Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 02:27:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/04_2023/8d1g_27129_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/04_2023/8d1g_27129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/04_2023/8d1g_27129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/04_2023/8d1g_27129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/04_2023/8d1g_27129_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1g_27129/04_2023/8d1g_27129_trim.pdb" } resolution = 2.07 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= 0.130 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: 7 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 80 5.16 5 Cl 1 4.86 5 C 10490 2.51 5 N 2355 2.21 5 O 3255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "E PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 303": "OD1" <-> "OD2" Residue "E GLU 333": "OE1" <-> "OE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C GLU 333": "OE1" <-> "OE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 303": "OD1" <-> "OD2" Residue "D GLU 333": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16201 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "B" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "E" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "C" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "D" Number of atoms: 2870 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 347, 2863 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 9, 'TRANS': 337} Chain breaks: 2 bond proxies already assigned to first conformer: 2931 Chain: "A" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 247 Unusual residues: {' CA': 1, ' CL': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Unusual residues: {' CA': 1, 'DU0': 1, 'MC3': 10} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 7, 'MC3:plan-1': 7} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "E" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "C" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Time building chain proxies: 15.31, per 1000 atoms: 0.95 Number of scatterers: 16201 At special positions: 0 Unit cell: (90.47, 92.13, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 5 19.99 Cl 1 17.00 S 80 16.00 P 15 15.00 O 3255 8.00 N 2355 7.00 C 10490 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: 7.02 Conformation dependent library (CDL) restraints added in 4.1 seconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU A 22 " --> pdb=" O GLN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 296 removed outlier: 4.498A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'B' and resid 6 through 10 Processing helix chain 'B' and resid 17 through 23 removed outlier: 3.593A pdb=" N LEU B 22 " --> pdb=" O GLN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 182 through 198 Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 296 removed outlier: 4.498A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 323 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU E 22 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 174 Processing helix chain 'E' and resid 182 through 198 Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 296 removed outlier: 4.497A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 323 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU C 22 " --> pdb=" O GLN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 53 removed outlier: 5.608A pdb=" N ARG C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 296 removed outlier: 4.498A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 323 Processing helix chain 'D' and resid 6 through 10 Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.594A pdb=" N LEU D 22 " --> pdb=" O GLN D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.607A pdb=" N ARG D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 174 Processing helix chain 'D' and resid 182 through 198 Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 296 removed outlier: 4.497A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 323 980 hydrogen bonds defined for protein. 2830 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: 4.71 Time building geometry restraints manager: 7.45 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: 2240 1.32 - 1.44: 4570 1.44 - 1.56: 8985 1.56 - 1.69: 30 1.69 - 1.81: 120 Bond restraints: 15945 Sorted by residual: bond pdb=" N VAL D 81 " pdb=" CA VAL D 81 " ideal model delta sigma weight residual 1.460 1.496 -0.037 1.21e-02 6.83e+03 9.18e+00 bond pdb=" N VAL C 81 " pdb=" CA VAL C 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.90e+00 bond pdb=" N VAL A 81 " pdb=" CA VAL A 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.86e+00 bond pdb=" N VAL B 81 " pdb=" CA VAL B 81 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.83e+00 bond pdb=" N VAL E 81 " pdb=" CA VAL E 81 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.58e+00 ... (remaining 15940 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.75: 250 105.75 - 112.85: 7971 112.85 - 119.94: 6207 119.94 - 127.04: 6791 127.04 - 134.13: 156 Bond angle restraints: 21375 Sorted by residual: angle pdb=" O3P MC3 E 505 " pdb=" P MC3 E 505 " pdb=" O4P MC3 E 505 " ideal model delta sigma weight residual 93.26 104.22 -10.96 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 A 504 " pdb=" P MC3 A 504 " pdb=" O4P MC3 A 504 " ideal model delta sigma weight residual 93.26 104.22 -10.96 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 B 504 " pdb=" P MC3 B 504 " pdb=" O4P MC3 B 504 " ideal model delta sigma weight residual 93.26 104.20 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 C 504 " pdb=" P MC3 C 504 " pdb=" O4P MC3 C 504 " ideal model delta sigma weight residual 93.26 104.20 -10.94 3.00e+00 1.11e-01 1.33e+01 angle pdb=" O3P MC3 D 505 " pdb=" P MC3 D 505 " pdb=" O4P MC3 D 505 " ideal model delta sigma weight residual 93.26 104.20 -10.94 3.00e+00 1.11e-01 1.33e+01 ... (remaining 21370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.46: 8458 27.46 - 54.91: 752 54.91 - 82.37: 100 82.37 - 109.83: 20 109.83 - 137.28: 10 Dihedral angle restraints: 9340 sinusoidal: 4190 harmonic: 5150 Sorted by residual: dihedral pdb=" C33 MC3 D 505 " pdb=" C31 MC3 D 505 " pdb=" C32 MC3 D 505 " pdb=" O2 MC3 D 505 " ideal model delta sinusoidal sigma weight residual 175.52 -47.20 -137.28 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C33 MC3 C 504 " pdb=" C31 MC3 C 504 " pdb=" C32 MC3 C 504 " pdb=" O2 MC3 C 504 " ideal model delta sinusoidal sigma weight residual 175.52 -47.20 -137.28 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C33 MC3 A 504 " pdb=" C31 MC3 A 504 " pdb=" C32 MC3 A 504 " pdb=" O2 MC3 A 504 " ideal model delta sinusoidal sigma weight residual 175.52 -47.22 -137.26 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 