Starting phenix.real_space_refine on Sun Aug 11 04:16:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/08_2024/7t0z_25585_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/08_2024/7t0z_25585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/08_2024/7t0z_25585.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/08_2024/7t0z_25585.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/08_2024/7t0z_25585_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t0z_25585/08_2024/7t0z_25585_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 86 5.16 5 C 10215 2.51 5 N 2568 2.21 5 O 2912 1.98 5 H 15348 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31129 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 5471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5471 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 5448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5448 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 5470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5470 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 5447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5447 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 5447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5447 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 319} Chain: "H" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1862 Classifications: {'peptide': 125} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1664 Classifications: {'peptide': 109} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 15.37, per 1000 atoms: 0.49 Number of scatterers: 31129 At special positions: 0 Unit cell: (145.665, 114.374, 132.717, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 O 2912 8.00 N 2568 7.00 C 10215 6.00 H 15348 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN M 8 " - " MAN M 9 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG D 401 " - " ASN D 111 " Time building additional restraints: 26.19 Conformation dependent library (CDL) restraints added in 3.1 seconds 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 14 sheets defined 36.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 7 through 21 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 170 through 173 Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 218 through 239 removed outlier: 4.854A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 3.846A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 242 No H-bonds generated for 'chain 'A' and resid 240 through 242' Processing helix chain 'A' and resid 246 through 272 Processing helix chain 'A' and resid 279 through 307 removed outlier: 4.330A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 339 Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 73 through 76 Processing helix chain 'B' and resid 87 through 92 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 223 through 246 removed outlier: 5.086A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.000A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 277 removed outlier: 3.550A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 311 Processing helix chain 'B' and resid 314 through 345 Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 8 through 21 Processing helix chain 'C' and resid 70 through 73 Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 170 through 173 Processing helix chain 'C' and resid 218 through 239 removed outlier: 5.404A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.796A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 272 removed outlier: 4.289A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 307 removed outlier: 4.650A pdb=" N PHE C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 339 removed outlier: 3.553A pdb=" N ALA C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 12 through 23 removed outlier: 4.052A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 Processing helix chain 'D' and resid 284 through 311 Processing helix chain 'D' and resid 314 through 347 Proline residue: D 330 - end of helix removed outlier: 4.147A pdb=" N ARG D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 Processing helix chain 'E' and resid 85 through 88 removed outlier: 4.003A pdb=" N LYS E 88 " --> pdb=" O ARG E 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 85 through 88' Processing helix chain 'E' and resid 233 through 256 removed outlier: 3.505A pdb=" N THR E 237 " --> pdb=" O MET E 233 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.750A pdb=" N SER E 251 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 283 removed outlier: 3.838A pdb=" N THR E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 321 Processing helix chain 'E' and resid 324 through 357 removed outlier: 3.608A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.727A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.656A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.875A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 51 removed outlier: 8.346A pdb=" N VAL A 38 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N ARG A 68 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N MET A 40 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ALA A 66 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE A 42 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLN A 64 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE A 44 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR A 62 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR A 58 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL A 50 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP A 56 " --> pdb=" O VAL A 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 68 current: chain 'A' and resid 123 through 135 