Starting phenix.real_space_refine on Wed Jul 24 14:27:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/07_2024/8uee_42161_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/07_2024/8uee_42161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/07_2024/8uee_42161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/07_2024/8uee_42161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/07_2024/8uee_42161_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uee_42161/07_2024/8uee_42161_neut.cif" } resolution = 3.2 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= 0.001 sd= 0.034 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 21 5.49 5 Mg 7 5.21 5 S 167 5.16 5 C 16337 2.51 5 N 4410 2.21 5 O 4982 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "H ASP 286": "OD1" <-> "OD2" Residue "I ASP 157": "OD1" <-> "OD2" Residue "I PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 207": "OE1" <-> "OE2" Residue "J TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 286": "OD1" <-> "OD2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K ASP 222": "OD1" <-> "OD2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 276": "OE1" <-> "OE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 195": "OE1" <-> "OE2" Residue "M GLU 224": "OE1" <-> "OE2" Residue "M ASP 244": "OD1" <-> "OD2" Residue "M GLU 361": "OE1" <-> "OE2" Residue "M GLU 364": "OE1" <-> "OE2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 569": "OD1" <-> "OD2" Residue "C PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 574": "OE1" <-> "OE2" Residue "C GLU 629": "OE1" <-> "OE2" Residue "D GLU 598": "OE1" <-> "OE2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 679": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 25924 Number of models: 1 Model: "" Number of chains: 19 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1348 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "C" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1348 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1348 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "A" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1348 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 14.54, per 1000 atoms: 0.56 Number of scatterers: 25924 At special positions: 0 Unit cell: (118.8, 111.24, 257.04, 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 167 16.00 P 21 15.00 Mg 7 11.99 O 4982 8.00 N 4410 7.00 C 16337 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.95 Conformation dependent library (CDL) restraints added in 5.3 seconds 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 41 sheets defined 53.5% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 91 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.226A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.522A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.563A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.808A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.122A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 4.025A 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 369 through 374 removed outlier: 3.845A pdb=" N LYS F 373 " --> pdb=" O ILE F 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 61 removed outlier: 3.532A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 112 through 125 removed outlier: 3.956A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET H 123 " --> pdb=" O MET H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 202 through 217 removed outlier: 3.548A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.526A pdb=" N CYS H 257 " --> pdb=" O GLU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 removed outlier: 3.508A pdb=" N LYS H 284 " --> pdb=" O ASN H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 288 removed outlier: 6.318A pdb=" N ASP H 288 " --> pdb=" O CYS H 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 285 through 288' Processing helix chain 'H' and resid 289 through 295 removed outlier: 3.753A pdb=" N ALA H 295 " --> pdb=" O LYS H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 305 Processing helix chain 'H' and resid 308 through 321 Processing helix chain 'H' and resid 334 through 336 No H-bonds generated for 'chain 'H' and resid 334 through 336' Processing helix chain 'H' and resid 337 through 349 Processing helix chain 'H' and resid 350 through 355 removed outlier: 3.553A pdb=" N GLN H 353 " --> pdb=" O SER H 350 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN H 354 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 Processing helix chain 'H' and resid 369 through 374 removed outlier: 3.535A pdb=" N CYS H 374 " --> pdb=" O VAL H 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 61 Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.688A pdb=" N LEU I 65 " --> pdb=" O ARG I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 removed outlier: 3.870A pdb=" N HIS I 101 " --> pdb=" O PRO I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 126 removed outlier: 3.849A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 145 Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 194 removed outlier: 3.776A pdb=" N THR I 194 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 222 through 233 Processing helix chain 'I' and resid 252 through 257 removed outlier: 3.522A pdb=" N CYS I 257 " --> pdb=" O GLU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 262 Processing helix chain 'I' and resid 263 through 268 Processing helix chain 'I' and resid 273 through 284 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA I 295 " --> pdb=" O LYS I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 306 removed outlier: 4.224A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 321 Processing helix chain 'I' and resid 334 through 336 No H-bonds generated for 'chain 'I' and resid 334 through 336' Processing helix chain 'I' and resid 337 through 349 Processing helix chain 'I' and resid 350 through 353 Processing helix chain 'I' and resid 359 through 366 removed outlier: 3.556A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 374 removed outlier: 3.983A pdb=" N ARG I 372 " --> pdb=" O SER I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'J' and resid 78 through 92 Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 112 through 126 removed outlier: 4.005A pdb=" N ARG J 116 " --> pdb=" O PRO J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 137 through 144 Processing helix chain 'J' and resid 172 through 175 Processing helix chain 'J' and resid 181 through 193 Processing helix chain 'J' and resid 194 through 197 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 222 through 233 Processing helix chain 'J' and resid 252 through 257 removed outlier: 3.629A pdb=" N CYS J 257 " --> pdb=" O GLU J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 262 Processing helix chain 'J' and resid 263 through 268 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 289 through 295 removed outlier: 3.763A pdb=" N ALA J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 305 Processing helix chain 'J' and resid 308 through 321 Processing helix chain 'J' and resid 337 through 349 Processing helix chain 'J' and resid 359 through 366 Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.971A pdb=" N ARG J 372 " --> pdb=" O SER J 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 removed outlier: 3.596A pdb=" N LYS K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 Processing helix chain 'K' and resid 97 through 101 removed outlier: 3.564A pdb=" N HIS K 101 " --> pdb=" O PRO K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 126 removed outlier: 4.207A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 145 removed outlier: 3.512A pdb=" N LEU K 142 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER K 145 " --> pdb=" O SER K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 194 removed outlier: 3.754A pdb=" N THR K 194 " --> pdb=" O MET K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 197 No H-bonds generated for 'chain 'K' and resid 195 through 197' Processing helix chain 'K' and resid 202 through 217 removed outlier: 3.735A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 252 through 257 removed outlier: 3.500A pdb=" N CYS K 257 " --> pdb=" O GLU K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 262 Processing helix chain 'K' and resid 263 through 268 Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 289 through 296 Processing helix chain 'K' and resid 301 through 305 Processing helix chain 'K' and resid 308 through 319 removed outlier: 3.668A pdb=" N ARG K 312 " --> pdb=" O GLY K 308 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 349 Processing helix chain 'K' and resid 350 through 353 Processing helix chain 'K' and resid 359 through 366 removed outlier: 3.802A pdb=" N GLU K 364 " --> pdb=" O GLN K 360 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA K 365 " --> pdb=" O GLU K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.618A pdb=" N CYS K 374 " --> pdb=" O VAL K 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 61 Processing helix chain 'L' and resid 78 through 92 Processing helix chain 'L' and resid 97 through 101 Processing helix chain 'L' and resid 112 through 126 removed outlier: 3.882A pdb=" N ARG L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 145 removed outlier: 3.534A pdb=" N TYR L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER L 145 " --> pdb=" O SER L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 175 Processing helix chain 'L' and resid 181 through 194 removed outlier: 3.882A pdb=" N THR L 194 " --> pdb=" O MET L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 197 No H-bonds generated for 'chain 'L' and resid 195 through 197' Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 222 through 231 Processing helix chain 'L' and resid 252 through 260 removed outlier: 3.620A pdb=" N CYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Proline residue: L 258 - end of helix Processing helix chain 'L' and resid 261 through 262 No H-bonds generated for 'chain 'L' and resid 261 through 262' Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 273 through 284 Processing helix chain 'L' and resid 289 through 295 removed outlier: 3.590A pdb=" N ALA L 295 " --> pdb=" O LYS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 306 removed outlier: 4.022A pdb=" N TYR L 306 " --> pdb=" O THR L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 334 through 336 No H-bonds generated for 'chain 'L' and resid 334 through 336' Processing helix chain 'L' and resid 337 through 348 Processing helix chain 'L' and resid 349 through 355 removed outlier: 3.599A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 368 through 374 removed outlier: 4.036A pdb=" N ARG L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 61 Processing helix chain 'M' and resid 78 through 92 removed outlier: 3.573A pdb=" N MET M 82 " --> pdb=" O ASN M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 101 Processing helix chain 'M' and resid 112 through 126 removed outlier: 4.034A pdb=" N ARG M 116 " --> pdb=" O PRO M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 145 Processing helix chain 'M' and resid 172 through 175 Processing helix chain 'M' and resid 181 through 193 Processing helix chain 'M' and resid 194 through 197 Processing helix chain 'M' and resid 202 through 217 removed outlier: 3.673A pdb=" N GLU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 233 Processing helix chain 'M' and resid 252 through 257 Processing helix chain 'M' and resid 258 through 262 Processing helix chain 'M' and resid 263 through 268 Processing helix chain 'M' and resid 273 through 284 Processing helix chain 'M' and resid 286 through 288 No H-bonds generated for 'chain 'M' and resid 286 through 288' Processing helix chain 'M' and resid 289 through 295 removed outlier: 3.607A pdb=" N ALA M 295 " --> pdb=" O LYS M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 301 through 306 removed outlier: 4.126A pdb=" N TYR M 306 " --> pdb=" O THR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 321 Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 337 through 348 Processing helix chain 'M' and resid 349 through 355 removed outlier: 3.783A pdb=" N GLN M 354 " --> pdb=" O THR M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 366 Processing helix chain 'M' and resid 367 through 372 removed outlier: 3.607A pdb=" N VAL M 370 " --> pdb=" O PRO M 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 536 removed outlier: 3.552A pdb=" N HIS B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 554 Processing helix chain 'B' and resid 561 through 576 Processing helix chain 'B' and resid 579 through 590 removed outlier: 3.655A pdb=" N GLN B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 612 removed outlier: 3.527A pdb=" N LYS B 602 " --> pdb=" O GLU B 598 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 611 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 630 Processing helix chain 'B' and resid 640 through 651 Processing helix chain 'B' and resid 654 through 659 removed outlier: 3.939A pdb=" N ARG B 657 " --> pdb=" O GLY B 654 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 658 " --> pdb=" O SER B 655 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY B 659 " --> pdb=" O TRP B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 654 through 659' Processing helix chain 'B' and resid 676 through 682 removed outlier: 3.971A pdb=" N LEU B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS B 682 " --> pdb=" O VAL B 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 536 removed outlier: 4.065A pdb=" N HIS C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 554 Processing helix chain 'C' and resid 561 through 576 Processing helix chain 'C' and resid 579 through 590 Processing helix chain 'C' and resid 591 through 595 removed outlier: 5.840A pdb=" N ASP C 594 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS C 595 " --> pdb=" O ASP C 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 591 through 595' Processing helix chain 'C' and resid 596 through 611 Processing helix chain 'C' and resid 615 through 629 Processing helix chain 'C' and resid 640 through 651 removed outlier: 3.526A pdb=" N VAL C 646 " --> pdb=" O VAL C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 658 Processing helix chain 'C' and resid 676 through 682 removed outlier: 3.604A pdb=" N LEU C 681 " --> pdb=" O THR C 677 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HIS C 682 " --> pdb=" O VAL C 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 537 Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 561 through 576 removed outlier: 3.507A pdb=" N ALA D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 574 " --> pdb=" O GLY D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 591 removed outlier: 3.540A pdb=" N GLN D 589 " --> pdb=" O ALA D 585 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 591 " --> pdb=" O LYS D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 removed outlier: 3.566A pdb=" N LYS D 595 " --> pdb=" O ASP D 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 592 through 595' Processing helix chain 'D' and resid 596 through 612 removed outlier: 3.828A pdb=" N LEU D 606 " --> pdb=" O LYS D 602 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU D 608 " --> pdb=" O GLU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 629 Processing helix chain 'D' and resid 640 through 651 Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 676 through 682 removed outlier: 3.782A pdb=" N HIS D 682 " --> pdb=" O VAL D 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.003A pdb=" N SER A 527 " --> pdb=" O SER A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 541 through 554 Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.508A pdb=" N ALA A 567 " --> pdb=" O PRO A 563 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 574 " --> pdb=" O GLY A 570 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 590 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 596 through 612 removed outlier: 3.652A pdb=" N LYS A 600 " --> pdb=" O HIS A 596 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 630 Processing helix chain 'A' and resid 641 through 651 removed outlier: 3.860A pdb=" N ASN A 645 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 646 " --> pdb=" O VAL A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.706A pdb=" N HIS A 682 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.534A pdb=" N PHE F 31 