Starting phenix.real_space_refine on Mon Nov 18 19:45:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/11_2024/8st4_40757_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/11_2024/8st4_40757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/11_2024/8st4_40757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/11_2024/8st4_40757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/11_2024/8st4_40757_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st4_40757/11_2024/8st4_40757_trim.cif" } resolution = 2.35 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 132 5.16 5 Na 1 4.78 5 C 16317 2.51 5 N 4102 2.21 5 O 4738 1.98 5 H 24869 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 50159 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "B" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5882 Classifications: {'peptide': 359} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 337} Chain breaks: 1 Chain: "C" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5882 Classifications: {'peptide': 359} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 337} Chain breaks: 1 Chain: "D" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 6257 Classifications: {'peptide': 379} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 359} Chain: "E" Number of atoms: 5882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 5882 Classifications: {'peptide': 359} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 337} Chain breaks: 1 Chain: "F" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "G" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "H" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "I" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "J" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "K" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3265 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "L" 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: 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: "N" 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: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {'ACH': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 22.94, per 1000 atoms: 0.46 Number of scatterers: 50159 At special positions: 0 Unit cell: (143.3, 205.325, 145.438, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 Na 1 11.00 O 4738 8.00 N 4102 7.00 C 16317 6.00 H 24869 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 199 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 202 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 701 " - " ASN A 31 " " NAG A 702 " - " ASN A 81 " " NAG A 703 " - " ASN A 148 " " NAG D 701 " - " ASN D 31 " " NAG D 702 " - " ASN D 81 " " NAG D 703 " - " ASN D 148 " " NAG L 1 " - " ASN B 143 " " NAG M 1 " - " ASN C 143 " " NAG N 1 " - " ASN E 143 " Time building additional restraints: 13.44 Conformation dependent library (CDL) restraints added in 3.7 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5996 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 51 sheets defined 27.6% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.94 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 75 through 80 removed outlier: 4.278A pdb=" N GLU A 80 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 234 through 235 No H-bonds generated for 'chain 'A' and resid 234 through 235' Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.723A pdb=" N GLY A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 268 Processing helix chain 'A' and resid 278 through 306 Processing helix chain 'A' and resid 315 through 330 removed outlier: 5.833A pdb=" N VAL A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 341 through 382 Proline residue: A 379 - end of helix Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.835A pdb=" N THR B 68 " --> pdb=" O TYR B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.025A pdb=" N ASP B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.223A pdb=" N ILE B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix removed outlier: 3.647A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 4.821A pdb=" N VAL B 230 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 239 through 262 Processing helix chain 'B' and resid 270 through 298 Processing helix chain 'B' and resid 307 through 315 Processing helix chain 'B' and resid 316 through 323 removed outlier: 3.933A pdb=" N ALA B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 364 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 70 through 75 removed outlier: 4.232A pdb=" N ASP C 75 " --> pdb=" O GLU C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 209 through 225 removed outlier: 4.627A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix Processing helix chain 'C' and resid 226 through 227 No H-bonds generated for 'chain 'C' and resid 226 through 227' Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.578A pdb=" N GLY C 238 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 262 Processing helix chain 'C' and resid 270 through 298 Processing helix chain 'C' and resid 307 through 315 Processing helix chain 'C' and resid 316 through 322 removed outlier: 3.777A pdb=" N ALA C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 363 Processing helix chain 'D' and resid 6 through 19 Processing helix chain 'D' and resid 75 through 80 removed outlier: 4.248A pdb=" N GLU D 80 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 217 through 233 removed outlier: 4.537A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix Processing helix chain 'D' and resid 234 through 235 No H-bonds generated for 'chain 'D' and resid 234 through 235' Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 247 through 268 Processing helix chain 'D' and resid 