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.950A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 54 removed outlier: 6.441A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 59 " --> pdb=" O PRO B 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 71 current: chain 'B' and resid 126 through 138 Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 101 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 99 through 101 current: chain 'B' and resid 209 through 221 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 47 removed outlier: 6.469A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 68 current: chain 'C' and resid 123 through 135 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.618A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 203 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 49 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 through 49 current: chain 'D' and resid 59 through 71 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 71 current: chain 'D' and resid 126 through 138 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 99 through 101 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 99 through 101 current: chain 'D' and resid 208 through 221 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 51 through 66 removed outlier: 6.418A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU E 71 " --> pdb=" O PRO E 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 71 through 83 current: chain 'E' and resid 138 through 150 Processing sheet with id=AB1, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.571A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'H' and resid 33 through 39 removed outlier: 6.973A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 113 through 114 Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 99 602 hydrogen bonds defined for protein. 1731 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: 10.31 Time building geometry restraints manager: 26.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14880 1.03 - 1.23: 1305 1.23 - 1.43: 6255 1.43 - 1.63: 8942 1.63 - 1.83: 149 Bond restraints: 31531 Sorted by residual: bond pdb=" N TYR A 205 " pdb=" H TYR A 205 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" N ARG L 91 " pdb=" H ARG L 91 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N TYR L 97 " pdb=" H TYR L 97 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.84e+01 bond pdb=" N THR B 130 " pdb=" H THR B 130 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" N PHE B 65 " pdb=" H PHE B 65 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 31526 not shown) Histogram of bond angle deviations from ideal: 97.63 - 104.97: 281 104.97 - 112.30: 35393 112.30 - 119.64: 8410 119.64 - 126.98: 12358 126.98 - 134.32: 203 Bond angle restraints: 56645 Sorted by residual: angle pdb=" N THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 110.65 102.42 8.23 1.47e+00 4.63e-01 3.13e+01 angle pdb=" C THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 109.55 118.14 -8.59 1.68e+00 3.54e-01 2.61e+01 angle pdb=" CA VAL H 104 " pdb=" C VAL H 104 " pdb=" O VAL H 104 " ideal model delta sigma weight residual 121.92 116.93 4.99 1.17e+00 7.31e-01 1.82e+01 angle pdb=" CA PRO C 206 " pdb=" C PRO C 206 " pdb=" O PRO C 206 " ideal model delta sigma weight residual 121.98 116.78 5.20 1.23e+00 6.61e-01 1.79e+01 angle pdb=" CA GLU C 155 " pdb=" C GLU C 155 " pdb=" O GLU C 155 " ideal model delta sigma weight residual 121.58 116.87 4.71 1.16e+00 7.43e-01 1.65e+01 ... (remaining 56640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 14394 21.62 - 43.24: 690 43.24 - 64.86: 156 64.86 - 86.48: 36 86.48 - 108.10: 14 Dihedral angle restraints: 15290 sinusoidal: 8338 harmonic: 6952 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -30.53 -55.47 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CA CYS E 165 " pdb=" C CYS E 165 " pdb=" N PRO E 166 " pdb=" CA PRO E 166 " ideal model delta harmonic sigma weight residual 180.00 -154.25 -25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ARG D 37 " pdb=" C ARG D 37 " pdb=" N VAL D 38 " pdb=" CA VAL D 38 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 15287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2049 0.056 - 0.113: 432 0.113 - 0.169: 62 0.169 - 0.225: 4 0.225 - 0.281: 3 Chirality restraints: 2550 Sorted by residual: chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2547 not shown) Planarity restraints: 4529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 303 " 0.170 2.00e-02 2.50e+03 4.99e-01 3.74e+03 pdb=" CG ASN A 303 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 303 " -0.167 2.00e-02 2.50e+03 pdb=" ND2 ASN A 303 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 303 " -0.842 2.00e-02 2.50e+03 pdb="HD22 ASN A 303 " 0.854 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 238 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C ILE E 238 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE E 238 " -0.019 2.00e-02 2.50e+03 pdb=" N GLN E 239 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 155 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C GLU C 155 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU C 155 " -0.016 2.00e-02 2.50e+03 pdb=" N SER C 156 " -0.015 2.00e-02 2.50e+03 ... (remaining 4526 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1040 2.15 - 2.76: 58938 2.76 - 3.37: 87142 3.37 - 3.99: 117843 3.99 - 4.60: 182369 Nonbonded interactions: 447332 Sorted by model distance: nonbonded pdb=" O ASP B 145 " pdb=" H MET B 148 " model vdw 1.533 2.450 nonbonded pdb=" O SER B 92 " pdb="HH12 ARG C 86 " model vdw 1.559 2.450 nonbonded pdb=" HH TYR B 60 " pdb=" O PRO B 154 " model vdw 1.580 2.450 nonbonded pdb=" OD1 ASP A 101 " pdb="HH22 