Starting phenix.real_space_refine on Fri Feb 16 19:28:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2024/8d1k_27133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2024/8d1k_27133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2024/8d1k_27133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2024/8d1k_27133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2024/8d1k_27133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2024/8d1k_27133_updated.pdb" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.129 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 5 5.49 5 S 80 5.16 5 C 10905 2.51 5 N 2550 2.21 5 O 2760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ASP 270": "OD1" <-> "OD2" Residue "D PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 328": "OD1" <-> "OD2" Residue "D GLU 371": "OE1" <-> "OE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 328": "OD1" <-> "OD2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "E TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ASP 270": "OD1" <-> "OD2" Residue "E PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 328": "OD1" <-> "OD2" Residue "E GLU 371": "OE1" <-> "OE2" Residue "C TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 328": "OD1" <-> "OD2" Residue "C GLU 371": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16305 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "E" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 178 Unusual residues: {' CA': 1, 'MC3': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 209 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 108 Unusual residues: {' CA': 1, 'MC3': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 143 Unusual residues: {' CA': 1, 'MC3': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 41 Time building chain proxies: 8.51, per 1000 atoms: 0.52 Number of scatterers: 16305 At special positions: 0 Unit cell: (107.9, 104.58, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 80 16.00 P 5 15.00 O 2760 8.00 N 2550 7.00 C 10905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.20 Conformation dependent library (CDL) restraints added in 2.6 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 0 sheets defined 61.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'D' and resid 6 through 9 Processing helix chain 'D' and resid 19 through 22 Processing helix chain 'D' and resid 28 through 52 removed outlier: 5.638A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.667A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 98 Processing helix chain 'D' and resid 104 through 113 Processing helix chain 'D' and resid 119 through 143 Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 204 through 229 Processing helix chain 'D' and resid 234 through 254 removed outlier: 3.882A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 275 through 294 removed outlier: 3.696A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 323 Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'B' and resid 6 through 9 Processing helix chain 'B' and resid 19 through 22 Processing helix chain 'B' and resid 28 through 52 removed outlier: 5.638A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 71 removed outlier: 3.667A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 98 Processing helix chain 'B' and resid 104 through 113 Processing helix chain 'B' and resid 119 through 143 Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 183 through 197 Processing helix chain 'B' and resid 204 through 229 Processing helix chain 'B' and resid 234 through 254 removed outlier: 3.883A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 275 through 294 removed outlier: 3.697A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 323 Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'A' and resid 6 through 9 Processing helix chain 'A' and resid 19 through 22 Processing helix chain 'A' and resid 28 through 52 removed outlier: 5.638A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 71 removed outlier: 3.667A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 98 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 119 through 143 Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 204 through 229 Processing helix chain 'A' and resid 234 through 254 removed