278 through 306 Processing helix chain 'D' and resid 315 through 330 removed outlier: 5.756A pdb=" N VAL D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 341 through 382 Proline residue: D 379 - end of helix Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 70 through 75 removed outlier: 3.681A pdb=" N ASP E 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 209 through 225 removed outlier: 4.492A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix Processing helix chain 'E' and resid 226 through 227 No H-bonds generated for 'chain 'E' and resid 226 through 227' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 239 through 262 Processing helix chain 'E' and resid 270 through 298 Processing helix chain 'E' and resid 307 through 323 removed outlier: 5.436A pdb=" N LEU E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Proline residue: E 319 - end of helix Processing helix chain 'E' and resid 338 through 363 Processing helix chain 'F' and resid 84 through 88 Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'G' and resid 29 through 33 removed outlier: 3.504A pdb=" N TYR G 33 " --> pdb=" O PHE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 193 through 198 removed outlier: 3.992A pdb=" N SER G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 210 Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 187 through 192 removed outlier: 3.638A pdb=" N GLU H 192 " --> pdb=" O LYS H 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.745A pdb=" N TYR I 33 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.593A pdb=" N ARG I 66 " --> pdb=" O GLU I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing helix chain 'J' and resid 84 through 88 Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 187 through 193 Processing helix chain 'K' and resid 29 through 33 removed outlier: 3.569A pdb=" N TYR K 33 " --> pdb=" O PHE K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'K' and resid 193 through 198 removed outlier: 4.428A pdb=" N SER K 197 " --> pdb=" O SER K 193 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.800A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY A 121 " --> pdb=" O ASP A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 3.800A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY A 121 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET A 56 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP A 49 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR A 58 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.464A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG A 214 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ILE A 185 " --> pdb=" O ARG A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 83 removed outlier: 4.064A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 83 removed outlier: 4.064A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 51 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VAL B 45 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR B 53 " --> pdb=" O ILE B 43 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP B 57 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU B 39 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR B 59 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL B 37 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLU B 61 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 35 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N GLU B 63 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL B 33 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.128A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE B 204 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.128A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 83 removed outlier: 4.132A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 83 removed outlier: 4.132A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER C 44 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN C 55 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU C 63 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR C 32 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.157A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.157A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.843A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY D 121 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.843A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY D 121 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET D 56 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASP D 49 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR D 58 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.371A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 189 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ARG D 214 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE D 185 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.022A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY E 116 " --> pdb=" O ASP E 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.022A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY E 116 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE E 51 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER E 44 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR E 53 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU E 42 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN E 55 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU E 63 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR E 32 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.224A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE E 204 " --> pdb=" O VAL E 