Starting phenix.real_space_refine on Tue Jul 23 23:25:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b27_44099/07_2024/9b27_44099_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b27_44099/07_2024/9b27_44099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b27_44099/07_2024/9b27_44099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b27_44099/07_2024/9b27_44099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b27_44099/07_2024/9b27_44099_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b27_44099/07_2024/9b27_44099_neut.cif" } resolution = 3.51 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= 0.020 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 P 12 5.49 5 Mg 6 5.21 5 S 163 5.16 5 C 15057 2.51 5 N 4024 2.21 5 O 4566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 915": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23828 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3259 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 13, 'TRANS': 383} Chain breaks: 1 Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3001 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.75, per 1000 atoms: 0.58 Number of scatterers: 23828 At special positions: 0 Unit cell: (132.84, 140.4, 232.2, 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 163 16.00 P 12 15.00 Mg 6 11.99 O 4566 8.00 N 4024 7.00 C 15057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.25 Conformation dependent library (CDL) restraints added in 4.4 seconds 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5612 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 37 sheets defined 53.3% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.157A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.845A pdb=" N GLY A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.724A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.554A pdb=" N ARG A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.695A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.747A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.761A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.245A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.725A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.614A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.767A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.143A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.794A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.156A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.583A pdb=" N GLU B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.709A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.603A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.573A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.945A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.613A pdb=" N PHE B 352 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 353' Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.528A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.710A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.054A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.746A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.960A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.535A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.586A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.765A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 306 removed outlier: 4.027A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 303 through 306' Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.809A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.533A pdb=" N PHE C 352 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 349 through 353' Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.600A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.616A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.027A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.684A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.547A pdb=" N ARG D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.568A pdb=" N GLU D 226 " --> pdb=" O ASP D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.683A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.548A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.960A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.567A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.619A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.673A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.076A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.904A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.661A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.682A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.866A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 347 removed outlier: 3.983A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 349 No H-bonds generated for 'chain 'E' and resid 348 through 349' Processing helix chain 'E' and resid 350 through 354 removed outlier: 3.719A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 350 through 354' Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.919A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.676A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.721A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.048A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.501A pdb=" N ARG F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.660A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 261 removed outlier: 3.541A pdb=" N LEU F 261 " --> pdb=" O PRO F 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 258 through 261' Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.586A pdb=" N LEU F 293 " --> pdb=" O ILE F 289 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.116A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.707A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 removed outlier: 3.668A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 354 removed outlier: 3.704A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.213A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 