outlier: 3.883A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 275 through 294 removed outlier: 3.696A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'E' and resid 6 through 9 Processing helix chain 'E' and resid 19 through 22 Processing helix chain 'E' and resid 28 through 52 removed outlier: 5.638A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.667A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 98 Processing helix chain 'E' and resid 104 through 113 Processing helix chain 'E' and resid 119 through 143 Processing helix chain 'E' and resid 145 through 150 Processing helix chain 'E' and resid 154 through 159 Processing helix chain 'E' and resid 165 through 173 Processing helix chain 'E' and resid 183 through 197 Processing helix chain 'E' and resid 204 through 229 Processing helix chain 'E' and resid 234 through 254 removed outlier: 3.882A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'E' and resid 275 through 294 removed outlier: 3.695A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'C' and resid 6 through 9 Processing helix chain 'C' and resid 19 through 22 Processing helix chain 'C' and resid 28 through 52 removed outlier: 5.638A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.667A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 98 Processing helix chain 'C' and resid 104 through 113 Processing helix chain 'C' and resid 119 through 143 Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 183 through 197 Processing helix chain 'C' and resid 204 through 229 Processing helix chain 'C' and resid 234 through 254 removed outlier: 3.882A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 275 through 294 removed outlier: 3.696A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 323 Processing helix chain 'C' and resid 352 through 354 No H-bonds generated for 'chain 'C' and resid 352 through 354' 810 hydrogen bonds defined for protein. 2400 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: 4.50 Time building geometry restraints manager: 6.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2769 1.32 - 1.45: 4504 1.45 - 1.58: 9317 1.58 - 1.71: 10 1.71 - 1.84: 135 Bond restraints: 16735 Sorted by residual: bond pdb=" C ARG A 105 " pdb=" O ARG A 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.31e+01 bond pdb=" C ARG E 105 " pdb=" O ARG E 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.31e+01 bond pdb=" C ARG B 105 " pdb=" O ARG B 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.31e+01 bond pdb=" C ARG D 105 " pdb=" O ARG D 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.30e+01 bond pdb=" C ARG C 105 " pdb=" O ARG C 105 " ideal model delta sigma weight residual 1.236 1.292 -0.055 1.15e-02 7.56e+03 2.30e+01 ... (remaining 16730 not shown) Histogram of bond angle deviations from ideal: 97.43 - 104.88: 366 104.88 - 112.33: 7698 112.33 - 119.77: 7478 119.77 - 127.22: 6808 127.22 - 134.67: 210 Bond angle restraints: 22560 Sorted by residual: angle pdb=" N PRO A 77 " pdb=" CA PRO A 77 " pdb=" CB PRO A 77 " ideal model delta sigma weight residual 102.81 99.30 3.51 6.70e-01 2.23e+00 2.74e+01 angle pdb=" N PRO E 77 " pdb=" CA PRO E 77 " pdb=" CB PRO E 77 " ideal model delta sigma weight residual 102.81 99.31 3.50 6.70e-01 2.23e+00 2.73e+01 angle pdb=" N PRO D 77 " pdb=" CA PRO D 77 " pdb=" CB PRO D 77 " ideal model delta sigma weight residual 102.81 99.32 3.49 6.70e-01 2.23e+00 2.71e+01 angle pdb=" N PRO B 77 " pdb=" CA PRO B 77 " pdb=" CB PRO B 77 " ideal model delta sigma weight residual 102.81 99.32 3.49 6.70e-01 2.23e+00 2.71e+01 angle pdb=" N PRO C 77 " pdb=" CA PRO C 77 " pdb=" CB PRO C 77 " ideal model delta sigma weight residual 102.81 99.32 3.49 6.70e-01 2.23e+00 2.71e+01 ... (remaining 22555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 9055 23.97 - 47.93: 655 47.93 - 71.90: 185 71.90 - 95.86: 35 95.86 - 119.83: 5 Dihedral angle restraints: 9935 sinusoidal: 4370 harmonic: 5565 Sorted by residual: dihedral pdb=" C33 MC3 B 603 " pdb=" C31 MC3 B 603 " pdb=" C32 MC3 B 603 " pdb=" O2 MC3 B 603 " ideal model delta sinusoidal sigma weight residual 175.52 55.69 119.83 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C33 MC3 E 603 " pdb=" C31 MC3 E 603 " pdb=" C32 MC3 E 603 " pdb=" O2 MC3 E 603 " ideal model delta sinusoidal sigma