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.647A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.540A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.565A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.560A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'I' and resid 8 through 12 Processing sheet with id=AB5, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'I' and resid 105 through 107 removed outlier: 6.542A pdb=" N LEU I 105 " --> pdb=" O ALA I 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 131 through 132 Processing sheet with id=AB8, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AB9, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.306A pdb=" N ASN I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'J' and resid 29 through 32 removed outlier: 3.538A pdb=" N PHE J 31 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR J 106 " --> pdb=" O CYS J 10 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN J 12 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.552A pdb=" N ARG J 37 " --> pdb=" O THR J 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 71 through 72 Processing sheet with id=AC5, first strand: chain 'J' and resid 176 through 178 removed outlier: 6.424A pdb=" N ASN J 297 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 176 through 178 removed outlier: 4.232A pdb=" N GLN K 41 " --> pdb=" O ALA J 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 238 through 241 Processing sheet with id=AC8, first strand: chain 'K' and resid 29 through 32 removed outlier: 3.878A pdb=" N THR K 106 " --> pdb=" O CYS K 10 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN K 12 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AD2, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'K' and resid 169 through 170 removed outlier: 6.232A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AD5, first strand: chain 'L' and resid 29 through 32 removed outlier: 3.502A pdb=" N PHE L 31 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR L 106 " --> pdb=" O CYS L 10 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASN L 12 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR L 133 " --> pdb=" O THR L 103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AD7, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AD8, first strand: chain 'L' and resid 169 through 170 removed outlier: 6.217A pdb=" N ILE L 151 " --> pdb=" O VAL L 298 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER L 300 " --> pdb=" O ILE L 151 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU L 153 " --> pdb=" O SER L 300 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN L 297 " --> pdb=" O ILE L 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AE1, first strand: chain 'M' and resid 29 through 32 removed outlier: 6.840A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 53 through 54 Processing sheet with id=AE3, first strand: chain 'M' and resid 169 through 170 Processing sheet with id=AE4, first strand: chain 'M' and resid 169 through 170 removed outlier: 6.541A pdb=" N ASN M 297 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 238 through 241 1236 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.26 Time building geometry restraints manager: 10.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4723 1.32 - 1.45: 6509 1.45 - 1.57: 14928 1.57 - 1.69: 21 1.69 - 1.81: 295 Bond restraints: 26476 Sorted by residual: bond pdb=" C ILE H 75 " pdb=" O ILE H 75 " ideal model delta sigma weight residual 1.236 1.202 0.034 1.02e-02 9.61e+03 1.13e+01 bond pdb=" CA HIC H 73 " pdb=" C HIC H 73 " ideal model delta sigma weight residual 1.525 1.455 0.070 2.10e-02 2.27e+03 1.10e+01 bond pdb=" O3 PO4 M 403 " pdb=" P PO4 M 403 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" CA ASN A 534 " pdb=" C ASN A 534 " ideal model delta sigma weight residual 1.522 1.478 0.045 1.41e-02 5.03e+03 9.97e+00 bond pdb=" CG HIC K 73 " pdb=" ND1 HIC K 73 " ideal model delta sigma weight residual 1.370 1.308 0.062 2.00e-02 2.50e+03 9.73e+00 ... (remaining 26471 not shown) Histogram of bond angle deviations from ideal: 96.35 - 104.34: 535 104.34 - 112.33: 13556 112.33 - 120.32: 11470 120.32 - 128.31: 10146 128.31 - 136.30: 198 Bond angle restraints: 35905 Sorted by residual: angle pdb=" N HIC H 73 " pdb=" CA HIC H 73 " pdb=" CB HIC H 73 " ideal model delta sigma weight residual 110.50 117.34 -6.84 1.70e+00 3.46e-01 1.62e+01 angle pdb=" C ILE I 71 " pdb=" CA ILE I 71 " pdb=" CB ILE I 71 " ideal model delta sigma weight residual 111.29 105.44 5.85 1.64e+00 3.72e-01 1.27e+01 angle pdb=" N ARG B 628 " pdb=" CA ARG B 628 " pdb=" C ARG B 628 " ideal model delta sigma weight residual 111.28 115.13 -3.85 1.09e+00 8.42e-01 1.25e+01 angle pdb=" O TYR H 69 " pdb=" C TYR H 69 " pdb=" N PRO H 70 " ideal model delta sigma weight residual 121.35 124.47 -3.12 9.20e-01 1.18e+00 1.15e+01 angle pdb=" N ASN A 534 " pdb=" CA ASN A 534 " pdb=" C ASN A 534 " ideal model delta sigma weight residual 112.38 108.33 4.05 1.22e+00 6.72e-01 1.10e+01 ... (remaining 35900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.70: 15627 34.70 - 69.41: 290 69.41 - 104.11: 41 104.11 - 138.81: 0 138.81 - 173.52: 7 Dihedral angle restraints: 15965 sinusoidal: 6477 harmonic: 9488 Sorted by residual: dihedral pdb=" C5' ADP K 401 " pdb=" O5' ADP K 401 " pdb=" PA ADP K 401 " pdb=" O2A ADP K 401 " ideal model delta sinusoidal sigma weight residual -60.00 113.52 -173.52 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP L 401 " pdb=" O5' ADP L 401 " pdb=" PA ADP L 401 " pdb=" O2A ADP L 401 " ideal model delta sinusoidal sigma weight residual 300.00 128.95 