785 through 790 Processing helix chain 'G' and resid 791 through 802 Processing helix chain 'G' and resid 836 through 851 Processing helix chain 'G' and resid 853 through 864 Processing helix chain 'G' and resid 870 through 880 removed outlier: 3.577A pdb=" N ILE G 874 " --> pdb=" O THR G 870 " (cutoff:3.500A) Processing helix chain 'G' and resid 883 through 892 Processing helix chain 'G' and resid 893 through 900 removed outlier: 3.725A pdb=" N GLU G 896 " --> pdb=" O LEU G 893 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR G 897 " --> pdb=" O LYS G 894 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASP G 898 " --> pdb=" O GLU G 895 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 900 " --> pdb=" O TYR G 897 " (cutoff:3.500A) Processing helix chain 'G' and resid 901 through 913 removed outlier: 3.776A pdb=" N VAL G 913 " --> pdb=" O VAL G 909 " (cutoff:3.500A) Processing helix chain 'G' and resid 916 through 952 removed outlier: 4.526A pdb=" N SER G 930 " --> pdb=" O LYS G 926 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU G 931 " --> pdb=" O LEU G 927 " (cutoff:3.500A) Proline residue: G 938 - end of helix Processing helix chain 'G' and resid 954 through 971 Processing helix chain 'G' and resid 984 through 991 removed outlier: 3.990A pdb=" N CYS G 988 " --> pdb=" O SER G 985 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG G 991 " --> pdb=" O CYS G 988 " (cutoff:3.500A) Processing helix chain 'G' and resid 1001 through 1013 Processing helix chain 'G' and resid 1016 through 1018 No H-bonds generated for 'chain 'G' and resid 1016 through 1018' Processing helix chain 'G' and resid 1019 through 1024 removed outlier: 3.514A pdb=" N GLU G1023 " --> pdb=" O LYS G1019 " (cutoff:3.500A) Processing helix chain 'G' and resid 1026 through 1031 Processing helix chain 'G' and resid 1034 through 1058 Processing helix chain 'G' and resid 1068 through 1105 removed outlier: 3.712A pdb=" N LYS G1072 " --> pdb=" O LYS G1068 " (cutoff:3.500A) Processing helix chain 'G' and resid 1114 through 1166 Processing helix chain 'H' and resid 746 through 750 removed outlier: 3.949A pdb=" N GLY H 749 " --> pdb=" O LEU H 746 " (cutoff:3.500A) Processing helix chain 'H' and resid 785 through 790 Processing helix chain 'H' and resid 791 through 802 Processing helix chain 'H' and resid 837 through 851 Processing helix chain 'H' and resid 853 through 864 Processing helix chain 'H' and resid 870 through 880 removed outlier: 3.514A pdb=" N ILE H 874 " --> pdb=" O THR H 870 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN H 880 " --> pdb=" O ASN H 876 " (cutoff:3.500A) Processing helix chain 'H' and resid 883 through 892 Processing helix chain 'H' and resid 893 through 897 removed outlier: 3.688A pdb=" N GLU H 896 " --> pdb=" O LEU H 893 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR H 897 " --> pdb=" O LYS H 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 893 through 897' Processing helix chain 'H' and resid 901 through 912 removed outlier: 3.620A pdb=" N THR H 912 " --> pdb=" O VAL H 908 " (cutoff:3.500A) Processing helix chain 'H' and resid 916 through 928 Processing helix chain 'H' and resid 928 through 953 Proline residue: H 938 - end of helix removed outlier: 3.778A pdb=" N LYS H 952 " --> pdb=" O GLU H 948 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER H 953 " --> pdb=" O GLU H 949 " (cutoff:3.500A) Processing helix chain 'H' and resid 953 through 971 Processing helix chain 'H' and resid 983 through 991 removed outlier: 4.189A pdb=" N CYS H 988 " --> pdb=" O SER H 985 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG H 991 " --> pdb=" O CYS H 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 1001 through 1013 Processing helix chain 'H' and resid 1016 through 1020 removed outlier: 3.977A pdb=" N LYS H1019 " --> pdb=" O GLU H1016 " (cutoff:3.500A) Processing helix chain 'H' and resid 1029 through 1033 removed outlier: 4.201A pdb=" N ARG H1032 " --> pdb=" O LYS H1029 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL H1033 " --> pdb=" O ALA H1030 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1029 through 1033' Processing helix chain 'H' and resid 1034 through 1059 Processing helix chain 'H' and resid 1068 through 1105 removed outlier: 3.505A pdb=" N GLU H1082 " --> pdb=" O LYS H1078 " (cutoff:3.500A) Processing helix chain 'H' and resid 1113 through 1143 removed outlier: 3.655A pdb=" N ASP H1120 " --> pdb=" O GLU H1116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.795A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.468A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.793A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.326A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.534A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.189A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.827A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.725A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.705A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.985A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.493A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.301A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.636A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.080A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'G' and resid 981 through 982 1167 hydrogen bonds defined for protein. 3210 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: 8.82 Time building geometry restraints manager: 10.