weight residual 175.52 55.75 119.77 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C33 MC3 D 603 " pdb=" C31 MC3 D 603 " pdb=" C32 MC3 D 603 " pdb=" O2 MC3 D 603 " ideal model delta sinusoidal sigma weight residual 175.52 55.76 119.76 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 9932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 968 0.040 - 0.080: 693 0.080 - 0.120: 486 0.120 - 0.160: 179 0.160 - 0.200: 59 Chirality restraints: 2385 Sorted by residual: chirality pdb=" CA LEU A 176 " pdb=" N LEU A 176 " pdb=" C LEU A 176 " pdb=" CB LEU A 176 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA LEU D 176 " pdb=" N LEU D 176 " pdb=" C LEU D 176 " pdb=" CB LEU D 176 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" CA LEU B 176 " pdb=" N LEU B 176 " pdb=" C LEU B 176 " pdb=" CB LEU B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 2382 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 97 " -0.036 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR D 97 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR D 97 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 97 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR D 97 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR D 97 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 97 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR D 97 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 97 " -0.036 2.00e-02 2.50e+03 3.05e-02 1.86e+01 pdb=" CG TYR C 97 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR C 97 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 97 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR C 97 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 97 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR C 97 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR C 97 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 97 " -0.035 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR E 97 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR E 97 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR E 97 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR E 97 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR E 97 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR E 97 " -0.039 2.00e-02 2.50e+03 pdb=" OH TYR E 97 " 0.026 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3766 2.81 - 3.33: 16808 3.33 - 3.85: 29250 3.85 - 4.38: 35657 4.38 - 4.90: 57240 Nonbonded interactions: 142721 Sorted by model distance: nonbonded pdb=" O ASN A 296 " pdb="CA CA A 602 " model vdw 2.287 2.510 nonbonded pdb=" O ASN C 296 " pdb="CA CA C 602 " model vdw 2.288 2.510 nonbonded pdb=" O ASN D 296 " pdb="CA CA D 601 " model vdw 2.288 2.510 nonbonded pdb=" O ASN B 296 " pdb="CA CA B 601 " model vdw 2.288 2.510 nonbonded pdb=" O ASN E 296 " pdb="CA CA E 601 " model vdw 2.288 2.510 ... (remaining 142716 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' and (resid 2 through 377 or resid 604 or (resid 605 and (name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41 or name C42)) or (resid 606 and (name C33 or name C34 or name C35 o \ r name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C \ 42 or name C43 or name C44)) or (resid 607 through 608 and (name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name \ C41 or name C42)))) selection = (chain 'B' and (resid 2 through 377 or (resid 604 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 605 and (name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42)) or (resid 606 and (name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name C44)) or (resid 607 through 608 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2)))) selection = (chain 'C' and (resid 2 through 377 or (resid 604 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 605 and (name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42)) or resid 606 or (resid 607 through 608 and (name C33 or name C34 or \ name C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 \ or name C42)))) selection = (chain 'D' and (resid 2 through 377 or (resid 604 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 605 and (name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42)) or (resid 606 and (name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name C44)) or (resid 607 through 608 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2)))) selection = (chain 'E' and (resid 2 through 377 or (resid 604 and (name C32 or name C33 or n \ ame C34 or name C35 or name C36)) or (resid 605 and (name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42)) or (resid 606 and (name C33 or name C34 or name C35 or name C36 or n \ ame C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 \ or name C44)) or (resid 607 through 608 and (name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or name C4 \ 2)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 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: 14.060 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 42.340 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.065 16735 Z= 0.837 Angle : 1.275 13.700 22560 Z= 0.940 Chirality : 0.074 0.200 2385 Planarity : 0.007 0.031 2770 Dihedral : 18.326 119.825 6345 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.65 % Allowed : 8.85 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 1870 helix: 0.79 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : 0.46 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.011 TRP A 309 HIS 0.007 0.003 HIS C 267 PHE 0.028 0.006 PHE E 162 TYR 0.051 0.008 TYR D 97 ARG 0.035 0.003 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 1.795 Fit side-chains REVERT: D 262 LYS cc_start: 0.6671 (OUTLIER) cc_final: 0.6338 (mppt) REVERT: D 264 TYR cc_start: 0.7597 (m-80) cc_final: 0.7144 (m-80) REVERT: D 360 MET cc_start: 0.9026 (mmm) cc_final: 0.8793 (mmm) REVERT: D 376 GLN cc_start: 0.6917 (mm-40) cc_final: 0.6656 (mm110) REVERT: B 119 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8293 (tt0) REVERT: B 376 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6645 (mm110) REVERT: A 119 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8254 (tt0) REVERT: A 360 MET cc_start: 0.9020 (mmm) cc_final: 0.8728 (mmm) REVERT: A 369 ASN cc_start: 0.7356 (m-40) cc_final: 0.7152 (m110) REVERT: A 373 MET cc_start: 0.8346 (mtp) cc_final: 0.8025 (mtm) REVERT: A 376 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6678 (mm110) REVERT: E 8 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8637 (mt0) REVERT: E 376 GLN cc_start: 0.6747 (mm-40) cc_final: 0.6453 (mm110) REVERT: C 373 MET cc_start: 0.8225 (mtp) cc_final: 0.7988 (mtm) REVERT: C 376 GLN cc_start: 0.6982 (mm-40) cc_final: 0.6698 (mm110) outliers start: 45 outliers final: 11 residues processed: 235 average time/residue: 1.4295 time to fit residues: 370.0094 Evaluate side-chains 175 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain E residue 8 GLN Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 178 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 208 GLN B 208 GLN B 369 ASN A 208 GLN E 208 GLN E 369 ASN C 208 GLN C 369 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16735 Z= 0.184 Angle : 0.525 7.790 22560 Z= 0.274 Chirality : 0.038 0.160 2385 Planarity : 0.003 0.024 2770 Dihedral : 14.875 118.232 2670 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.36 % Allowed : 11.21 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 1870 helix: 1.20 (0.15), residues: 1250 sheet: None (None), residues: 0 loop : -0.03 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 309 HIS 0.004 0.001 HIS C 178 PHE 0.022 0.002 PHE B 248 TYR 0.022 0.002 TYR C 97 ARG 0.005 0.001 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.684 Fit side-chains REVERT: D 72 TYR cc_start: 0.7151 (m-10) cc_final: 0.6445 (m-80) REVERT: D 262 LYS cc_start: 0.7010 (mmtm) cc_final: 0.6801 (mppt) REVERT: D 360 MET cc_start: 0.8928 (mmm) cc_final: 0.8643 (mmm) REVERT: D 376 GLN cc_start: 0.6919 (mm-40) cc_final: 0.6597 (mm110) REVERT: B 68 TYR cc_start: 0.6920 (t80) cc_final: 0.6639 (t80) REVERT: B 119 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8297 (tt0) REVERT: B 376 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6679 (mm110) REVERT: A 72 TYR cc_start: 0.7088 (m-80) cc_final: 0.6750 (m-10) REVERT: A 119 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8259 (tt0) REVERT: A 360 MET cc_start: 0.8948 (mmm) cc_final: 0.8608 (mmm) REVERT: A 376 GLN cc_start: 0.6783 (mm-40) cc_final: 0.6452 (mm110) REVERT: E 68 TYR cc_start: 0.7143 (t80) cc_final: 0.6763 (t80) REVERT: E 72 TYR cc_start: 0.6929 (m-80) cc_final: 0.6664 (m-10) REVERT: E 373 MET cc_start: 0.8184 (mtt) cc_final: 0.7969 (mtp) REVERT: C 72 TYR cc_start: 0.6968 (m-80) cc_final: 0.6666 (m-80) REVERT: C 376 GLN cc_start: 0.6850 (mm-40) cc_final: 0.6534 (mm110) outliers start: 23 outliers final: 13 residues processed: 195 average time/residue: 1.4149 time to fit residues: 303.6351 Evaluate side-chains 177 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 178 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 46 optimal weight: 0.0570 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 166 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 369 ASN E 259 ASN E 369 ASN C 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16735 Z= 0.161 Angle : 0.485 7.337 22560 Z= 0.254 Chirality : 0.037 0.159 2385 Planarity : 0.003 0.027 2770 Dihedral : 14.110 113.979 2660 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.65 % Allowed : 10.91 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 1870 helix: 1.38 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.16 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 309 HIS 0.004 0.001 HIS C 178 PHE 0.020 0.001 PHE B 248 TYR 0.021 0.001 TYR C 97 ARG 0.003 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 2.384 Fit side-chains REVERT: D 72 TYR cc_start: 0.7016 (m-10) cc_final: 0.6468 (m-80) REVERT: D 262 LYS cc_start: 0.7075 (mmtm) cc_final: 0.6865 (mppt) REVERT: D 376 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6631 (mm110) REVERT: B 119 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8298 (tt0) REVERT: B 376 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6687 (mm110) REVERT: A 72 TYR cc_start: 0.6998 (m-80) cc_final: 0.6736 (m-80) REVERT: A 119 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8265 (tt0) REVERT: A 178 HIS cc_start: 0.9076 (OUTLIER) cc_final: 0.8640 (m-70) REVERT: A 360 MET cc_start: 0.8894 (mmm) cc_final: 0.8514 (mmm) REVERT: A 369 ASN cc_start: 0.7334 (m-40) cc_final: 0.7124 (m110) REVERT: A 376 GLN cc_start: 0.6776 (mm-40) cc_final: 0.6450 (mm110) REVERT: E 40 LEU cc_start: 0.8156 (tp) cc_final: 0.7832 (mt) REVERT: E 68 TYR cc_start: 0.7144 (t80) cc_final: 0.6625 (t80) REVERT: E 178 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.8644 (m-70) REVERT: E 373 MET cc_start: 0.8198 (mtt) cc_final: 0.7970 (mtp) REVERT: C 72 TYR cc_start: 0.6974 (m-80) cc_final: 0.6728 (m-80) REVERT: C 376 GLN cc_start: 0.6842 (mm-40) cc_final: 0.6546 (mm110) outliers start: 28 outliers final: 11 residues processed: 204 average time/residue: 1.3505 time to fit residues: 304.4841 Evaluate side-chains 188 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 178 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 0.0980 chunk 178 optimal weight: 6.9990 chunk 88 optimal weight: 0.2980 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 HIS B 369 ASN E 369 ASN C 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16735 Z= 0.198 Angle : 0.507 7.697 22560 Z= 0.264 Chirality : 0.038 0.158 2385 Planarity : 0.004 0.029 2770 Dihedral : 13.742 111.889 2658 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.77 % Allowed : 11.86 % Favored : 86.37 % 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: 1.14 (0.19), residues: 1870 helix: 1.25 (0.15), residues: 1250 sheet: None (None), residues: 0 loop : -0.12 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 309 HIS 0.005 0.001 HIS D 178 PHE 0.023 0.002 PHE B 248 TYR 0.024 0.002 TYR C 97 ARG 0.003 0.000 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 190 time to evaluate : 1.962 Fit side-chains REVERT: D 72 TYR cc_start: 0.7007 (m-10) cc_final: 0.6498 (m-80) REVERT: D 262 LYS cc_start: 0.7125 (mmtm) cc_final: 0.6896 (mppt) REVERT: D 376 GLN cc_start: 0.6916 (mm-40) cc_final: 0.6622 (mm110) REVERT: B 119 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8312 (tt0) REVERT: B 262 LYS cc_start: 0.7004 (mppt) cc_final: 0.6748 (mppt) REVERT: B 376 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6627 (mm110) REVERT: A 68 TYR cc_start: 0.7112 (t80) cc_final: 0.6890 (t80) REVERT: A 72 TYR cc_start: 0.6985 (m-80) cc_final: 0.6689 (m-80) REVERT: A 119 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8275 (tt0) REVERT: A 178 HIS cc_start: 0.9117 (OUTLIER) cc_final: 