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.224A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.768A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP F 40 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.873A pdb=" N ASN F 142 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER F 179 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 149 through 152 removed outlier: 3.530A pdb=" N ASN F 150 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AC6, first strand: chain 'F' and resid 196 through 198 Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.051A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.428A pdb=" N ILE G 35 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU G 51 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 130 removed outlier: 3.605A pdb=" N CYS G 147 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.534A pdb=" N VAL G 143 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 158 through 161 Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.007A pdb=" N GLY H 89 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP H 40 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.549A pdb=" N ASN H 142 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASN H 142 " --> pdb=" O MET H 180 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N MET H 180 " --> pdb=" O ASN H 142 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER H 179 " --> pdb=" O THR H 169 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.549A pdb=" N ASN H 142 " --> pdb=" O THR H 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 149 through 152 removed outlier: 3.794A pdb=" N LYS H 212 " --> pdb=" O CYS H 199 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 154 through 155 Processing sheet with id=AD9, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE1, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.368A pdb=" N ILE I 35 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU I 51 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.587A pdb=" N LYS I 150 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 143 " --> pdb=" O VAL I 190 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.587A pdb=" N LYS I 150 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER I 187 " --> pdb=" O HIS I 171 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 158 through 161 removed outlier: 4.319A pdb=" N CYS I 202 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS I 215 " --> pdb=" O CYS I 202 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.841A pdb=" N GLY J 89 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU J 38 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR J 54 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TRP J 40 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 119 through 123 removed outlier: 6.085A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER J 179 " --> pdb=" O THR J 169 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 119 through 123 Processing sheet with id=AE9, first strand: chain 'J' and resid 158 through 160 removed outlier: 4.494A pdb=" N TRP J 153 " --> pdb=" O ARG J 160 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS J 152 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N HIS J 203 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER J 208 " --> pdb=" O HIS J 203 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AF2, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.359A pdb=" N ILE K 35 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU K 51 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP K 37 " --> pdb=" O ILE K 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 129 through 131 removed outlier: 3.916A pdb=" N GLY K 146 " --> pdb=" O LEU K 131 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL K 149 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR K 182 " --> pdb=" O GLY K 151 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N SER K 185 " --> pdb=" O PRO K 174 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 142 through 144 removed outlier: 3.523A pdb=" N VAL K 143 " --> pdb=" O VAL K 190 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 203 through 206 1193 hydrogen bonds defined for protein. 3264 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: 23.19 Time building geometry restraints manager: 15.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 24844 1.02 - 1.22: 44 1.22 - 1.43: 10950 1.43 - 1.63: 14787 1.63 - 1.84: 201 Bond restraints: 50826 Sorted by residual: bond pdb=" NE ARG C 155 " pdb=" HE ARG C 155 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" N ASN B 97 " pdb=" CA ASN B 97 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.32e-02 5.74e+03 7.90e+00 bond pdb=" C ARG C 155 " pdb=" O ARG C 155 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.29e-02 6.01e+03 7.84e+00 bond pdb=" N ASP B 99 " pdb=" CA ASP B 99 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.06e-02 8.90e+03 7.59e+00 bond pdb=" C ILE B 51 " pdb=" O ILE B 51 " ideal model delta sigma weight residual 1.236 1.208 0.027 1.00e-02 1.00e+04 7.44e+00 ... (remaining 50821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 91161 1.96 - 3.92: 617 3.92 - 5.88: 56 5.88 - 7.85: 5 7.85 - 9.81: 3 Bond angle restraints: 91842 Sorted by residual: angle pdb=" N ASP G 180 " pdb=" CA ASP G 180 " pdb=" C ASP G 180 " ideal model delta sigma weight residual 114.56 107.89 6.67 1.27e+00 6.20e-01 2.76e+01 angle pdb=" C TYR J 145 " pdb=" N PRO J 146 " pdb=" CD PRO J 146 " ideal model delta sigma weight residual 120.60 111.75 8.85 2.20e+00 2.07e-01 1.62e+01 angle pdb=" CA ASN B 97 " pdb=" C ASN B 97 " pdb=" O ASN B 97 " ideal model delta sigma weight residual 121.87 117.50 4.37 1.10e+00 8.26e-01 1.58e+01 angle pdb=" CA SER C 113 " pdb=" C SER C 113 " pdb=" O SER C 113 " ideal model delta sigma weight residual 121.72 117.17 4.55 1.18e+00 7.18e-01 1.48e+01 angle pdb=" CA ILE C 43 " pdb=" C ILE C 43 " pdb=" O ILE C 43 " ideal model delta sigma weight residual 121.17 117.49 3.68 1.06e+00 8.90e-01 1.21e+01 ... (remaining 91837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.01: 22746 22.01 - 44.01: 1324 44.01 - 66.02: 274 66.02 - 88.02: 65 88.02 - 110.03: 13 Dihedral angle restraints: 24422 sinusoidal: 13201 harmonic: 11221 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual 93.00 158.99 -65.99 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS E 130 " pdb=" SG CYS E 130 " pdb=" SG CYS E 144 " pdb=" CB CYS E 144 " ideal model delta sinusoidal sigma weight residual 93.00 36.39 56.61 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 149.15 -56.15 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 24419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3737 0.082 - 0.164: 354 0.164 - 0.246: 3 0.246 - 0.328: 3 0.328 - 0.411: 1 Chirality restraints: 4098 Sorted by residual: chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 81 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 4095 not shown) Planarity restraints: 7336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 97 " -0.137 2.00e-02 2.50e+03 1.48e-01 3.29e+02 pdb=" CG ASN B 97 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN B 97 " 0.132 2.00e-02 2.50e+03 pdb=" ND2 ASN B 97 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 97 " -0.222 2.00e-02 2.50e+03 pdb="HD22 ASN B 97 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR J 145 " 0.081 5.00e-02 4.00e+02 1.24e-01 2.45e+01 pdb=" N PRO J 146 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO J 146 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO J 146 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 81 " -0.029 2.00e-02 2.50e+03 3.29e-02 1.35e+01 pdb=" CG ASN A 81 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 81 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 81 " 0.054 2.00e-02 2.50e+03 pdb=" C1 NAG A 702 " -0.039 2.00e-02 2.50e+03 ... (remaining 7333 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 85 1.80 - 2.50: 37119 2.50 - 3.20: 151523 3.20 - 3.90: 205476 3.90 - 4.60: 321795 Nonbonded interactions: 715998 Sorted by model distance: nonbonded pdb=" O PRO B 234 " pdb=" HG CYS B 237 " model vdw 1.103 2.620 nonbonded pdb=" HH TYR E 95 " pdb=" HA TRP E 151 " model vdw 1.435 2.270 nonbonded pdb=" OE1 GLU F 86 " pdb=" H GLU F 86 " model vdw 1.475 2.450 nonbonded pdb=" HH TYR B 196 " pdb=" OD2 ASP B 198 " model vdw 1.482 2.450 nonbonded pdb=" HD1 HIS J 203 " pdb=" OG1 THR J 205 " model vdw 1.597 2.450 ... (remaining 715993 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' selection = chain 'D' } ncs_group { reference = (chain 'B' and resid 1 through 365) selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.640 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: 0.830 Extract box with map and model: 1.850 Check model and map are aligned: 0.330 Set scattering table: 0.470 Process input model: 102.420 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.230 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25957 Z= 0.274 Angle : 0.579 9.371 35403 Z= 0.305 Chirality : 0.046 0.411 4098 Planarity : 0.004 0.124 4377 Dihedral : 15.892 110.029 9566 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.03 % Allowed : 14.08 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3115 helix: 1.76 (0.20), residues: 668 sheet: -0.25 (0.16), residues: 1000 loop : -0.51 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 69 HIS 0.004 0.001 HIS E 329 PHE 0.018 0.001 PHE C 254 TYR 0.017 0.002 TYR E 95 ARG 0.007 0.001 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 3.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 2.9098 time to fit residues: 914.9642 Evaluate side-chains 233 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 257 optimal weight: 9.9990 chunk 231 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 239 optimal weight: 30.0000 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 177 optimal weight: 2.9990 chunk 276 optimal weight: 40.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN B 297 HIS C 60 GLN F 27 GLN F 171 GLN G 60 ASN H 43 GLN H 143 ASN I 203 ASN J 35 ASN J 171 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25957 Z= 0.201 Angle : 0.546 5.527 35403 Z= 0.288 Chirality : 0.044 0.156 4098 Planarity : 0.004 0.071 4377 Dihedral : 6.881 69.679 3709 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.08 % Allowed : 14.04 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3115 helix: 1.91 (0.20), residues: 678 sheet: -0.21 (0.16), residues: 1007 loop : -0.52 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 62 HIS 0.003 0.001 HIS F 194 PHE 0.014 0.001 PHE C 254 TYR 0.014 0.001 TYR E 344 ARG 0.007 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7576 (m-30) REVERT: G 83 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7501 (tt0) outliers start: 31 outliers final: 10 residues processed: 262 average time/residue: 2.8112 time to fit residues: 862.0548 Evaluate side-chains 237 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 225 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 152 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 153 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 277 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 275 optimal weight: 30.0000 chunk 94 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN F 194 HIS G 60 ASN J 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25957 Z= 0.237 Angle : 0.539 6.489 35403 Z= 0.283 Chirality : 0.044 0.151 4098 Planarity : 0.004 0.058 4377 Dihedral : 5.575 46.268 3709 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.22 % Allowed : 13.83 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3115 helix: 1.69 (0.19), residues: 690 sheet: -0.21 (0.16), residues: 1014 loop : -0.59 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 62 HIS 0.003 0.001 HIS C 298 PHE 0.016 0.001 PHE C 254 TYR 0.017 0.001 TYR K 105 ARG 0.012 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 240 time to evaluate : 4.