171.05 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C5' ADP I 401 " pdb=" O5' ADP I 401 " pdb=" PA ADP I 401 " pdb=" O2A ADP I 401 " ideal model delta sinusoidal sigma weight residual -60.00 107.61 -167.61 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 15962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2298 0.033 - 0.067: 1164 0.067 - 0.100: 341 0.100 - 0.133: 181 0.133 - 0.167: 9 Chirality restraints: 3993 Sorted by residual: chirality pdb=" CB THR C 633 " pdb=" CA THR C 633 " pdb=" OG1 THR C 633 " pdb=" CG2 THR C 633 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" C2' ADP J 401 " pdb=" C1' ADP J 401 " pdb=" C3' ADP J 401 " pdb=" O2' ADP J 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ILE K 75 " pdb=" N ILE K 75 " pdb=" C ILE K 75 " pdb=" CB ILE K 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 3990 not shown) Planarity restraints: 4597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 340 " -0.021 2.00e-02 2.50e+03 1.95e-02 9.52e+00 pdb=" CG TRP F 340 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP F 340 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 340 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 340 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP F 340 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 340 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 340 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 340 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP F 340 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN J 111 " -0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO J 112 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO J 112 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO J 112 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR H 304 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C THR H 304 " 0.026 2.00e-02 2.50e+03 pdb=" O THR H 304 " -0.009 2.00e-02 2.50e+03 pdb=" N MET H 305 " -0.009 2.00e-02 2.50e+03 ... (remaining 4594 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 110 2.49 - 3.10: 18505 3.10 - 3.70: 38151 3.70 - 4.30: 56814 4.30 - 4.90: 95076 Nonbonded interactions: 208656 Sorted by model distance: nonbonded pdb=" O1B ADP L 401 " pdb="MG MG L 402 " model vdw 1.893 2.170 nonbonded pdb=" O1B ADP J 401 " pdb="MG MG J 402 " model vdw 1.902 2.170 nonbonded pdb="MG MG H 402 " pdb=" O2 PO4 H 403 " model vdw 1.904 2.170 nonbonded pdb=" O1B ADP H 401 " pdb="MG MG H 402 " model vdw 1.907 2.170 nonbonded pdb="MG MG F 402 " pdb=" O4 PO4 F 403 " model vdw 1.987 2.170 ... (remaining 208651 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' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 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: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.210 Set scattering table: 0.250 Process input model: 72.210 Find NCS groups from input model: 2.290 Set up NCS constraints: 0.170 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.005 0.070 26476 Z= 0.321 Angle : 0.634 11.042 35905 Z= 0.313 Chirality : 0.045 0.167 3993 Planarity : 0.004 0.046 4597 Dihedral : 14.505 173.516 9875 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % 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: 0.29 (0.15), residues: 3242 helix: 0.44 (0.14), residues: 1419 sheet: -0.05 (0.23), residues: 483 loop : 0.24 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP F 340 HIS 0.011 0.001 HIS A 682 PHE 0.012 0.001 PHE L 200 TYR 0.022 0.001 TYR D 662 ARG 0.006 0.001 ARG A 565 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 436 time to evaluate : 2.977 Fit side-chains REVERT: F 43 VAL cc_start: 0.8948 (t) cc_final: 0.8741 (t) REVERT: F 44 MET cc_start: 0.5682 (mmm) cc_final: 0.5273 (mmm) REVERT: F 76 ILE cc_start: 0.8962 (mt) cc_final: 0.8753 (mt) REVERT: F 107 GLU cc_start: 0.8121 (tt0) cc_final: 0.7846 (pt0) REVERT: H 65 LEU cc_start: 0.9311 (mt) cc_final: 0.9107 (mt) REVERT: H 227 MET cc_start: 0.8006 (tpp) cc_final: 0.7775 (tpp) REVERT: H 305 MET cc_start: 0.8397 (mmm) cc_final: 0.8179 (mmt) REVERT: H 326 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7837 (tttm) REVERT: I 374 CYS cc_start: 0.7039 (m) cc_final: 0.6665 (m) REVERT: K 191 LYS cc_start: 0.8057 (ttpt) cc_final: 0.7846 (ttpt) REVERT: K 206 ARG cc_start: 0.7349 (ttp-170) cc_final: 0.7102 (tpp80) REVERT: L 118 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7350 (tppp) REVERT: B 536 HIS cc_start: 0.7751 (m170) cc_final: 0.7464 (m-70) REVERT: D 538 MET cc_start: 0.8422 (tpp) cc_final: 0.8150 (ttm) REVERT: A 638 GLU cc_start: 0.6603 (pm20) cc_final: 0.6013 (tm-30) outliers start: 12 outliers final: 3 residues processed: 443 average time/residue: 0.3386 time to fit residues: 243.7537 Evaluate side-chains 348 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 344 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain L residue 118 LYS Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain A residue 533 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 84 optimal weight: 0.0070 chunk 167 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 190 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 12 ASN H 162 ASN K 101 HIS K 162 ASN L 225 ASN C 645 ASN ** A 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26476 Z= 0.173 Angle : 0.571 10.121 35905 Z= 0.280 Chirality : 0.043 0.144 3993 Planarity : 0.004 0.039 4597 Dihedral : 8.167 171.771 3668 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.12 % Allowed : 7.16 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3242 helix: 1.01 (0.15), residues: 