9337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1453 0.034 - 0.067: 590 0.067 - 0.101: 141 0.101 - 0.135: 46 0.135 - 0.168: 15 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CA VAL B 232 " pdb=" N VAL B 232 " pdb=" C VAL B 232 " pdb=" CB VAL B 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CA VAL D 232 " pdb=" N VAL D 232 " pdb=" C VAL D 232 " pdb=" CB VAL D 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA VAL A 232 " pdb=" N VAL A 232 " pdb=" C VAL A 232 " pdb=" CB VAL A 232 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 2242 not shown) Planarity restraints: 2530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE E 282 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C PHE E 282 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE E 282 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE E 283 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 282 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C PHE D 282 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE D 282 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE D 283 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 282 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C PHE B 282 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE B 282 " -0.010 2.00e-02 2.50e+03 pdb=" N PHE B 283 " -0.009 2.00e-02 2.50e+03 ... (remaining 2527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1879 2.75 - 3.28: 16364 3.28 - 3.82: 31540 3.82 - 4.36: 38590 4.36 - 4.90: 60758 Nonbonded interactions: 149131 Sorted by model distance: nonbonded pdb=" O HOH B 655 " pdb=" O HOH C 704 " model vdw 2.207 2.440 nonbonded pdb=" O HOH A 704 " pdb=" O HOH E 655 " model vdw 2.215 2.440 nonbonded pdb=" O HOH A 655 " pdb=" O HOH B 704 " model vdw 2.215 2.440 nonbonded pdb=" O HOH E 704 " pdb=" O HOH D 656 " model vdw 2.219 2.440 nonbonded pdb=" O HOH C 655 " pdb=" O HOH D 704 " model vdw 2.226 2.440 ... (remaining 149126 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 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 through 507 or (resid 508 and (name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or na \ me C42 or name C43 or name C44)) or resid 509 through 511 or (resid 512 and (nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44)))) selection = (chain 'B' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 through 507 or (resid 508 and (name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or na \ me C42 or name C43 or name C44)) or resid 509 through 511 or (resid 512 and (nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44)))) selection = (chain 'C' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 through 507 or (resid 508 and (name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or na \ me C42 or name C43 or name C44)) or resid 509 through 511 or (resid 512 and (nam \ e C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or \ name C44)))) selection = (chain 'D' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 or (resid 505 through 506 and (name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C40 or name C41 or name C42 or name C43 or name C44)) or (resid 507 through 5 \ 08 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 name C43 or name C44)) or resid \ 509 or (resid 510 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 name C43 or name \ C44)) or (resid 511 through 512 and (name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43 or name C44)))) selection = (chain 'E' and (resid 2 through 204 or resid 206 through 239 or resid 241 throug \ h 365 or resid 504 or (resid 505 through 506 and (name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or na \ me C40 or name C41 or name C42 or name C43 or name C44)) or (resid 507 through 5 \ 08 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 name C43 or name C44)) or resid \ 509 or (resid 510 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 name C43 or name \ C44)) or (resid 511 through 512 and (name C37 or name C38 or name C39 or name C4 \ 0 or name C41 or name C42 or name C43 or name C44)))) } 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=0.50 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: 3.430 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: 0.020 Extract box with map and model: 14.700 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 51.130 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.006 0.050 15945 Z= 0.376 Angle : 0.690 10.959 21375 Z= 0.368 Chirality : 0.041 0.168 2245 Planarity : 0.003 0.018 2530 Dihedral : 19.814 137.282 6040 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 0.66 % 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: 1.81 (0.20), residues: 1715 helix: 1.80 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.14 (0.28), residues: 515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 212 time to evaluate : 1.806 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 218 average time/residue: 1.6764 time to fit residues: 397.1374 Evaluate side-chains 179 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.4289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 316 GLN B 173 ASN B 175 ASN B 316 GLN E 173 ASN E 175 ASN E 316 GLN C 175 ASN C 316 GLN D 19 GLN D 316 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15945 Z= 0.164 Angle : 0.487 4.987 21375 Z= 0.276 Chirality : 0.037 0.162 2245 Planarity : 0.003 0.025 2530 Dihedral : 17.644 118.663 2770 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.18 % 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: 1.97 (0.20), residues: 1715 helix: 1.91 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.15 (0.29), residues: 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 1.879 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 200 average time/residue: 1.5876 time to fit residues: 347.0100 Evaluate side-chains 190 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 183 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.6181 time to fit residues: 4.6061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 0.0970 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 175 ASN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15945 Z= 0.158 Angle : 0.471 5.149 21375 Z= 0.268 Chirality : 0.036 0.159 2245 Planarity : 0.003 0.029 2530 Dihedral : 15.945 109.893 2770 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.20), residues: 1715 helix: 1.94 (0.14), residues: 1245 sheet: None (None), residues: 0 loop : -0.23 (0.28), residues: 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 198 time to evaluate : 1.729 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 204 average time/residue: 1.6097 time to fit residues: 358.6133 Evaluate side-chains 198 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 193 time to evaluate : 1.764 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1518 