0.8763 (m-70) REVERT: A 353 GLN cc_start: 0.8131 (pt0) cc_final: 0.7854 (pt0) REVERT: A 360 MET cc_start: 0.8918 (mmm) cc_final: 0.8543 (mmm) REVERT: A 376 GLN cc_start: 0.6869 (mm-40) cc_final: 0.6586 (mm110) REVERT: E 40 LEU cc_start: 0.8162 (tp) cc_final: 0.7767 (mt) REVERT: E 68 TYR cc_start: 0.7344 (t80) cc_final: 0.7083 (t80) REVERT: E 72 TYR cc_start: 0.7000 (m-80) cc_final: 0.6777 (m-80) REVERT: E 373 MET cc_start: 0.8273 (mtt) cc_final: 0.8059 (mtp) REVERT: C 373 MET cc_start: 0.8279 (mtm) cc_final: 0.8040 (mtm) REVERT: C 376 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6520 (mm110) outliers start: 30 outliers final: 15 residues processed: 216 average time/residue: 1.4155 time to fit residues: 336.1986 Evaluate side-chains 200 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 184 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 178 HIS Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 371 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 0.0870 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 369 ASN E 178 HIS E 369 ASN C 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16735 Z= 0.210 Angle : 0.512 7.715 22560 Z= 0.267 Chirality : 0.038 0.158 2385 Planarity : 0.004 0.029 2770 Dihedral : 13.425 110.178 2656 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.53 % Allowed : 12.27 % Favored : 86.19 % 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: 1.13 (0.19), residues: 1870 helix: 1.24 (0.15), residues: 1255 sheet: None (None), residues: 0 loop : -0.14 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 309 HIS 0.004 0.001 HIS E 178 PHE 0.024 0.002 PHE B 248 TYR 0.024 0.002 TYR C 97 ARG 0.002 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 1.887 Fit side-chains REVERT: D 72 TYR cc_start: 0.7025 (m-10) cc_final: 0.6532 (m-80) REVERT: D 262 LYS cc_start: 0.7120 (mmtm) cc_final: 0.6907 (mppt) REVERT: D 376 GLN cc_start: 0.6935 (mm-40) cc_final: 0.6645 (mm110) REVERT: B 119 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8312 (tt0) REVERT: B 178 HIS cc_start: 0.9160 (OUTLIER) cc_final: 0.8882 (m-70) REVERT: B 376 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6667 (mm110) REVERT: A 119 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8277 (tt0) REVERT: A 353 GLN cc_start: 0.8128 (pt0) cc_final: 0.7895 (pt0) REVERT: A 360 MET cc_start: 0.8940 (mmm) cc_final: 0.8565 (mmm) REVERT: A 376 GLN cc_start: 0.6916 (mm-40) cc_final: 0.6624 (mm110) REVERT: E 40 LEU cc_start: 0.8167 (tp) cc_final: 0.7751 (mt) REVERT: E 72 TYR cc_start: 0.7044 (m-80) cc_final: 0.6802 (m-80) REVERT: E 373 MET cc_start: 0.8291 (mtt) cc_final: 0.8074 (mtp) REVERT: C 72 TYR cc_start: 0.7059 (m-80) cc_final: 0.6776 (m-80) REVERT: C 373 MET cc_start: 0.8308 (mtm) cc_final: 0.8058 (mtm) REVERT: C 376 GLN cc_start: 0.6800 (mm-40) cc_final: 0.6528 (mm110) outliers start: 26 outliers final: 11 residues processed: 212 average time/residue: 1.4475 time to fit residues: 337.4831 Evaluate side-chains 201 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 369 ASN E 369 ASN C 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16735 Z= 0.416 Angle : 0.645 8.703 22560 Z= 0.335 Chirality : 0.046 0.165 2385 Planarity : 0.005 0.039 2770 Dihedral : 13.892 112.404 2652 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.12 % Allowed : 11.80 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1870 helix: 0.98 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -0.20 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 309 HIS 0.008 0.002 HIS A 178 PHE 0.039 0.003 PHE E 248 TYR 0.030 0.003 TYR C 97 ARG 0.005 0.001 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 1.798 Fit side-chains REVERT: D 262 LYS cc_start: 0.7048 (mmtm) cc_final: 0.6836 (mppt) REVERT: D 376 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6610 (mm110) REVERT: B 119 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8322 (tt0) REVERT: A 119 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8271 (tt0) REVERT: A 353 GLN cc_start: 0.8178 (pt0) cc_final: 0.7852 (pt0) REVERT: A 360 MET cc_start: 0.8953 (mmm) cc_final: 0.8681 (mmm) REVERT: E 72 TYR cc_start: 0.7024 (m-80) cc_final: 0.6766 (m-80) REVERT: E 373 MET cc_start: 0.8393 (mtt) cc_final: 0.8160 (mtp) REVERT: C 72 TYR cc_start: 0.7039 (m-80) cc_final: 