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7602 (m-30) REVERT: J 18 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6491 (tt0) REVERT: K 47 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7412 (mt-10) outliers start: 35 outliers final: 17 residues processed: 263 average time/residue: 2.5863 time to fit residues: 809.0352 Evaluate side-chains 251 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 4.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain J residue 18 GLN Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 274 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 278 optimal weight: 40.0000 chunk 294 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 79 optimal weight: 0.3980 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 171 GLN G 60 ASN H 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25957 Z= 0.239 Angle : 0.537 7.343 35403 Z= 0.282 Chirality : 0.044 0.149 4098 Planarity : 0.004 0.078 4377 Dihedral : 5.027 32.553 3709 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.36 % Allowed : 13.87 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3115 helix: 1.70 (0.19), residues: 688 sheet: -0.20 (0.16), residues: 1030 loop : -0.59 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 62 HIS 0.003 0.001 HIS D 9 PHE 0.015 0.001 PHE C 254 TYR 0.014 0.001 TYR G 104 ARG 0.014 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 237 time to evaluate : 4.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: C 347 MET cc_start: 0.8492 (mtp) cc_final: 0.8252 (mtp) REVERT: H 32 SER cc_start: 0.4901 (OUTLIER) cc_final: 0.4605 (p) outliers start: 39 outliers final: 23 residues processed: 264 average time/residue: 2.6426 time to fit residues: 829.8792 Evaluate side-chains 259 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 time to evaluate : 3.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain J residue 154 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 245 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 219 optimal weight: 0.0470 chunk 121 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN F 171 GLN G 60 ASN H 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25957 Z= 0.212 Angle : 0.521 7.284 35403 Z= 0.272 Chirality : 0.044 0.147 4098 Planarity : 0.004 0.079 4377 Dihedral : 4.765 25.564 3709 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.40 % Allowed : 14.04 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.15), residues: 3115 helix: 1.75 (0.20), residues: 688 sheet: -0.17 (0.16), residues: 1030 loop : -0.57 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 101 HIS 0.003 0.001 HIS D 9 PHE 0.019 0.001 PHE I 173 TYR 0.014 0.001 TYR K 105 ARG 0.014 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7601 (m-30) REVERT: C 347 MET cc_start: 0.8485 (mtp) cc_final: 0.8227 (mtp) REVERT: H 32 SER cc_start: 0.4899 (OUTLIER) cc_final: 0.4603 (p) REVERT: K 47 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7411 (mt-10) outliers start: 40 outliers final: 24 residues processed: 268 average time/residue: 2.6399 time to fit residues: 835.3415 Evaluate side-chains 259 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 4.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 76 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 99 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 295 optimal weight: 4.9990 chunk 244 optimal weight: 0.4980 chunk 136 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 ASN H 18 GLN H 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25957 Z= 0.154 Angle : 0.493 7.461 35403 Z= 0.256 Chirality : 0.043 0.143 4098 Planarity : 0.004 0.056 4377 Dihedral : 4.513 24.938 3709 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.98 % Allowed : 14.39 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.15), residues: 3115 helix: 2.01 (0.20), residues: 678 sheet: -0.13 (0.16), residues: 1036 loop : -0.53 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 168 HIS 0.002 0.001 HIS E 136 PHE 0.018 0.001 PHE I 173 TYR 0.011 0.001 TYR I 104 ARG 0.008 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 4.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: C 347 MET cc_start: 0.8467 (mtp) cc_final: 0.8202 (mtp) outliers start: 28 outliers final: 18 residues processed: 261 average time/residue: 2.7261 time to fit residues: 840.4626 Evaluate side-chains 261 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain J residue 154 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 284 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 215 optimal weight: 0.0980 chunk 166 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN F 171 GLN G 60 ASN H 18 GLN H 43 GLN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25957 Z= 0.193 Angle : 0.505 7.639 35403 Z= 0.262 Chirality : 0.043 0.147 4098 Planarity : 0.004 0.057 4377 Dihedral : 4.540 25.585 3709 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.01 % Allowed : 14.29 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3115 helix: 2.02 (0.20), residues: 678 sheet: -0.11 (0.15), residues: 1070 loop : -0.50 (0.17), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 168 HIS 0.003 0.001 HIS C 298 PHE 0.014 0.001 PHE I 173 TYR 0.012 0.001 TYR G 104 ARG 0.010 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 4.