time to fit residues: 2.6388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 175 ASN E 19 GLN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15945 Z= 0.173 Angle : 0.489 5.612 21375 Z= 0.277 Chirality : 0.037 0.161 2245 Planarity : 0.004 0.030 2530 Dihedral : 15.269 105.642 2770 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer Outliers : 1.18 % 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: 1.98 (0.20), residues: 1715 helix: 1.92 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.18 (0.28), residues: 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 191 time to evaluate : 1.854 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 198 average time/residue: 1.5793 time to fit residues: 342.5292 Evaluate side-chains 193 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 5 residues processed: 5 average time/residue: 0.7327 time to fit residues: 6.7186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 175 ASN E 19 GLN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 15945 Z= 0.211 Angle : 0.532 5.966 21375 Z= 0.297 Chirality : 0.039 0.163 2245 Planarity : 0.004 0.033 2530 Dihedral : 15.102 102.187 2770 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.20), residues: 1715 helix: 1.86 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.22 (0.28), residues: 500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 1.764 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 192 average time/residue: 1.5261 time to fit residues: 321.8594 Evaluate side-chains 184 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 1.844 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1470 time to fit residues: 2.9909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 32 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 175 ASN E 19 GLN E 58 GLN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15945 Z= 0.190 Angle : 0.504 6.319 21375 Z= 0.284 Chirality : 0.038 0.162 2245 Planarity : 0.004 0.032 2530 Dihedral : 14.813 100.917 2770 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 0.79 % 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: 1.91 (0.20), residues: 1715 helix: 1.89 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.22 (0.28), residues: 500 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.729 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 186 average time/residue: 1.6166 time to fit residues: 329.8444 Evaluate side-chains 185 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 1.791 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.6201 time to fit residues: 4.6511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 175 ASN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 15945 Z= 0.164 Angle : 0.478 6.409 21375 Z= 0.271 Chirality : 0.037 0.160 2245 Planarity : 0.003 0.032 2530 Dihedral : 14.284 100.735 2770 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer Outliers : 0.79 % 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: 1.98 (0.20), residues: 1715 helix: 1.91 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.14 (0.28), residues: 495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 1.786 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 191 average time/residue: 1.5226 time to fit residues: 319.3694 Evaluate side-chains 187 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 1.799 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.6073 time to fit residues: 4.6064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 175 ASN E 71 GLN E 173 ASN E 175 ASN C 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 15945 Z= 0.156 Angle : 0.471 6.958 21375 Z= 0.267 Chirality : 0.036 0.159 2245 Planarity : 0.003 0.032 2530 Dihedral : 13.911 101.155 2770 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.20), residues: 1715 helix: 1.94 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.13 (0.28), residues: 495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.883 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 190 average time/residue: 1.5115 time to fit residues: 315.5052 Evaluate side-chains 185 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.1547 time to fit residues: 2.6150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 19 GLN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 15945 Z= 0.214 Angle : 0.531 8.087 21375 Z= 0.296 Chirality : 0.039 0.163 2245 Planarity : 0.004 0.033 2530 Dihedral : 14.094 101.270 2770 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 0.59 % 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: 1.89 (0.20), residues: 1715 helix: 1.83 (0.14), residues: 1220 sheet: None (None), residues: 0 loop : -0.12 (0.28), residues: 495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.853 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 185 average time/residue: 1.4894 time to fit residues: 303.7277 Evaluate side-chains 188 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 1.5317 time to fit residues: 4.0576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 19 GLN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 15945 Z= 0.182 Angle : 0.501 7.825 21375 Z= 0.282 Chirality : 0.037 0.161 2245 Planarity : 0.004 0.033 2530 Dihedral : 13.903 101.097 2770 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 0.52 % 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: 1.93 (0.20), residues: 1715 helix: 1.90 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.23 (0.28), residues: 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 187 time to evaluate : 1.821 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 192 average time/residue: 1.5214 time to fit residues: 321.2876 Evaluate side-chains 185 residues out of total 1505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 180 time to evaluate : 1.821 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 1.6176 time to fit residues: 4.1958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN B 173 ASN B 175 ASN E 19 GLN E 173 ASN E 175 ASN C 175 ASN D 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.133960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.103863 restraints weight = 31747.622| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.51 r_work: 0.3138 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 15945 Z= 0.356 Angle : 0.664 9.040 21375 Z= 0.361 Chirality : 0.045 0.184 2245 Planarity : 0.005 0.049 2530 Dihedral : 14.820 102.138 2770 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 0.59 % 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: 1.57 (0.19), residues: 1715 helix: 1.60 (0.14), residues: 1215 sheet: None (None), residues: 0 loop : -0.24 (0.27), residues: 500 =============================================================================== Job complete usr+sys time: 6049.13 seconds wall clock time: 108 minutes 30.28 seconds (6510.28 seconds total)