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6318 1.33 - 1.45: 4178 1.45 - 1.57: 13516 1.57 - 1.69: 18 1.69 - 1.81: 288 Bond restraints: 24318 Sorted by residual: bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.15e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.80e+00 ... (remaining 24313 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.48: 579 105.48 - 113.21: 13036 113.21 - 120.94: 11940 120.94 - 128.67: 7208 128.67 - 136.40: 145 Bond angle restraints: 32908 Sorted by residual: angle pdb=" C PHE H1105 " pdb=" N VAL H1106 " pdb=" CA VAL H1106 " ideal model delta sigma weight residual 121.97 131.27 -9.30 1.80e+00 3.09e-01 2.67e+01 angle pdb=" C LYS H 952 " pdb=" N SER H 953 " pdb=" CA SER H 953 " ideal model delta sigma weight residual 122.36 129.01 -6.65 1.42e+00 4.96e-01 2.19e+01 angle pdb=" C LEU A 110 " pdb=" N ASN A 111 " pdb=" CA ASN A 111 " ideal model delta sigma weight residual 120.49 126.99 -6.50 1.42e+00 4.96e-01 2.10e+01 angle pdb=" CA VAL H1106 " pdb=" CB VAL H1106 " pdb=" CG1 VAL H1106 " ideal model delta sigma weight residual 110.40 117.78 -7.38 1.70e+00 3.46e-01 1.88e+01 angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 122.08 128.38 -6.30 1.47e+00 4.63e-01 1.84e+01 ... (remaining 32903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 14506 35.66 - 71.32: 241 71.32 - 106.97: 15 106.97 - 142.63: 8 142.63 - 178.29: 9 Dihedral angle restraints: 14779 sinusoidal: 6076 harmonic: 8703 Sorted by residual: dihedral pdb=" CD ARG G 915 " pdb=" NE ARG G 915 " pdb=" CZ ARG G 915 " pdb=" NH1 ARG G 915 " ideal model delta sinusoidal sigma weight residual 0.00 -82.84 82.84 1 1.00e+01 1.00e-02 8.40e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 121.71 178.29 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 106.12 -166.12 1 2.00e+01 2.50e-03 4.73e+01 ... (remaining 14776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3235 0.082 - 0.164: 360 0.164 - 0.246: 32 0.246 - 0.328: 13 0.328 - 0.410: 1 Chirality restraints: 3641 Sorted by residual: chirality pdb=" CB VAL H1106 " pdb=" CA VAL H1106 " pdb=" CG1 VAL H1106 " pdb=" CG2 VAL H1106 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3638 not shown) Planarity restraints: 4227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 915 " -1.081 9.50e-02 1.11e+02 4.84e-01 1.41e+02 pdb=" NE ARG G 915 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG G 915 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 915 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG G 915 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO B 112 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 111 " 0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO D 112 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO D 112 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 112 " 0.043 5.00e-02 4.00e+02 ... (remaining 4224 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 12 2.20 - 2.87: 8180 2.87 - 3.55: 30284 3.55 - 4.22: 55941 4.22 - 4.90: 95472 Nonbonded interactions: 189889 Sorted by model distance: nonbonded pdb=" NH1 ARG G 915 " pdb=" N ARG G 917 " model vdw 1.519 3.200 nonbonded pdb=" NH1 ARG G 915 " pdb=" CB ARG G 917 " model vdw 2.007 3.520 nonbonded pdb=" NH1 ARG G 915 " pdb=" CA ARG G 917 " model vdw 2.092 3.550 nonbonded pdb=" O3A ADP D 401 " pdb="MG MG D 402 " model vdw 2.093 2.170 nonbonded pdb=" O2A ADP E 401 " pdb="MG MG E 402 " model vdw 2.104 2.170 ... (remaining 189884 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 750 through 803 or resid 836 through 1143)) selection = (chain 'H' and (resid 750 through 803 or resid 836 through 1143)) } 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 group one per residue 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: 9.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.170 Set scattering table: 0.250 Process input model: 65.030 Find NCS groups from input model: 1.770 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 0.074 24318 Z= 0.286 Angle : 0.819 11.004 32908 Z= 0.441 Chirality : 0.053 0.410 3641 Planarity : 0.011 0.484 4227 Dihedral : 15.443 178.291 9167 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.73 % Favored : 96.14 % Rotamer: Outliers : 0.23 % Allowed : 0.27 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.13), residues: 2953 helix: -3.33 (0.08), residues: 1378 sheet: -0.42 (0.25), residues: 396 loop : -0.97 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 767 HIS 0.005 0.001 HIS C 161 PHE 0.029 0.002 PHE G1020 TYR 0.015 0.001 TYR H1104 ARG 0.007 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 362 time to evaluate : 2.682 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: A 34 ILE cc_start: 0.8877 (pt) cc_final: 0.8538 (tp) REVERT: A 51 ASP cc_start: 0.8659 (p0) cc_final: 0.8449 (t0) REVERT: A 225 ASN cc_start: 0.8689 (m-40) cc_final: 0.8455 (t0) REVERT: A 269 MET cc_start: 0.8561 (mtp) cc_final: 0.8267 (mtt) REVERT: A 305 MET cc_start: 0.8701 (mmm) cc_final: 0.8499 (mmm) REVERT: B 123 MET cc_start: 0.8599 (mmt) cc_final: 0.8156 (mmm) REVERT: B 257 CYS cc_start: 0.8991 (t) cc_final: 0.8752 (p) REVERT: B 283 MET cc_start: 0.7367 (mmm) cc_final: 0.6840 (tmm) REVERT: D 25 ASP cc_start: 0.7489 (m-30) cc_final: 0.7077 (p0) REVERT: D 82 MET cc_start: 0.8832 (tpt) cc_final: 0.8305 (mmm) REVERT: D 190 MET cc_start: 0.7896 (mtp) cc_final: 0.7545 (mtt) REVERT: D 299 MET cc_start: 0.8200 (mtm) cc_final: 0.7627 (mtt) REVERT: D 363 ASP cc_start: 0.8911 (m-30) cc_final: 0.8562 (p0) REVERT: E 10 CYS cc_start: 0.8374 (t) cc_final: 0.7899 (t) REVERT: E 12 ASN cc_start: 0.7608 (m110) cc_final: 0.6932 (m-40) REVERT: E 121 GLN cc_start: 0.9280 (tt0) cc_final: 0.8969 (tm-30) REVERT: E 132 MET cc_start: 0.8322 (ppp) cc_final: 0.8024 (ptt) REVERT: E 142 LEU cc_start: 0.7239 (tp) cc_final: 0.6852 (tp) REVERT: E 149 THR cc_start: 0.8340 (t) cc_final: 0.8132 (m) REVERT: E 325 MET cc_start: 0.8172 (mmm) cc_final: 0.7840 (mpp) REVERT: E 354 GLN cc_start: 0.9245 (pt0) cc_final: 0.9011 (pp30) REVERT: E 355 MET cc_start: 0.8388 (mtp) cc_final: 0.7943 (mtp) REVERT: F 119 MET cc_start: 0.8625 (mtp) cc_final: 0.8359 (mtm) REVERT: F 191 LYS cc_start: 0.9092 (tttm) cc_final: 0.8864 (ttmt) REVERT: F 340 TRP cc_start: 0.7089 (t60) cc_final: 0.6318 (t60) REVERT: G 869 LEU cc_start: 0.7166 (mt) cc_final: 0.6931 (mt) REVERT: G 1019 LYS cc_start: 0.9596 (mttt) cc_final: 0.9306 (mtmm) REVERT: G 1026 HIS cc_start: 0.8657 (m90) cc_final: 0.8354 (m-70) REVERT: G 1090 MET cc_start: 0.8786 (mtp) cc_final: 0.8307 (mmm) REVERT: G 1118 PHE cc_start: 0.9349 (m-80) cc_final: 0.9121 (m-80) REVERT: G 1143 GLU cc_start: 0.9012 (tt0) cc_final: 