0.6754 (m-80) REVERT: C 373 MET cc_start: 0.8328 (mtm) cc_final: 0.8107 (mtm) REVERT: C 376 GLN cc_start: 0.6939 (mm-40) cc_final: 0.6615 (mm110) outliers start: 36 outliers final: 14 residues processed: 213 average time/residue: 1.3130 time to fit residues: 310.0005 Evaluate side-chains 187 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 178 HIS Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 178 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 369 ASN E 178 HIS E 369 ASN C 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16735 Z= 0.158 Angle : 0.495 7.728 22560 Z= 0.257 Chirality : 0.037 0.158 2385 Planarity : 0.003 0.029 2770 Dihedral : 12.989 108.426 2652 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.42 % Allowed : 12.98 % Favored : 85.60 % 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: 0.99 (0.19), residues: 1870 helix: 1.17 (0.15), residues: 1255 sheet: None (None), residues: 0 loop : -0.27 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 309 HIS 0.005 0.001 HIS A 178 PHE 0.020 0.001 PHE D 283 TYR 0.020 0.001 TYR B 68 ARG 0.004 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 194 time to evaluate : 1.791 Fit side-chains REVERT: D 262 LYS cc_start: 0.7084 (mmtm) cc_final: 0.6847 (mppt) REVERT: D 376 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6612 (mm110) REVERT: B 119 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8302 (tt0) REVERT: A 119 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8274 (tt0) REVERT: A 353 GLN cc_start: 0.8138 (pt0) cc_final: 0.7872 (pt0) REVERT: A 376 GLN cc_start: 0.6953 (mm-40) cc_final: 0.6701 (mm110) REVERT: E 40 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7669 (mt) REVERT: E 72 TYR cc_start: 0.7034 (m-80) cc_final: 0.6799 (m-80) REVERT: E 373 MET cc_start: 0.8263 (mtt) cc_final: 0.8032 (mtp) REVERT: C 72 TYR cc_start: 0.7002 (m-80) cc_final: 0.6759 (m-80) REVERT: C 376 GLN cc_start: 0.6924 (mm-40) cc_final: 0.6652 (mm110) outliers start: 24 outliers final: 12 residues processed: 215 average time/residue: 1.3016 time to fit residues: 310.2053 Evaluate side-chains 201 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 0.0270 chunk 121 optimal weight: 0.0040 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.5250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 178 HIS B 369 ASN A 316 GLN A 369 ASN E 369 ASN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16735 Z= 0.138 Angle : 0.473 8.432 22560 Z= 0.243 Chirality : 0.036 0.158 2385 Planarity : 0.003 0.029 2770 Dihedral : 11.998 101.248 2650 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.30 % Allowed : 13.33 % Favored : 85.37 % 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: 1.40 (0.18), residues: 1870 helix: 1.51 (0.15), residues: 1195 sheet: None (None), residues: 0 loop : -0.03 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 309 HIS 0.003 0.001 HIS A 178 PHE 0.023 0.001 PHE C 283 TYR 0.022 0.001 TYR E 68 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 1.692 Fit side-chains REVERT: D 40 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7815 (mt) REVERT: D 262 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6859 (mppt) REVERT: D 376 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6600 (mm110) REVERT: B 119 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8286 (tt0) REVERT: A 119 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8265 (tt0) REVERT: A 353 GLN cc_start: 0.8088 (pt0) cc_final: 0.7862 (pt0) REVERT: A 376 GLN cc_start: 0.6958 (mm-40) cc_final: 0.6713 (mm110) REVERT: E 40 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7693 (OUTLIER) REVERT: E 72 TYR cc_start: 0.7117 (m-80) cc_final: 0.6852 (m-80) REVERT: C 72 TYR cc_start: 0.6975 (m-80) cc_final: 0.6758 (m-80) REVERT: C 376 GLN cc_start: 0.6927 (mm-40) cc_final: 0.6674 (mm110) outliers start: 22 outliers final: 14 residues processed: 216 average time/residue: 1.3606 time to fit residues: 324.4647 Evaluate side-chains 202 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 187 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 165 optimal weight: 0.0030 chunk 109 optimal weight: 0.