 202 ARG cc_start: 0.9060 (mtp180) cc_final: 0.8335 (ptt90) REVERT: F 206 LYS cc_start: 0.9212 (ptpt) cc_final: 0.9007 (mttp) REVERT: F 209 PHE cc_start: 0.9441 (m-10) cc_final: 0.9156 (m-80) REVERT: F 227 GLU cc_start: 0.9776 (mm-30) cc_final: 0.9494 (mm-30) outliers start: 13 outliers final: 9 residues processed: 310 average time/residue: 0.2491 time to fit residues: 101.5137 Evaluate side-chains 297 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 285 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 202 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.042088 restraints weight = 63631.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.043004 restraints weight = 45285.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.043704 restraints weight = 35065.655| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9504 Z= 0.278 Angle : 1.042 16.527 12900 Z= 0.546 Chirality : 0.050 0.288 1476 Planarity : 0.005 0.078 1548 Dihedral : 4.683 22.809 1218 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 33.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.37 % Allowed : 35.00 % Favored : 63.63 % 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: 0.73 (0.24), residues: 1110 helix: 1.00 (0.17), residues: 870 sheet: 0.67 (0.61), residues: 60 loop : -1.86 (0.40), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.102 0.003 TRP E 78 HIS 0.008 0.001 HIS E 74 PHE 0.027 0.002 PHE E 212 TYR 0.021 0.001 TYR F 230 ARG 0.016 0.001 ARG C 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.93 seconds wall clock time: 46 minutes 9.16 seconds (2769.16 seconds total)