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: C 347 MET cc_start: 0.8474 (mtp) cc_final: 0.8213 (mtp) REVERT: H 32 SER cc_start: 0.4879 (OUTLIER) cc_final: 0.4597 (p) outliers start: 29 outliers final: 18 residues processed: 261 average time/residue: 2.8553 time to fit residues: 888.5502 Evaluate side-chains 256 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 76 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 181 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 186 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 231 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25957 Z= 0.149 Angle : 0.490 8.364 35403 Z= 0.253 Chirality : 0.043 0.142 4098 Planarity : 0.004 0.061 4377 Dihedral : 4.398 24.864 3709 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.94 % Allowed : 14.46 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3115 helix: 2.19 (0.20), residues: 672 sheet: -0.09 (0.16), residues: 1033 loop : -0.44 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 168 HIS 0.002 0.001 HIS E 136 PHE 0.014 0.001 PHE I 173 TYR 0.011 0.001 TYR G 104 ARG 0.010 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 243 time to evaluate : 4.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: C 347 MET cc_start: 0.8461 (mtp) cc_final: 0.8186 (mtp) REVERT: H 32 SER cc_start: 0.4966 (OUTLIER) cc_final: 0.4602 (p) outliers start: 27 outliers final: 16 residues processed: 263 average time/residue: 2.7620 time to fit residues: 855.4316 Evaluate side-chains 255 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 154 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 267 optimal weight: 0.2980 chunk 281 optimal weight: 40.0000 chunk 256 optimal weight: 20.0000 chunk 273 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 84 optimal weight: 0.6980 chunk 247 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 chunk 272 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 ASN H 43 GLN J 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25957 Z= 0.215 Angle : 0.518 9.158 35403 Z= 0.268 Chirality : 0.043 0.149 4098 Planarity : 0.004 0.085 4377 Dihedral : 4.541 27.577 3709 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.01 % Allowed : 14.53 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3115 helix: 2.06 (0.20), residues: 678 sheet: -0.10 (0.16), residues: 1067 loop : -0.46 (0.17), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 168 HIS 0.003 0.001 HIS C 298 PHE 0.015 0.001 PHE C 254 TYR 0.013 0.001 TYR E 95 ARG 0.013 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 4.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: C 347 MET cc_start: 0.8454 (mtp) cc_final: 0.8188 (mtp) REVERT: H 32 SER cc_start: 0.4961 (OUTLIER) cc_final: 0.4671 (p) outliers start: 29 outliers final: 22 residues processed: 260 average time/residue: 2.7986 time to fit residues: 865.1868 Evaluate side-chains 262 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 76 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 179 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 201 optimal weight: 5.9990 chunk 303 optimal weight: 8.9990 chunk 279 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 148 optimal weight: 0.0170 overall best weight: 1.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 ASN H 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25957 Z= 0.249 Angle : 0.538 9.408 35403 Z= 0.280 Chirality : 0.044 0.151 4098 Planarity : 0.004 0.072 4377 Dihedral : 4.671 27.114 3709 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.98 % Allowed : 14.57 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.15), residues: 3115 helix: 2.01 (0.20), residues: 672 sheet: -0.13 (0.15), residues: 1069 loop : -0.46 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 168 HIS 0.003 0.001 HIS C 298 PHE 0.016 0.001 PHE C 254 TYR 0.021 0.001 TYR E 275 ARG 0.013 0.000 ARG F 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 4.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7609 (m-30) REVERT: C 347 MET cc_start: 0.8476 (mtp) cc_final: 0.8218 (mtp) REVERT: H 32 SER cc_start: 0.5066 (OUTLIER) cc_final: 0.4726 (p) outliers start: 28 outliers final: 25 residues processed: 257 average time/residue: 2.6931 time to fit residues: 816.1820 Evaluate side-chains 263 residues out of total 2863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 3.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 168 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain C residue 2 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 169 HIS Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain I residue 60 ASN Chi-restraints excluded: chain J residue 154 LYS Chi-restraints excluded: chain K residue 76 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 305 random chunks: chunk 192 optimal weight: 50.0000 chunk 257 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.159355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103736 restraints weight = 83278.170| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.42 r_work: 0.2983 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25957 Z= 0.186 Angle : 0.518 9.554 35403 Z= 0.267 Chirality : 0.043 0.147 4098 Planarity : 0.004 0.065 4377 Dihedral : 4.597 26.244 3709 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.94 % Allowed : 14.53 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3115 helix: 2.06 (0.20), residues: 672 sheet: -0.12 (0.15), residues: 1067 loop : -0.46 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 101 HIS 0.003 0.001 HIS D 9 PHE 0.013 0.001 PHE C 254 TYR 0.018 0.001 TYR E 275 ARG 0.012 0.000 ARG I 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15842.94 seconds wall clock time: 275 minutes 43.66 seconds (16543.66 seconds total)