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 369 ASN E 369 ASN C 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16735 Z= 0.196 Angle : 0.515 8.583 22560 Z= 0.266 Chirality : 0.038 0.159 2385 Planarity : 0.004 0.029 2770 Dihedral : 11.828 99.098 2650 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.18 % Allowed : 13.69 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1870 helix: 1.39 (0.15), residues: 1225 sheet: None (None), residues: 0 loop : -0.20 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 309 HIS 0.006 0.001 HIS A 178 PHE 0.032 0.002 PHE C 283 TYR 0.023 0.002 TYR D 97 ARG 0.003 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 2.061 Fit side-chains REVERT: D 262 LYS cc_start: 0.7116 (mmtm) cc_final: 0.6618 (mppt) REVERT: D 264 TYR cc_start: 0.7640 (m-80) cc_final: 0.7380 (m-80) REVERT: D 376 GLN cc_start: 0.6861 (mm-40) cc_final: 0.6597 (mm110) REVERT: B 119 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8311 (tt0) REVERT: A 119 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8276 (tt0) REVERT: A 353 GLN cc_start: 0.8106 (pt0) cc_final: 0.7857 (pt0) REVERT: A 376 GLN cc_start: 0.6963 (mm-40) cc_final: 0.6707 (mm110) REVERT: E 72 TYR cc_start: 0.7092 (m-80) cc_final: 0.6869 (m-80) REVERT: C 51 ARG cc_start: 0.8004 (mmt90) cc_final: 0.7728 (mmt90) REVERT: C 376 GLN cc_start: 0.6928 (mm-40) cc_final: 0.6652 (mm110) outliers start: 20 outliers final: 12 residues processed: 207 average time/residue: 1.4338 time to fit residues: 330.4597 Evaluate side-chains 200 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 169 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 316 GLN A 369 ASN E 369 ASN C 369 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16735 Z= 0.251 Angle : 0.555 8.641 22560 Z= 0.288 Chirality : 0.040 0.160 2385 Planarity : 0.004 0.029 2770 Dihedral : 12.013 99.212 2650 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.12 % Allowed : 13.86 % Favored : 85.01 % 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: 1.11 (0.19), residues: 1870 helix: 1.30 (0.15), residues: 1225 sheet: None (None), residues: 0 loop : -0.23 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 309 HIS 0.008 0.001 HIS A 178 PHE 0.037 0.002 PHE C 283 TYR 0.026 0.002 TYR D 97 ARG 0.003 0.000 ARG C 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 1.721 Fit side-chains REVERT: D 8 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8512 (mt0) REVERT: D 262 LYS cc_start: 0.7143 (mmtm) cc_final: 0.6586 (mppt) REVERT: D 264 TYR cc_start: 0.7664 (m-80) cc_final: 0.7390 (m-80) REVERT: D 376 GLN cc_start: 0.6871 (mm-40) cc_final: 0.6604 (mm110) REVERT: B 72 TYR cc_start: 0.7152 (m-80) cc_final: 0.6929 (m-10) REVERT: B 119 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8317 (tt0) REVERT: A 119 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8279 (tt0) REVERT: A 353 GLN cc_start: 0.8143 (pt0) cc_final: 0.7865 (pt0) REVERT: E 373 MET cc_start: 0.8356 (mtt) cc_final: 0.8131 (mtp) REVERT: C 51 ARG cc_start: 0.8024 (mmt90) cc_final: 0.7751 (mmt90) REVERT: C 376 GLN cc_start: 0.6926 (mm-40) cc_final: 0.6645 (mm110) outliers start: 19 outliers final: 14 residues processed: 201 average time/residue: 1.3830 time to fit residues: 307.0042 Evaluate side-chains 198 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 183 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 307 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN A 369 ASN E 369 ASN C 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.124557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.099250 restraints weight = 18748.529| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.30 r_work: 0.3059 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16735 Z= 0.185 Angle : 0.521 8.380 22560 Z= 0.269 Chirality : 0.038 0.160 2385 Planarity : 0.004 0.029 2770 Dihedral : 11.864 98.705 2650 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.88 % Allowed : 14.10 % Favored : 85.01 % 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: 1.10 (0.18), residues: 1870 helix: 1.31 (0.15), residues: 1225 sheet: None (None), residues: 0 loop : -0.28 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 309 HIS 0.006 0.001 HIS A 178 PHE 0.034 0.002 PHE D 283 TYR 0.023 0.002 TYR B 97 ARG 0.003 0.000 ARG D 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5897.13 seconds wall clock time: 105 minutes 46.13 seconds (6346.13 seconds total)