0.8590 (pt0) REVERT: H 889 MET cc_start: 0.8166 (mtm) cc_final: 0.7852 (tmm) REVERT: H 1071 GLU cc_start: 0.8417 (tt0) cc_final: 0.7871 (mp0) REVERT: H 1127 MET cc_start: 0.6912 (mtt) cc_final: 0.6620 (ptp) outliers start: 6 outliers final: 2 residues processed: 368 average time/residue: 0.3720 time to fit residues: 212.3721 Evaluate side-chains 210 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 208 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 915 ARG Chi-restraints excluded: chain G residue 1113 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 92 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN B 12 ASN D 137 GLN D 162 ASN E 162 ASN E 246 GLN F 41 GLN ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1037 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24318 Z= 0.172 Angle : 0.578 7.180 32908 Z= 0.287 Chirality : 0.042 0.192 3641 Planarity : 0.005 0.073 4227 Dihedral : 11.307 178.915 3318 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.01 % Allowed : 6.25 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 2953 helix: -0.55 (0.12), residues: 1387 sheet: -0.11 (0.26), residues: 396 loop : -0.49 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 781 HIS 0.006 0.001 HIS H1122 PHE 0.018 0.001 PHE G1107 TYR 0.017 0.001 TYR G 969 ARG 0.007 0.000 ARG E 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 2.918 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: symmetry clash REVERT: A 8 LEU cc_start: 0.8988 (mt) cc_final: 0.8752 (mm) REVERT: A 269 MET cc_start: 0.8514 (mtp) cc_final: 0.8217 (mtt) REVERT: A 355 MET cc_start: 0.8815 (tpp) cc_final: 0.8537 (ttm) REVERT: B 44 MET cc_start: 0.8326 (mmp) cc_final: 0.7437 (ptp) REVERT: B 123 MET cc_start: 0.8849 (mmt) cc_final: 0.8529 (mmm) REVERT: B 132 MET cc_start: 0.8714 (ptm) cc_final: 0.8083 (ppp) REVERT: B 283 MET cc_start: 0.7375 (mmm) cc_final: 0.6865 (tmm) REVERT: C 123 MET cc_start: 0.8830 (tpp) cc_final: 0.8592 (tpp) REVERT: D 25 ASP cc_start: 0.7514 (m-30) cc_final: 0.7145 (p0) REVERT: D 82 MET cc_start: 0.8959 (tpt) cc_final: 0.8066 (mmm) REVERT: D 190 MET cc_start: 0.8043 (mtp) cc_final: 0.7694 (mtt) REVERT: D 299 MET cc_start: 0.8134 (mtm) cc_final: 0.7790 (mtm) REVERT: D 361 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8358 (mp0) REVERT: E 44 MET cc_start: 0.8540 (mpp) cc_final: 0.8332 (tpp) REVERT: E 132 MET cc_start: 0.7769 (ppp) cc_final: 0.7525 (ptt) REVERT: E 142 LEU cc_start: 0.7114 (tp) cc_final: 0.6842 (tp) REVERT: E 227 MET cc_start: 0.7100 (mmm) cc_final: 0.6650 (mmm) REVERT: E 355 MET cc_start: 0.8443 (mtp) cc_final: 0.8062 (mtp) REVERT: F 82 MET cc_start: 0.7894 (tpp) cc_final: 0.7683 (tpp) REVERT: F 340 TRP cc_start: 0.7262 (t60) cc_final: 0.5954 (t60) REVERT: G 1019 LYS cc_start: 0.9609 (mttt) cc_final: 0.9370 (mtmm) REVERT: G 1026 HIS cc_start: 0.8676 (m90) cc_final: 0.8255 (m90) REVERT: G 1143 GLU cc_start: 0.8970 (tt0) cc_final: 0.8608 (pt0) REVERT: H 889 MET cc_start: 0.8155 (mtm) cc_final: 0.7818 (tmm) REVERT: H 902 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8498 (pm20) REVERT: H 1071 GLU cc_start: 0.8679 (tt0) cc_final: 0.8315 (pm20) REVERT: H 1089 MET cc_start: 0.8731 (ptt) cc_final: 0.8362 (mmp) REVERT: H 1090 MET cc_start: 0.7282 (mmt) cc_final: 0.6979 (mmt) outliers start: 26 outliers final: 13 residues processed: 232 average time/residue: 0.3186 time to fit residues: 120.9288 Evaluate side-chains 201 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 1113 SER Chi-restraints excluded: chain H residue 1065 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 224 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 270 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 267 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 216 optimal weight: 0.0670 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 HIS A 297 ASN B 161 HIS C 225 ASN C 297 ASN D 40 HIS D 162 ASN E 246 GLN F 59 GLN ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 HIS F 162 ASN G1037 ASN G1093 ASN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1091 HIS H1130 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 24318 Z= 0.515 Angle : 0.808 12.572 32908 Z= 0.410 Chirality : 0.049 0.191 3641 Planarity : 0.006 0.064 4227 Dihedral : 10.824 172.898 3314 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.32 % Allowed : 9.15 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 2953 helix: 0.28 (0.14), residues: 1416 sheet: -0.67 (0.30), residues: 294 loop : -0.40 (0.19), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 767 HIS 0.008 0.002 HIS E 87 PHE 0.027 0.003 PHE E 255 TYR 0.028 0.002 TYR B 306 ARG 0.008 0.001 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 180 time to evaluate : 2.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8918 (mt) cc_final: 0.8696 (mm) REVERT: A 269 MET cc_start: 0.8701 (mtp) cc_final: 0.8435 (ttm) REVERT: B 44 MET cc_start: 0.8229 (mmp) cc_final: 0.7276 (ptt) REVERT: B 82 MET cc_start: 0.9244 (tpt) cc_final: 0.8778 (mmm) REVERT: B 123 MET cc_start: 0.9038 (mmt) cc_final: 0.8649 (mmm) REVERT: B 283 MET cc_start: 0.7447 (mmm) cc_final: 0.6953 (tmm) REVERT: B 355 MET cc_start: 0.8505 (tpt) cc_final: 0.8119 (tpt) REVERT: D 299 MET cc_start: 0.8315 (mtm) cc_final: 0.7982 (mtm) REVERT: D 361 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8306 (mp0) REVERT: E 44 MET cc_start: 0.8866 (mpp) cc_final: 0.7989 (mmm) REVERT: E 132 MET cc_start: 0.8263 (ppp) cc_final: 0.7702 (ppp) REVERT: E 142 LEU cc_start: 0.7007 (tp) cc_final: 0.6699 (tp) REVERT: F 119 MET cc_start: 0.9054 (mtm) cc_final: 0.8768 (mtp) REVERT: F 132 MET cc_start: 0.7925 (tmm) cc_final: 0.7648 (tmm) REVERT: G 1000 MET cc_start: 0.9157 (ptm) cc_final: 0.8684 (ptm) REVERT: G 1019 LYS cc_start: 0.9587 (mttt) cc_final: 0.9374 (mtmm) REVERT: G 1026 HIS cc_start: 0.8799 (m90) cc_final: 0.8361 (m170) REVERT: G 1127 MET cc_start: 0.9590 (mtm) cc_final: 0.9154 (mtm) REVERT: H 889 MET cc_start: 0.8364 (mtm) cc_final: 0.8004 (tmm) REVERT: H 1066 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5340 (ttpt) REVERT: H 1071 GLU cc_start: 0.8809 (tt0) cc_final: 