ARG B 132 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLU D 59 " pdb=" HZ2 LYS D 105 " model vdw 1.583 2.450 ... (remaining 447327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD22)) or resid 150 through 340)) selection = (chain 'C' and resid 7 through 340) } ncs_group { reference = (chain 'B' and (resid 10 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 112 through 347)) selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.500 Extract box with map and model: 1.210 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 97.940 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 0.087 16183 Z= 0.402 Angle : 0.743 10.463 22014 Z= 0.411 Chirality : 0.048 0.281 2550 Planarity : 0.005 0.049 2705 Dihedral : 14.331 108.098 6183 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: -0.22 (0.19), residues: 1898 helix: 1.48 (0.20), residues: 621 sheet: -0.78 (0.22), residues: 540 loop : -0.97 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 246 HIS 0.005 0.001 HIS C 267 PHE 0.022 0.002 PHE D 258 TYR 0.029 0.002 TYR C 299 ARG 0.006 0.001 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 THR cc_start: 0.8798 (t) cc_final: 0.7741 (t) REVERT: D 20 ASP cc_start: 0.8115 (m-30) cc_final: 0.7853 (m-30) REVERT: D 131 MET cc_start: 0.8553 (mtp) cc_final: 0.8222 (mtp) REVERT: D 190 GLN cc_start: 0.8162 (pt0) cc_final: 0.7306 (pm20) REVERT: E 99 ASN cc_start: 0.8120 (m110) cc_final: 0.7819 (m-40) REVERT: E 162 GLU cc_start: 0.6620 (tm-30) cc_final: 0.6175 (tm-30) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 2.5723 time to fit residues: 942.7323 Evaluate side-chains 254 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 169 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 GLN E 60 ASN H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.003 0.050 16183 Z= 0.199 Angle : 0.566 8.224 22014 Z= 0.295 Chirality : 0.042 0.154 2550 Planarity : 0.005 0.061 2705 Dihedral : 8.542 74.789 2619 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.65 % Allowed : 9.41 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.11 (0.19), residues: 1898 helix: 1.70 (0.20), residues: 626 sheet: -0.42 (0.23), residues: 502 loop : -0.88 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 246 HIS 0.003 0.001 HIS C 267 PHE 0.015 0.001 PHE A 31 TYR 0.029 0.001 TYR C 299 ARG 0.007 0.001 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 266 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.7860 (mp0) cc_final: 0.7494 (mp0) REVERT: B 332 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6162 (mp) REVERT: C 294 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7048 (mpt) REVERT: D 17 ARG cc_start: 0.7265 (mtm110) cc_final: 0.6979 (mtm110) REVERT: D 20 ASP cc_start: 0.8071 (m-30) cc_final: 0.7854 (m-30) REVERT: D 78 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6645 (tmmt) REVERT: D 112 MET cc_start: 0.8089 (ttp) cc_final: 0.7861 (ttp) REVERT: D 131 MET cc_start: 0.8484 (mtp) cc_final: 0.8191 (mtp) REVERT: D 190 GLN cc_start: 0.8151 (pt0) cc_final: 0.7282 (pm20) REVERT: E 162 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6394 (tm-30) REVERT: E 214 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8311 (mtmm) REVERT: H 76 LYS cc_start: 0.8074 (mttt) cc_final: 0.7398 (mmtm) outliers start: 28 outliers final: 13 residues processed: 278 average time/residue: 2.4234 time to fit residues: 755.5069 Evaluate side-chains 263 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 246 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 170 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN E 60 ASN E 99 ASN L 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16183 Z= 0.268 Angle : 0.558 6.987 22014 Z= 0.291 Chirality : 0.042 0.153 2550 Planarity : 0.004 0.051 2705 Dihedral : 7.273 68.288 2619 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.82 % Allowed : 10.94 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.27 % 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: 0.17 (0.19), residues: 1898 helix: 1.81 (0.20), residues: 626 sheet: -0.38 (0.22), residues: 513 loop : -0.92 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 246 HIS 0.004 0.001 HIS C 267 PHE 0.015 0.001 PHE H 106 TYR 0.029 0.002 TYR C 299 ARG 0.006 0.001 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3796 Ramachandran restraints generated. 1898 Oldfield, 0 Emsley, 1898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6907 (mtt-85) REVERT: B 312 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6854 (tptm) REVERT: B 332 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6215 (mp) REVERT: C 207 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8279 (ttm-80) REVERT: C 294 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7034 (mpt) REVERT: C 305 ILE cc_start: 0.8320 (tp) cc_final: 0.7976 (mt) REVERT: D 17 ARG cc_start: 0.7319 (mtm110) cc_final: 0.7039 (mtm110) REVERT: D 20 ASP cc_start: 0.8013 (m-30) cc_final: 0.7715 (m-30) REVERT: D 131 MET cc_start: 0.8521 (mtp) cc_final: 0.8269 (mtp) REVERT: D 190 GLN cc_start: 0.8171 (pt0) cc_final: 0.7289 (pm20) REVERT: D 294 TYR cc_start: 0.7371 (t80) cc_final: 0.6955 (t80) REVERT: E 162 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6620 (tm-30) REVERT: E 214 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8349 (mtmm) outliers start: 31 outliers final: 18 residues processed: 269 average time/residue: 2.2715 time to fit residues: 688.7813 Evaluate side-chains 264 residues out of total 1700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 17 ARG Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 244 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 345 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 170 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: