Starting phenix.real_space_refine (version: dev) on Wed Feb 22 02:40:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2023/8d1k_27133_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2023/8d1k_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_2023/8d1k_27133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2023/8d1k_27133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2023/8d1k_27133_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1k_27133/02_2023/8d1k_27133_updated.pdb" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 130 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: 130 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: 133 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: 127 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: 130 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: 9.16, per 1000 atoms: 0.56 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: 6.61 Conformation dependent library (CDL) restraints added in 2.0 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: 1.36 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: 4.35 Time building geometry restraints manager: 6.88 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: 9035 23.97 - 47.93: 635 47.93 - 71.90: 175 71.90 - 95.86: 35 95.86 - 119.83: 5 Dihedral angle restraints: 9885 sinusoidal: 4320 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 9882 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 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. 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: 3.570 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: 15.250 Check model and map are aligned: 0.230 Process input model: 40.340 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.150 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9113 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 : 18.103 119.825 6295 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 % 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 *********************** 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 : 1.960 Fit side-chains outliers start: 45 outliers final: 11 residues processed: 235 average time/residue: 1.3988 time to fit residues: 362.5296 Evaluate side-chains 170 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 2.067 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 2.5976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 A 369 ASN E 208 GLN E 369 ASN E 376 GLN C 208 GLN C 369 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 16735 Z= 0.214 Angle : 0.545 7.836 22560 Z= 0.284 Chirality : 0.039 0.158 2385 Planarity : 0.004 0.027 2770 Dihedral : 13.715 118.655 2590 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer Outliers : 1.47 % 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: 1.08 (0.19), residues: 1870 helix: 1.20 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : -0.06 (0.23), residues: 650 *********************** 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 193 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.777 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 189 average time/residue: 1.4241 time to fit residues: 296.7449 Evaluate side-chains 175 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 161 time to evaluate : 1.755 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 2.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 149 optimal weight: 4.9990 chunk 166 optimal weight: 0.0370 chunk 57 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 GLN A 369 ASN E 259 ASN E 369 ASN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1391 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= 0.164 Angle : 0.485 7.403 22560 Z= 0.254 Chirality : 0.037 0.158 2385 Planarity : 0.003 0.027 2770 Dihedral : 12.865 114.469 2590 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 1.59 % 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: 1.35 (0.19), residues: 1870 helix: 1.37 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.14 (0.23), residues: 650 *********************** 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 207 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.856 Fit side-chains outliers start: 27 outliers final: 20 residues processed: 204 average time/residue: 1.3742 time to fit residues: 309.9863 Evaluate side-chains 193 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 2 average time/residue: 0.8961 time to fit residues: 4.5095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 0.0970 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 0.0070 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 GLN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1426 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= 0.211 Angle : 0.518 7.806 22560 Z= 0.270 Chirality : 0.039 0.158 2385 Planarity : 0.004 0.029 2770 Dihedral : 12.594 113.570 2590 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 1.89 % 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 (0.19), residues: 1870 helix: 1.21 (0.15), residues: 1250 sheet: None (None), residues: 0 loop : -0.11 (0.23), residues: 620 *********************** 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 211 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 1.880 Fit side-chains outliers start: 32 outliers final: 17 residues processed: 206 average time/residue: 1.4640 time to fit residues: 333.0859 Evaluate side-chains 194 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 2.044 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 1.6745 time to fit residues: 4.3934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.6980 chunk 101 optimal weight: 0.0470 chunk 2 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 chunk 160 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 GLN A 369 ASN E 369 ASN E 376 GLN C 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 16735 Z= 0.180 Angle : 0.497 7.631 22560 Z= 0.258 Chirality : 0.037 0.159 2385 Planarity : 0.003 0.029 2770 Dihedral : 12.150 112.058 2590 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer Outliers : 2.06 % 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: 1255 sheet: None (None), residues: 0 loop : -0.14 (0.23), residues: 615 *********************** 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 219 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.983 Fit side-chains outliers start: 35 outliers final: 20 residues processed: 214 average time/residue: 1.3611 time to fit residues: 322.4665 Evaluate side-chains 199 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 1.6149 time to fit residues: 4.1814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 GLN A 369 ASN E 369 ASN C 369 ASN ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.1544 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= 0.223 Angle : 0.526 7.875 22560 Z= 0.273 Chirality : 0.039 0.158 2385 Planarity : 0.004 0.029 2770 Dihedral : 11.869 110.983 2590 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer Outliers : 2.01 % 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 (0.19), residues: 1870 helix: 1.22 (0.15), residues: 1255 sheet: None (None), residues: 0 loop : -0.14 (0.23), residues: 615 *********************** 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 218 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 1.928 Fit side-chains outliers start: 34 outliers final: 21 residues processed: 215 average time/residue: 1.3417 time to fit residues: 319.8430 Evaluate side-chains 202 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 1.930 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 1.5044 time to fit residues: 4.0872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 3.9990 chunk 20 optimal weight: 0.0570 chunk 101 optimal weight: 0.0000 chunk 130 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 0.3980 chunk 178 optimal weight: 2.9990 chunk 111 optimal weight: 0.0040 chunk 108 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN B 376 GLN A 369 ASN E 369 ASN C 369 ASN ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 16735 Z= 0.126 Angle : 0.457 7.467 22560 Z= 0.235 Chirality : 0.035 0.157 2385 Planarity : 0.003 0.029 2770 Dihedral : 10.736 107.090 2590 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 1.89 % 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: 1.32 (0.19), residues: 1870 helix: 1.39 (0.15), residues: 1240 sheet: None (None), residues: 0 loop : -0.03 (0.23), residues: 630 *********************** 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 238 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 206 time to evaluate : 1.974 Fit side-chains outliers start: 32 outliers final: 22 residues processed: 233 average time/residue: 1.3383 time to fit residues: 347.6458 Evaluate side-chains 198 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 1.955 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 2.5731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 chunk 34 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 0.0060 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 316 GLN B 259 ASN B 369 ASN B 376 GLN A 369 ASN E 369 ASN E 376 GLN C 369 ASN ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 16735 Z= 0.138 Angle : 0.462 8.253 22560 Z= 0.238 Chirality : 0.036 0.159 2385 Planarity : 0.003 0.029 2770 Dihedral : 10.274 101.856 2590 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 1.65 % 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: 1.41 (0.19), residues: 1870 helix: 1.44 (0.15), residues: 1240 sheet: None (None), residues: 0 loop : 0.06 (0.23), residues: 630 *********************** 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 208 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 2.052 Fit side-chains outliers start: 28 outliers final: 22 residues processed: 206 average time/residue: 1.3067 time to fit residues: 299.9192 Evaluate side-chains 196 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 22 residues processed: 0 time to fit residues: 2.3321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 100 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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: 0.9089 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 16735 Z= 0.295 Angle : 0.573 8.629 22560 Z= 0.298 Chirality : 0.042 0.158 2385 Planarity : 0.004 0.030 2770 Dihedral : 10.959 99.826 2590 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer Outliers : 1.65 % 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: 1255 sheet: None (None), residues: 0 loop : -0.13 (0.23), residues: 615 *********************** 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 205 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 177 time to evaluate : 1.998 Fit side-chains outliers start: 28 outliers final: 20 residues processed: 203 average time/residue: 1.2876 time to fit residues: 291.1532 Evaluate side-chains 195 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 2.4090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 chunk 169 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.9031 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 16735 Z= 0.150 Angle : 0.481 7.932 22560 Z= 0.249 Chirality : 0.037 0.159 2385 Planarity : 0.003 0.028 2770 Dihedral : 10.415 97.050 2590 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer Outliers : 1.30 % 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: 1.36 (0.19), residues: 1870 helix: 1.41 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.06 (0.23), residues: 650 ********************** 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 196 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.754 Fit side-chains outliers start: 22 outliers final: 21 residues processed: 196 average time/residue: 1.2857 time to fit residues: 282.1648 Evaluate side-chains 192 residues out of total 1695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 21 residues processed: 0 time to fit residues: 2.4196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 129 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3504 r_free = 0.3504 target = 0.123431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097685 restraints weight = 18749.834| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.32 r_work: 0.3043 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 16735 Z= 0.283 Angle : 0.561 8.282 22560 Z= 0.292 Chirality : 0.041 0.159 2385 Planarity : 0.004 0.030 2770 Dihedral : 10.894 96.826 2590 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer Outliers : 1.59 % 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: 1.18 (0.19), residues: 1870 helix: 1.32 (0.15), residues: 1225 sheet: None (None), residues: 0 loop : -0.14 (0.22), residues: 645 =============================================================================== Job complete usr+sys time: 5666.39 seconds wall clock time: 101 minutes 28.59 seconds (6088.59 seconds total)