0.8422 (pm20) REVERT: H 1089 MET cc_start: 0.8474 (ptt) cc_final: 0.8040 (mmp) REVERT: H 1090 MET cc_start: 0.7266 (mmt) cc_final: 0.6955 (mmt) outliers start: 34 outliers final: 20 residues processed: 207 average time/residue: 0.3216 time to fit residues: 109.7756 Evaluate side-chains 190 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 115 ASN Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 369 ILE Chi-restraints excluded: chain G residue 872 SER Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 128 optimal weight: 0.6980 chunk 181 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 256 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS F 115 ASN G1037 ASN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1123 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24318 Z= 0.162 Angle : 0.559 10.418 32908 Z= 0.272 Chirality : 0.042 0.154 3641 Planarity : 0.004 0.055 4227 Dihedral : 9.562 161.505 3313 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.93 % Allowed : 10.28 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2953 helix: 0.92 (0.14), residues: 1422 sheet: -0.33 (0.31), residues: 282 loop : -0.19 (0.19), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 79 HIS 0.004 0.001 HIS E 87 PHE 0.017 0.001 PHE G1107 TYR 0.019 0.001 TYR A 143 ARG 0.003 0.000 ARG G1139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 182 time to evaluate : 2.752 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: A 269 MET cc_start: 0.8647 (mtp) cc_final: 0.8343 (mtt) REVERT: A 355 MET cc_start: 0.8912 (mtp) cc_final: 0.8468 (mtp) REVERT: B 44 MET cc_start: 0.8205 (mmp) cc_final: 0.7264 (ptt) REVERT: B 123 MET cc_start: 0.8915 (mmt) cc_final: 0.8650 (mmm) REVERT: B 283 MET cc_start: 0.7306 (mmm) cc_final: 0.6827 (tmm) REVERT: B 355 MET cc_start: 0.8447 (tpt) cc_final: 0.8245 (tpt) REVERT: C 76 ILE cc_start: 0.8629 (mt) cc_final: 0.8368 (mt) REVERT: C 82 MET cc_start: 0.8553 (mtp) cc_final: 0.8022 (mtp) REVERT: C 299 MET cc_start: 0.8698 (mtp) cc_final: 0.8203 (mtp) REVERT: D 299 MET cc_start: 0.8269 (mtm) cc_final: 0.7921 (mtm) REVERT: D 361 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8234 (mp0) REVERT: E 44 MET cc_start: 0.8896 (mpp) cc_final: 0.8133 (mmm) REVERT: E 132 MET cc_start: 0.8172 (ppp) cc_final: 0.7571 (ppp) REVERT: E 142 LEU cc_start: 0.6936 (tp) cc_final: 0.6644 (tp) REVERT: E 227 MET cc_start: 0.7152 (mmm) cc_final: 0.6809 (mmm) REVERT: F 44 MET cc_start: 0.9190 (mmm) cc_final: 0.8676 (mmm) REVERT: F 119 MET cc_start: 0.9032 (mtm) cc_final: 0.8749 (mtp) REVERT: F 132 MET cc_start: 0.8026 (tmm) cc_final: 0.7792 (tmm) REVERT: F 340 TRP cc_start: 0.7219 (t60) cc_final: 0.5921 (t60) REVERT: G 1000 MET cc_start: 0.9175 (ptm) cc_final: 0.8672 (ptm) REVERT: G 1019 LYS cc_start: 0.9603 (mttt) cc_final: 0.9368 (mtmm) REVERT: G 1026 HIS cc_start: 0.8797 (m90) cc_final: 0.8335 (m170) REVERT: H 852 MET cc_start: 0.5990 (ttp) cc_final: 0.5726 (ttp) REVERT: H 889 MET cc_start: 0.8130 (mtm) cc_final: 0.7733 (tmm) REVERT: H 902 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8548 (pm20) REVERT: H 1026 HIS cc_start: 0.6052 (OUTLIER) cc_final: 0.5821 (t-90) REVERT: H 1066 LYS cc_start: 0.6289 (OUTLIER) cc_final: 0.5798 (ttpt) REVERT: H 1071 GLU cc_start: 0.8784 (tt0) cc_final: 0.8395 (pm20) REVERT: H 1089 MET cc_start: 0.8420 (ptt) cc_final: 0.8005 (mmp) REVERT: H 1090 MET cc_start: 0.7438 (mmt) cc_final: 0.7228 (mmt) outliers start: 24 outliers final: 11 residues processed: 200 average time/residue: 0.3143 time to fit residues: 105.1859 Evaluate side-chains 189 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain H residue 1026 HIS Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 6.9990 chunk 162 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN E 162 ASN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1026 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 24318 Z= 0.392 Angle : 0.680 11.586 32908 Z= 0.338 Chirality : 0.046 0.171 3641 Planarity : 0.005 0.058 4227 Dihedral : 9.179 176.266 3313 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.02 % Allowed : 10.74 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2953 helix: 0.77 (0.14), residues: 1455 sheet: -0.55 (0.31), residues: 282 loop : -0.47 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 86 HIS 0.007 0.001 HIS E 87 PHE 0.023 0.002 PHE E 255 TYR 0.019 0.002 TYR E 337 ARG 0.004 0.001 ARG E 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 171 time to evaluate : 2.876 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: A 82 MET cc_start: 0.9137 (tpp) cc_final: 0.8847 (tpp) REVERT: A 269 MET cc_start: 0.8700 (mtp) cc_final: 0.8455 (ttm) REVERT: A 355 MET cc_start: 0.8964 (mtp) cc_final: 0.8567 (mtp) REVERT: B 82 MET cc_start: 0.9286 (mmm) cc_final: 0.8816 (mmm) REVERT: B 123 MET cc_start: 0.9010 (mmt) cc_final: 0.8688 (mmm) REVERT: B 283 MET cc_start: 0.7419 (mmm) cc_final: 0.6966 (tmm) REVERT: B 355 MET cc_start: 0.8539 (tpt) cc_final: 0.8322 (tpt) REVERT: C 82 MET cc_start: 0.8679 (mtp) cc_final: 0.8221 (mtp) REVERT: C 299 MET cc_start: 0.8776 (mtp) cc_final: 0.8251 (mtp) REVERT: D 82 MET cc_start: 0.8733 (tpp) cc_final: 0.7577 (mmm) REVERT: D 299 MET cc_start: 0.8322 (mtm) cc_final: 0.7990 (mtm) REVERT: D 361 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8252 (mp0) REVERT: E 44 MET cc_start: 0.8963 (mpp) cc_final: 0.8322 (mmm) REVERT: E 47 MET cc_start: 0.6763 (ptt) cc_final: 0.6280 (ptp) REVERT: E 132 MET cc_start: 0.8277 (ppp) cc_final: 0.7817 (ppp) REVERT: E 142 LEU cc_start: 0.7098 (tp) cc_final: 0.6803 (tp) REVERT: E 227 MET cc_start: 0.7157 (mmm) cc_final: 0.6855 (mmm) REVERT: E 294 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: F 119 MET cc_start: 0.9032 (mtm) cc_final: 0.8686 (mtp) REVERT: G 1000 MET cc_start: 0.9199 (ptm) cc_final: 0.8671 (ptm) REVERT: G 1019 LYS cc_start: 0.9608 (mttt) cc_final: 0.9389 (mtmm) REVERT: G 1026 HIS cc_start: 0.8889 (m90) cc_final: 0.8489 (m170) REVERT: G 1119 MET cc_start: 0.9275 (mtt) cc_final: 0.8913 (mmt) REVERT: G 1127 MET cc_start: 0.9601 (mtm) cc_final: 0.9152 (mtm) REVERT: H 852 MET cc_start: 0.6134 (ttp) cc_final: 0.5860 (ttp) REVERT: H 889 MET cc_start: 0.8349 (mtm) cc_final: 0.7968 (tmm) REVERT: H 1071 GLU cc_start: 0.8776 (tt0) cc_final: 0.8362 (pm20) REVERT: H 1127 MET cc_start: 0.4887 (ttp) cc_final: 0.4679 (ppp) outliers start: 52 outliers final: 27 residues processed: 206 average time/residue: 0.3199 time to fit residues: 110.0750 Evaluate side-chains 195 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 167 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 287 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24318 Z= 0.171 Angle : 0.566 10.848 32908 Z= 0.273 Chirality : 0.042 0.167 3641 Planarity : 0.004 0.050 4227 Dihedral : 8.427 171.632 3313 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.01 % Allowed : 12.06 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 2953 helix: 1.22 (0.14), residues: 1428 sheet: -0.46 (0.27), residues: 378 loop : 0.16 (0.20), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 79 HIS 0.004 0.001 HIS F 161 PHE 0.015 0.001 PHE G1107 TYR 0.014 0.001 TYR A 143 ARG 0.003 0.000 ARG G 915 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 181 time to evaluate : 2.683 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: A 82 MET cc_start: 0.9142 (tpp) cc_final: 0.8826 (tpp) REVERT: A 143 TYR cc_start: 0.8157 (m-80) cc_final: 0.7840 (m-80) REVERT: A 269 MET cc_start: 0.8610 (mtp) cc_final: 0.8405 (ttm) REVERT: A 355 MET cc_start: 0.8906 (mtp) cc_final: 0.8500 (mtp) REVERT: A 362 TYR cc_start: 0.9055 (t80) cc_final: 0.8459 (t80) REVERT: B 82 MET cc_start: 0.9248 (mmm) cc_final: 0.8863 (mmm) REVERT: B 283 MET cc_start: 0.7296 (mmm) cc_final: 0.6846 (tmm) REVERT: B 355 MET cc_start: 0.8545 (tpt) cc_final: 0.8324 (tpt) REVERT: C 82 MET cc_start: 0.8693 (mtp) cc_final: 0.8245 (mtp) REVERT: C 123 MET cc_start: 0.8861 (tpp) cc_final: 0.8516 (tpp) REVERT: C 299 MET cc_start: 0.8706 (mtp) cc_final: 0.8443 (mtm) REVERT: D 82 MET cc_start: 0.8631 (tpp) cc_final: 0.8234 (mmm) REVERT: D 299 MET cc_start: 0.8343 (mtm) cc_final: 0.7774 (mtt) REVERT: D 361 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8333 (mp0) REVERT: E 44 MET cc_start: 0.8930 (mpp) cc_final: 0.8313 (tpp) REVERT: E 132 MET cc_start: 0.8162 (ppp) cc_final: 0.7662 (ppp) REVERT: E 142 LEU cc_start: 0.7042 (tp) cc_final: 0.6814 (tp) REVERT: E 151 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.6058 (tt) REVERT: E 227 MET cc_start: 0.7283 (mmm) cc_final: 0.6904 (mmm) REVERT: E 294 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: F 44 MET cc_start: 0.9213 (mmm) cc_final: 0.8685 (mmm) REVERT: F 119 MET cc_start: 0.9014 (mtm) cc_final: 0.8701 (mtp) REVERT: G 1000 MET cc_start: 0.9195 (ptm) cc_final: 0.8671 (ptm) REVERT: G 1019 LYS cc_start: 0.9622 (mttt) cc_final: 0.9365 (mtmm) REVERT: G 1026 HIS cc_start: 0.8881 (m90) cc_final: 0.8433 (m90) REVERT: H 852 MET cc_start: 0.6272 (ttp) cc_final: 0.5623 (ttt) REVERT: H 889 MET cc_start: 0.8169 (mtm) cc_final: 0.7743 (tmm) REVERT: H 902 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8635 (pm20) REVERT: H 1071 GLU cc_start: 0.8741 (tt0) cc_final: 0.8315 (pm20) outliers start: 26 outliers final: 16 residues processed: 201 average time/residue: 0.3241 time to fit residues: 107.7945 Evaluate side-chains 189 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 326 LYS Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain G residue 762 LEU Chi-restraints excluded: chain G residue 859 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 241 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 GLN ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24318 Z= 0.273 Angle : 0.613 11.128 32908 Z= 0.299 Chirality : 0.043 0.206 3641 Planarity : 0.004 0.063 4227 Dihedral : 8.303 158.138 3313 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.28 % Allowed : 12.65 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2953 helix: 1.04 (0.14), residues: 1463 sheet: -0.40 (0.27), residues: 372 loop : -0.06 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 767 HIS 0.005 0.001 HIS E 87 PHE 0.019 0.001 PHE E 255 TYR 0.017 0.001 TYR A 143 ARG 0.005 0.000 ARG F 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 2.709 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: A 123 MET cc_start: 0.8802 (tpp) cc_final: 0.7980 (tpp) REVERT: A 143 TYR cc_start: 0.8152 (m-80) cc_final: 0.7925 (m-80) REVERT: A 269 MET cc_start: 0.8654 (mtp) cc_final: 0.8434 (ttm) REVERT: A 355 MET cc_start: 0.8905 (mtp) cc_final: 0.8538 (mtp) REVERT: A 362 TYR cc_start: 0.9065 (t80) cc_final: 0.8340 (t80) REVERT: B 82 MET cc_start: 0.9277 (mmm) cc_final: 0.8907 (mmm) REVERT: B 283 MET cc_start: 0.7318 (mmm) cc_final: 0.6881 (tmm) REVERT: B 355 MET cc_start: 0.8541 (tpt) cc_final: 0.8301 (tpt) REVERT: C 44 MET cc_start: 0.8142 (mmm) cc_final: 0.7903 (mmm) REVERT: C 82 MET cc_start: 0.8741 (mtp) cc_final: 0.8267 (mtp) REVERT: C 299 MET cc_start: 0.8852 (mtp) cc_final: 0.8371 (mtp) REVERT: D 82 MET cc_start: 0.8649 (tpp) cc_final: 0.7633 (mmm) REVERT: D 299 MET cc_start: 0.8323 (mtm) cc_final: 0.7809 (mtt) REVERT: D 361 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8367 (mp0) REVERT: E 44 MET cc_start: 0.8980 (mpp) cc_final: 0.8320 (tpp) REVERT: E 132 MET cc_start: 0.8195 (ppp) cc_final: 0.7756 (ppp) REVERT: E 142 LEU cc_start: 0.7035 (tp) cc_final: 0.6767 (tp) REVERT: E 294 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: F 44 MET cc_start: 0.9212 (mmm) cc_final: 0.8645 (mmm) REVERT: F 119 MET cc_start: 0.9042 (mtm) cc_final: 0.8726 (mtp) REVERT: F 305 MET cc_start: 0.8555 (mmm) cc_final: 0.8317 (mmm) REVERT: G 1000 MET cc_start: 0.9199 (ptm) cc_final: 0.8664 (ptm) REVERT: G 1019 LYS cc_start: 0.9625 (mttt) cc_final: 0.9374 (mtmm) REVERT: G 1026 HIS cc_start: 0.8909 (m90) cc_final: 0.8455 (m90) REVERT: G 1090 MET cc_start: 0.8744 (mmm) cc_final: 0.8235 (mtt) REVERT: H 852 MET cc_start: 0.6425 (ttp) cc_final: 0.5731 (ttt) REVERT: H 889 MET cc_start: 0.8369 (mtm) cc_final: 0.7964 (tmm) REVERT: H 902 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8627 (pm20) REVERT: H 1066 LYS cc_start: 0.6010 (OUTLIER) cc_final: 0.5504 (tmtt) REVERT: H 1071 GLU cc_start: 0.8689 (tt0) cc_final: 0.8288 (pm20) REVERT: H 1089 MET cc_start: 0.8863 (ptt) cc_final: 0.8508 (mmp) REVERT: H 1090 MET cc_start: 0.6803 (mmt) cc_final: 0.6486 (mmt) outliers start: 33 outliers final: 23 residues processed: 192 average time/residue: 0.3157 time to fit residues: 101.4245 Evaluate side-chains 188 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 4.9990 chunk 114 optimal weight: 0.1980 chunk 170 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1093 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24318 Z= 0.199 Angle : 0.585 10.691 32908 Z= 0.282 Chirality : 0.042 0.169 3641 Planarity : 0.004 0.049 4227 Dihedral : 7.856 152.674 3313 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.40 % Allowed : 12.76 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2953 helix: 1.17 (0.14), residues: 1463 sheet: -0.36 (0.27), residues: 372 loop : 0.06 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.024 0.001 HIS H1026 PHE 0.015 0.001 PHE G1107 TYR 0.014 0.001 TYR A 143 ARG 0.004 0.000 ARG F 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 3.010 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: A 8 LEU cc_start: 0.8600 (mm) cc_final: 0.8295 (pp) REVERT: A 123 MET cc_start: 0.8762 (tpp) cc_final: 0.7944 (tpp) REVERT: A 143 TYR cc_start: 0.8137 (m-80) cc_final: 0.7887 (m-80) REVERT: A 269 MET cc_start: 0.8620 (mtp) cc_final: 0.8412 (ttm) REVERT: A 355 MET cc_start: 0.8912 (mtp) cc_final: 0.8545 (mtp) REVERT: A 362 TYR cc_start: 0.9080 (t80) cc_final: 0.8404 (t80) REVERT: B 44 MET cc_start: 0.8187 (mmp) cc_final: 0.7121 (mtm) REVERT: B 82 MET cc_start: 0.9259 (mmm) cc_final: 0.8895 (mmm) REVERT: B 283 MET cc_start: 0.7283 (mmm) cc_final: 0.6852 (tmm) REVERT: B 355 MET cc_start: 0.8560 (tpt) cc_final: 0.8327 (tpt) REVERT: C 82 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8321 (mtp) REVERT: C 123 MET cc_start: 0.8848 (tpp) cc_final: 0.8526 (tpp) REVERT: C 227 MET cc_start: 0.7425 (tmm) cc_final: 0.6614 (tpt) REVERT: C 299 MET cc_start: 0.8823 (mtp) cc_final: 0.8415 (mtp) REVERT: D 82 MET cc_start: 0.8681 (tpp) cc_final: 0.8398 (mmm) REVERT: D 294 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: D 299 MET cc_start: 0.8291 (mtm) cc_final: 0.7730 (mtt) REVERT: D 361 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8353 (mp0) REVERT: E 44 MET cc_start: 0.8946 (tpp) cc_final: 0.8309 (tpp) REVERT: E 132 MET cc_start: 0.8181 (ppp) cc_final: 0.7757 (ppp) REVERT: E 142 LEU cc_start: 0.7032 (tp) cc_final: 0.6761 (tp) REVERT: E 294 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: F 44 MET cc_start: 0.9170 (mmm) cc_final: 0.8643 (mmm) REVERT: F 119 MET cc_start: 0.9051 (mtm) cc_final: 0.8723 (mtp) REVERT: F 305 MET cc_start: 0.8553 (mmm) cc_final: 0.8320 (mmm) REVERT: G 1000 MET cc_start: 0.9206 (ptm) cc_final: 0.8690 (ptm) REVERT: G 1019 LYS cc_start: 0.9611 (mttt) cc_final: 0.9363 (mmtm) REVERT: G 1026 HIS cc_start: 0.8968 (m90) cc_final: 0.8521 (m90) REVERT: G 1090 MET cc_start: 0.8747 (mmm) cc_final: 0.8244 (mtt) REVERT: H 756 TYR cc_start: 0.5647 (m-80) cc_final: 0.4112 (m-10) REVERT: H 852 MET cc_start: 0.6416 (ttp) cc_final: 0.5616 (ttt) REVERT: H 889 MET cc_start: 0.8445 (mtm) cc_final: 0.8061 (tmm) REVERT: H 902 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8576 (pm20) REVERT: H 1066 LYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5666 (tmtt) REVERT: H 1071 GLU cc_start: 0.8667 (tt0) cc_final: 0.8294 (pm20) REVERT: H 1089 MET cc_start: 0.8830 (ptt) cc_final: 0.8507 (mmp) REVERT: H 1090 MET cc_start: 0.6711 (mmt) cc_final: 0.6438 (mmt) outliers start: 36 outliers final: 25 residues processed: 195 average time/residue: 0.3094 time to fit residues: 101.0541 Evaluate side-chains 197 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain H residue 787 ASP Chi-restraints excluded: chain H residue 1066 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 241 optimal weight: 9.9990 chunk 252 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24318 Z= 0.272 Angle : 0.622 11.252 32908 Z= 0.303 Chirality : 0.043 0.176 3641 Planarity : 0.004 0.066 4227 Dihedral : 7.748 151.851 3313 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.59 % Allowed : 12.84 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2953 helix: 1.10 (0.14), residues: 1462 sheet: -0.41 (0.27), residues: 372 loop : 0.02 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 767 HIS 0.018 0.001 HIS H1026 PHE 0.017 0.001 PHE G1107 TYR 0.018 0.001 TYR A 143 ARG 0.004 0.000 ARG F 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 3.056 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: A 8 LEU cc_start: 0.8585 (mm) cc_final: 0.8270 (pp) REVERT: A 123 MET cc_start: 0.8785 (tpp) cc_final: 0.7966 (tpp) REVERT: A 269 MET cc_start: 0.8610 (mtp) cc_final: 0.8391 (ttm) REVERT: A 355 MET cc_start: 0.8910 (mtp) cc_final: 0.8558 (mtp) REVERT: A 362 TYR cc_start: 0.9095 (t80) cc_final: 0.8374 (t80) REVERT: B 44 MET cc_start: 0.8136 (mmp) cc_final: 0.7059 (mtm) REVERT: B 82 MET cc_start: 0.9278 (mmm) cc_final: 0.8919 (mmm) REVERT: B 283 MET cc_start: 0.7273 (mmm) cc_final: 0.6857 (tmm) REVERT: B 355 MET cc_start: 0.8589 (tpt) cc_final: 0.8342 (tpt) REVERT: C 82 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8333 (mtp) REVERT: C 123 MET cc_start: 0.8939 (tpp) cc_final: 0.8632 (tpp) REVERT: C 299 MET cc_start: 0.8883 (mtp) cc_final: 0.8382 (mtp) REVERT: D 82 MET cc_start: 0.8724 (tpp) cc_final: 0.7689 (mmm) REVERT: D 294 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: D 299 MET cc_start: 0.8306 (mtm) cc_final: 0.7829 (mtt) REVERT: D 361 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8354 (mp0) REVERT: E 44 MET cc_start: 0.8957 (tpp) cc_final: 0.8280 (tpp) REVERT: E 132 MET cc_start: 0.8217 (ppp) cc_final: 0.7817 (ppp) REVERT: E 142 LEU cc_start: 0.7029 (tp) cc_final: 0.6765 (tp) REVERT: E 294 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: F 44 MET cc_start: 0.9151 (mmm) cc_final: 0.8705 (mmm) REVERT: F 119 MET cc_start: 0.9091 (mtm) cc_final: 0.8755 (mtp) REVERT: F 305 MET cc_start: 0.8553 (mmm) cc_final: 0.8335 (mmm) REVERT: G 852 MET cc_start: 0.5431 (tmm) cc_final: 0.5111 (ppp) REVERT: G 1000 MET cc_start: 0.9202 (ptm) cc_final: 0.8685 (ptm) REVERT: G 1019 LYS cc_start: 0.9613 (mttt) cc_final: 0.9379 (mmtm) REVERT: G 1026 HIS cc_start: 0.8947 (m90) cc_final: 0.8501 (m90) REVERT: G 1089 MET cc_start: 0.9226 (ppp) cc_final: 0.8981 (ppp) REVERT: G 1090 MET cc_start: 0.8762 (mmm) cc_final: 0.8288 (mtt) REVERT: H 756 TYR cc_start: 0.5752 (m-80) cc_final: 0.4242 (m-10) REVERT: H 852 MET cc_start: 0.6466 (ttp) cc_final: 0.6017 (ttt) REVERT: H 889 MET cc_start: 0.8460 (mtm) cc_final: 0.8034 (tmm) REVERT: H 902 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8622 (pm20) REVERT: H 1071 GLU cc_start: 0.8654 (tt0) cc_final: 0.8336 (pm20) REVERT: H 1089 MET cc_start: 0.8831 (ptt) cc_final: 0.8513 (mmp) REVERT: H 1090 MET cc_start: 0.6665 (mmt) cc_final: 0.6409 (mmt) outliers start: 41 outliers final: 30 residues processed: 198 average time/residue: 0.3035 time to fit residues: 102.1399 Evaluate side-chains 198 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 25 ASP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain H residue 787 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.9980 chunk 282 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 295 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 235 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24318 Z= 0.180 Angle : 0.587 12.720 32908 Z= 0.280 Chirality : 0.042 0.225 3641 Planarity : 0.004 0.049 4227 Dihedral : 7.397 150.599 3313 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.20 % Allowed : 13.30 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.16), residues: 2953 helix: 1.19 (0.14), residues: 1468 sheet: -0.31 (0.27), residues: 372 loop : 0.11 (0.20), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 79 HIS 0.017 0.001 HIS H1026 PHE 0.015 0.001 PHE G1117 TYR 0.022 0.001 TYR A 143 ARG 0.004 0.000 ARG F 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5906 Ramachandran restraints generated. 2953 Oldfield, 0 Emsley, 2953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 2.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8549 (mm) cc_final: 0.8284 (pp) REVERT: A 123 MET cc_start: 0.8750 (tpp) cc_final: 0.7940 (tpp) REVERT: A 355 MET cc_start: 0.8915 (mtp) cc_final: 0.8558 (mtp) REVERT: A 362 TYR cc_start: 0.9046 (t80) cc_final: 0.8376 (t80) REVERT: B 44 MET cc_start: 0.8239 (mmp) cc_final: 0.7059 (mtm) REVERT: B 82 MET cc_start: 0.9256 (mmm) cc_final: 0.8896 (mmm) REVERT: B 283 MET cc_start: 0.7272 (mmm) cc_final: 0.6804 (tmm) REVERT: B 355 MET cc_start: 0.8552 (tpt) cc_final: 0.8316 (tpt) REVERT: C 82 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8304 (mtp) REVERT: C 123 MET cc_start: 0.8860 (tpp) cc_final: 0.8532 (tpp) REVERT: C 227 MET cc_start: 0.7370 (tmm) cc_final: 0.6556 (tpt) REVERT: C 299 MET cc_start: 0.8830 (mtp) cc_final: 0.8565 (mtm) REVERT: D 82 MET cc_start: 0.8654 (tpp) cc_final: 0.8390 (mmm) REVERT: D 294 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: D 299 MET cc_start: 0.8306 (mtm) cc_final: 0.7804 (mtt) REVERT: D 361 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8350 (mp0) REVERT: E 44 MET cc_start: 0.8859 (tpp) cc_final: 0.8224 (tpp) REVERT: E 47 MET cc_start: 0.6433 (ptt) cc_final: 0.5047 (ppp) REVERT: E 132 MET cc_start: 0.8163 (ppp) cc_final: 0.7746 (ppp) REVERT: E 142 LEU cc_start: 0.7026 (tp) cc_final: 0.6751 (tp) REVERT: E 294 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: F 44 MET cc_start: 0.9141 (mmm) cc_final: 0.8712 (mmm) REVERT: F 119 MET cc_start: 0.9117 (mtm) cc_final: 0.8791 (mtp) REVERT: F 305 MET cc_start: 0.8557 (mmm) cc_final: 0.8334 (mmm) REVERT: G 852 MET cc_start: 0.5620 (tmm) cc_final: 0.5260 (ppp) REVERT: G 1019 LYS cc_start: 0.9624 (mttt) cc_final: 0.9390 (mmtm) REVERT: G 1026 HIS cc_start: 0.8964 (m90) cc_final: 0.8515 (m90) REVERT: G 1089 MET cc_start: 0.9190 (ppp) cc_final: 0.8942 (ppp) REVERT: G 1090 MET cc_start: 0.8729 (mmm) cc_final: 0.8266 (mtt) REVERT: H 756 TYR cc_start: 0.5696 (m-80) cc_final: 0.4158 (m-10) REVERT: H 852 MET cc_start: 0.6439 (ttp) cc_final: 0.5945 (ttp) REVERT: H 889 MET cc_start: 0.8406 (mtm) cc_final: 0.7976 (tmm) REVERT: H 902 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8581 (pm20) REVERT: H 1071 GLU cc_start: 0.8645 (tt0) cc_final: 0.8323 (pm20) REVERT: H 1089 MET cc_start: 0.8822 (ptt) cc_final: 0.8496 (mmp) REVERT: H 1090 MET cc_start: 0.6673 (mmt) cc_final: 0.6425 (mmt) outliers start: 31 outliers final: 25 residues processed: 193 average time/residue: 0.3070 time to fit residues: 99.3181 Evaluate side-chains 196 residues out of total 2578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 168 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain F residue 294 TYR Chi-restraints excluded: chain G residue 859 ASN Chi-restraints excluded: chain H residue 787 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.7980 chunk 250 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 217 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1123 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.075400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.054738 restraints weight = 107030.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.056301 restraints weight = 49497.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.057325 restraints weight = 29167.254| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24318 Z= 0.290 Angle : 0.645 14.460 32908 Z= 0.313 Chirality : 0.044 0.198 3641 Planarity : 0.004 0.049 4227 Dihedral : 7.569 148.917 3313 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.32 % Allowed : 13.30 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2953 helix: 1.09 (0.14), residues: 1469 sheet: -0.36 (0.27), residues: 372 loop : 0.04 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 767 HIS 0.016 0.001 HIS H1026 PHE 0.018 0.001 PHE C 255 TYR 0.027 0.001 TYR A 143 ARG 0.005 0.000 ARG F 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3915.94 seconds wall clock time: 73 minutes 14.35 seconds (4394.35 seconds total)