1399 sheet: 0.27 (0.23), residues: 490 loop : 0.42 (0.18), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 340 HIS 0.004 0.001 HIS C 613 PHE 0.010 0.001 PHE A 626 TYR 0.034 0.001 TYR C 641 ARG 0.004 0.000 ARG K 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 368 time to evaluate : 3.171 Fit side-chains REVERT: F 41 GLN cc_start: 0.7981 (pm20) cc_final: 0.7183 (tp40) REVERT: F 44 MET cc_start: 0.5498 (mmm) cc_final: 0.5280 (mtp) REVERT: F 59 GLN cc_start: 0.8461 (mm110) cc_final: 0.8225 (tp40) REVERT: F 225 ASN cc_start: 0.8047 (t0) cc_final: 0.7826 (t0) REVERT: H 47 MET cc_start: 0.5576 (ppp) cc_final: 0.5345 (ppp) REVERT: H 65 LEU cc_start: 0.9346 (mt) cc_final: 0.9097 (mt) REVERT: H 227 MET cc_start: 0.7991 (tpp) cc_final: 0.7704 (tpp) REVERT: I 148 THR cc_start: 0.8682 (p) cc_final: 0.8407 (m) REVERT: I 286 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: I 291 LYS cc_start: 0.8817 (tptp) cc_final: 0.8602 (tptp) REVERT: I 358 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8354 (m) REVERT: I 374 CYS cc_start: 0.6875 (m) cc_final: 0.6527 (m) REVERT: J 132 MET cc_start: 0.8690 (ppp) cc_final: 0.8484 (ptm) REVERT: K 82 MET cc_start: 0.8247 (tpt) cc_final: 0.7711 (tpt) REVERT: K 191 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7768 (ttpt) REVERT: L 25 ASP cc_start: 0.8013 (p0) cc_final: 0.7639 (t0) REVERT: L 136 ILE cc_start: 0.8570 (mm) cc_final: 0.8350 (mm) REVERT: M 96 VAL cc_start: 0.9081 (m) cc_final: 0.8872 (p) REVERT: M 270 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8675 (tp30) REVERT: B 536 HIS cc_start: 0.7724 (m170) cc_final: 0.7426 (m-70) REVERT: B 541 ASP cc_start: 0.6196 (OUTLIER) cc_final: 0.5947 (t70) REVERT: B 574 GLU cc_start: 0.7300 (tt0) cc_final: 0.6981 (pt0) outliers start: 31 outliers final: 19 residues processed: 386 average time/residue: 0.3392 time to fit residues: 213.0800 Evaluate side-chains 362 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 339 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 286 ASP Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 162 ASN Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 321 optimal weight: 4.9990 chunk 264 optimal weight: 9.9990 chunk 295 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN I 162 ASN K 101 HIS K 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 26476 Z= 0.482 Angle : 0.702 8.533 35905 Z= 0.354 Chirality : 0.050 0.167 3993 Planarity : 0.005 0.043 4597 Dihedral : 7.881 163.505 3664 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.94 % Allowed : 10.65 % Favored : 87.41 % 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: 0.32 (0.15), residues: 3242 helix: 0.78 (0.14), residues: 1385 sheet: -0.14 (0.23), residues: 483 loop : -0.09 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 340 HIS 0.008 0.002 HIS J 161 PHE 0.019 0.002 PHE H 375 TYR 0.027 0.002 TYR C 641 ARG 0.005 0.001 ARG I 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 339 time to evaluate : 3.325 Fit side-chains REVERT: F 41 GLN cc_start: 0.8056 (pm20) cc_final: 0.7235 (tp40) REVERT: F 59 GLN cc_start: 0.8520 (mm110) cc_final: 0.8284 (tp40) REVERT: F 82 MET cc_start: 0.7794 (mmm) cc_final: 0.6728 (tmm) REVERT: F 216 LEU cc_start: 0.8318 (mt) cc_final: 0.8070 (mp) REVERT: F 222 ASP cc_start: 0.8090 (t0) cc_final: 0.7588 (t0) REVERT: F 225 ASN cc_start: 0.8207 (t0) cc_final: 0.7987 (t0) REVERT: F 340 TRP cc_start: 0.8577 (t60) cc_final: 0.8098 (t60) REVERT: H 41 GLN cc_start: 0.7210 (tp-100) cc_final: 0.6994 (pt0) REVERT: H 221 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8561 (tt) REVERT: H 227 MET cc_start: 0.8182 (tpp) cc_final: 0.7870 (tpp) REVERT: H 269 MET cc_start: 0.8961 (mtt) cc_final: 0.8654 (mmt) REVERT: H 286 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8538 (m-30) REVERT: H 305 MET cc_start: 0.8269 (mmm) cc_final: 0.8007 (mmm) REVERT: H 326 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7985 (tttt) REVERT: I 72 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: I 291 LYS cc_start: 0.8930 (tptp) cc_final: 0.8382 (tptt) REVERT: I 358 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8584 (m) REVERT: I 374 CYS cc_start: 0.7294 (m) cc_final: 0.6963 (m) REVERT: J 291 LYS cc_start: 0.8443 (ttpp) cc_final: 0.8134 (tptt) REVERT: K 123 MET cc_start: 0.9068 (mmt) cc_final: 0.8853 (mmm) REVERT: K 126 THR cc_start: 0.8720 (m) cc_final: 0.8407 (p) REVERT: K 191 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7928 (ttpt) REVERT: L 25 ASP cc_start: 0.8256 (p0) cc_final: 0.7936 (t0) REVERT: L 83 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7593 (tm-30) REVERT: L 227 MET cc_start: 0.7982 (mmm) cc_final: 0.7693 (mmm) REVERT: L 269 MET cc_start: 0.9035 (mtp) cc_final: 0.8690 (mtt) REVERT: L 334 GLU cc_start: 0.7588 (pm20) cc_final: 0.7195 (pm20) REVERT: M 270 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8660 (tp30) REVERT: B 536 HIS cc_start: 0.7653 (m170) cc_final: 0.7322 (m-70) REVERT: B 683 MET cc_start: 0.7313 (ptm) cc_final: 0.7051 (ptm) REVERT: C 537 SER cc_start: 0.9046 (t) cc_final: 0.8674 (t) REVERT: A 638 GLU cc_start: 0.6864 (pm20) cc_final: 0.6385 (tm-30) REVERT: A 648 ASP cc_start: 0.7733 (m-30) cc_final: 0.7483 (m-30) REVERT: A 675 ILE cc_start: 0.8653 (mm) cc_final: 0.8112 (mm) outliers start: 54 outliers final: 37 residues processed: 375 average time/residue: 0.3421 time to fit residues: 208.6003 Evaluate side-chains 357 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 315 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain I residue 370 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 516 SER Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 199 optimal weight: 0.9980 chunk 298 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN K 101 HIS M 88 HIS ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 26476 Z= 0.177 Angle : 0.545 7.322 35905 Z= 0.265 Chirality : 0.043 0.186 3993 Planarity : 0.004 0.037 4597 Dihedral : 7.485 161.502 3663 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.58 % Allowed : 12.27 % Favored : 86.15 % 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: 0.70 (0.15), residues: 3242 helix: 1.16 (0.15), residues: 1378 sheet: -0.02 (0.23), residues: 469 loop : 0.07 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 340 HIS 0.005 0.001 HIS H 101 PHE 0.010 0.001 PHE H 375 TYR 0.030 0.001 TYR C 641 ARG 0.005 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 348 time to evaluate : 2.791 Fit side-chains revert: symmetry clash REVERT: F 41 GLN cc_start: 0.8004 (pm20) cc_final: 0.7267 (tp40) REVERT: F 59 GLN cc_start: 0.8526 (mm110) cc_final: 0.8248 (tp40) REVERT: F 216 LEU cc_start: 0.8227 (mt) cc_final: 0.7943 (mp) REVERT: F 222 ASP cc_start: 0.8023 (t0) cc_final: 0.7563 (t0) REVERT: F 225 ASN cc_start: 0.8062 (t0) cc_final: 0.7831 (t0) REVERT: H 227 MET cc_start: 0.8065 (tpp) cc_final: 0.7832 (tpp) REVERT: H 286 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8508 (m-30) REVERT: I 72 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: I 358 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8413 (m) REVERT: I 374 CYS cc_start: 0.7182 (m) cc_final: 0.6881 (m) REVERT: J 119 MET cc_start: 0.8585 (mtp) cc_final: 0.8357 (mtm) REVERT: K 77 THR cc_start: 0.8983 (m) cc_final: 0.8661 (p) REVERT: K 123 MET cc_start: 0.8985 (mmt) cc_final: 0.8764 (mmm) REVERT: K 191 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7838 (ttpt) REVERT: L 25 ASP cc_start: 0.8152 (p0) cc_final: 0.7927 (t0) REVERT: L 83 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7333 (tt0) REVERT: L 227 MET cc_start: 0.8010 (mmm) cc_final: 0.7723 (mmm) REVERT: L 334 GLU cc_start: 0.7473 (pm20) cc_final: 0.7149 (pm20) REVERT: L 340 TRP cc_start: 0.8936 (t60) cc_final: 0.8443 (t60) REVERT: M 82 MET cc_start: 0.7916 (tpp) cc_final: 0.7373 (tpt) REVERT: M 270 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8706 (tp30) REVERT: B 536 HIS cc_start: 0.7743 (m170) cc_final: 0.7413 (m-70) REVERT: C 535 MET cc_start: 0.7440 (mmt) cc_final: 0.7212 (mtt) REVERT: A 638 GLU cc_start: 0.6817 (pm20) cc_final: 0.6377 (tm-30) REVERT: A 648 ASP cc_start: 0.7849 (m-30) cc_final: 0.7508 (m-30) REVERT: A 675 ILE cc_start: 0.8642 (mm) cc_final: 0.8088 (mm) outliers start: 44 outliers final: 27 residues processed: 374 average time/residue: 0.3185 time to fit residues: 196.5108 Evaluate side-chains 349 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 318 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 283 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN I 162 ASN K 101 HIS L 40 HIS ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26476 Z= 0.228 Angle : 0.560 8.650 35905 Z= 0.271 Chirality : 0.044 0.170 3993 Planarity : 0.004 0.037 4597 Dihedral : 7.204 155.041 3663 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.12 % Allowed : 12.95 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3242 helix: 1.24 (0.15), residues: 1378 sheet: 0.01 (0.23), residues: 469 loop : 0.10 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 656 HIS 0.005 0.001 HIS I 371 PHE 0.010 0.001 PHE I 200 TYR 0.032 0.001 TYR C 641 ARG 0.003 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 334 time to evaluate : 3.037 Fit side-chains REVERT: F 216 LEU cc_start: 0.8244 (mt) cc_final: 0.7920 (mp) REVERT: F 222 ASP cc_start: 0.8032 (t0) cc_final: 0.7545 (t0) REVERT: F 225 ASN cc_start: 0.8074 (t0) cc_final: 0.7843 (t0) REVERT: F 313 MET cc_start: 0.9064 (tpp) cc_final: 0.8822 (mmm) REVERT: H 221 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8600 (tt) REVERT: H 227 MET cc_start: 0.8098 (tpp) cc_final: 0.7840 (tpp) REVERT: H 286 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8015 (m-30) REVERT: I 72 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7479 (mt-10) REVERT: I 269 MET cc_start: 0.8860 (mtm) cc_final: 0.8550 (mtm) REVERT: I 358 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8433 (m) REVERT: I 374 CYS cc_start: 0.7337 (m) cc_final: 0.7113 (m) REVERT: K 77 THR cc_start: 0.8962 (m) cc_final: 0.8621 (p) REVERT: K 82 MET cc_start: 0.8326 (tpt) cc_final: 0.7826 (tpt) REVERT: K 191 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7877 (ttpt) REVERT: K 364 GLU cc_start: 0.8760 (tp30) cc_final: 0.8376 (pt0) REVERT: L 25 ASP cc_start: 0.8176 (p0) cc_final: 0.7955 (t0) REVERT: L 83 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7364 (tt0) REVERT: L 334 GLU cc_start: 0.7455 (pm20) cc_final: 0.7199 (pm20) REVERT: L 340 TRP cc_start: 0.8967 (t60) cc_final: 0.8448 (t60) REVERT: M 82 MET cc_start: 0.7838 (tpp) cc_final: 0.7436 (tpt) REVERT: M 270 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8717 (tp30) REVERT: B 536 HIS cc_start: 0.7753 (m170) cc_final: 0.7413 (m-70) REVERT: A 555 GLU cc_start: 0.7873 (tt0) cc_final: 0.7633 (tt0) REVERT: A 638 GLU cc_start: 0.6797 (pm20) cc_final: 0.6377 (tm-30) REVERT: A 648 ASP cc_start: 0.7927 (m-30) cc_final: 0.7597 (m-30) REVERT: A 675 ILE cc_start: 0.8616 (mm) cc_final: 0.8060 (mm) outliers start: 59 outliers final: 38 residues processed: 368 average time/residue: 0.3255 time to fit residues: 197.3568 Evaluate side-chains 359 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 316 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 316 optimal weight: 20.0000 chunk 262 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 40 HIS H 162 ASN ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26476 Z= 0.348 Angle : 0.620 8.756 35905 Z= 0.305 Chirality : 0.047 0.154 3993 Planarity : 0.004 0.035 4597 Dihedral : 7.254 154.167 3662 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.59 % Allowed : 13.28 % Favored : 84.13 % 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: 0.54 (0.15), residues: 3242 helix: 1.10 (0.15), residues: 1378 sheet: -0.15 (0.23), residues: 469 loop : -0.09 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 656 HIS 0.007 0.001 HIS J 161 PHE 0.014 0.002 PHE I 200 TYR 0.031 0.002 TYR C 641 ARG 0.004 0.000 ARG I 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 326 time to evaluate : 3.262 Fit side-chains REVERT: F 216 LEU cc_start: 0.8288 (mt) cc_final: 0.7976 (mp) REVERT: F 222 ASP cc_start: 0.8058 (t0) cc_final: 0.7553 (t0) REVERT: F 225 ASN cc_start: 0.8150 (t0) cc_final: 0.7913 (t0) REVERT: F 227 MET cc_start: 0.8216 (mmm) cc_final: 0.7803 (mmm) REVERT: H 221 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8619 (tt) REVERT: H 227 MET cc_start: 0.8117 (tpp) cc_final: 0.7772 (tpp) REVERT: H 286 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: H 305 MET cc_start: 0.8244 (mmm) cc_final: 0.8043 (mmm) REVERT: I 44 MET cc_start: 0.8475 (mtp) cc_final: 0.8235 (mtm) REVERT: I 72 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7500 (mt-10) REVERT: I 358 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8498 (m) REVERT: I 374 CYS cc_start: 0.7275 (m) cc_final: 0.6978 (m) REVERT: J 119 MET cc_start: 0.8615 (mtp) cc_final: 0.8393 (mtm) REVERT: J 291 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8128 (tptt) REVERT: K 82 MET cc_start: 0.8350 (tpt) cc_final: 0.7763 (tpt) REVERT: K 123 MET cc_start: 0.9008 (mmt) cc_final: 0.8762 (mmm) REVERT: K 126 THR cc_start: 0.8855 (m) cc_final: 0.8492 (p) REVERT: K 328 LYS cc_start: 0.8462 (mttp) cc_final: 0.7577 (ptmm) REVERT: K 364 GLU cc_start: 0.8755 (tp30) cc_final: 0.8373 (pt0) REVERT: L 25 ASP cc_start: 0.8256 (p0) cc_final: 0.8054 (t0) REVERT: L 83 GLU cc_start: 0.7748 (tm-30) cc_final: 0.7316 (tt0) REVERT: L 334 GLU cc_start: 0.7454 (pm20) cc_final: 0.7232 (pm20) REVERT: L 340 TRP cc_start: 0.9018 (t60) cc_final: 0.8509 (t60) REVERT: L 364 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8537 (tp30) REVERT: M 270 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8543 (tp30) REVERT: B 536 HIS cc_start: 0.7782 (m170) cc_final: 0.7430 (m-70) REVERT: B 665 TYR cc_start: 0.7433 (m-80) cc_final: 0.7114 (m-80) REVERT: C 537 SER cc_start: 0.8969 (t) cc_final: 0.8607 (t) REVERT: D 666 LEU cc_start: 0.7854 (tp) cc_final: 0.7157 (pt) REVERT: A 640 ASP cc_start: 0.7588 (t0) cc_final: 0.6595 (p0) REVERT: A 648 ASP cc_start: 0.7964 (m-30) cc_final: 0.7575 (m-30) REVERT: A 675 ILE cc_start: 0.8679 (mm) cc_final: 0.8116 (mm) outliers start: 72 outliers final: 53 residues processed: 373 average time/residue: 0.3302 time to fit residues: 203.0992 Evaluate side-chains 373 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 315 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 288 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 297 ASN Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 24 ASP Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 299 MET Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 201 VAL Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 303 THR Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 555 GLU Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 653 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 chunk 231 optimal weight: 0.8980 chunk 179 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 315 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26476 Z= 0.164 Angle : 0.544 10.667 35905 Z= 0.261 Chirality : 0.043 0.141 3993 Planarity : 0.004 0.037 4597 Dihedral : 6.982 150.412 3662 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.91 % Allowed : 14.21 % Favored : 83.88 % 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: 0.82 (0.15), residues: 3242 helix: 1.33 (0.15), residues: 1378 sheet: -0.07 (0.23), residues: 469 loop : 0.11 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 656 HIS 0.004 0.001 HIS I 371 PHE 0.009 0.001 PHE H 255 TYR 0.032 0.001 TYR C 641 ARG 0.005 0.000 ARG D 551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 335 time to evaluate : 3.148 Fit side-chains REVERT: F 216 LEU cc_start: 0.8245 (mt) cc_final: 0.7907 (mp) REVERT: F 222 ASP cc_start: 0.8068 (t0) cc_final: 0.7570 (t0) REVERT: H 221 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8643 (tt) REVERT: H 227 MET cc_start: 0.8093 (tpp) cc_final: 0.7811 (tpp) REVERT: H 286 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: I 72 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: I 269 MET cc_start: 0.8807 (mtm) cc_final: 0.8490 (mtm) REVERT: I 358 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8368 (m) REVERT: I 374 CYS cc_start: 0.7220 (m) cc_final: 0.6915 (m) REVERT: J 119 MET cc_start: 0.8570 (mtp) cc_final: 0.8343 (mtm) REVERT: J 291 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8100 (tptt) REVERT: K 77 THR cc_start: 0.8980 (m) cc_final: 0.8648 (p) REVERT: K 82 MET cc_start: 0.8284 (tpt) cc_final: 0.7734 (tpt) REVERT: K 123 MET cc_start: 0.8977 (mmt) cc_final: 0.8721 (mmm) REVERT: K 328 LYS cc_start: 0.8406 (mttp) cc_final: 0.7688 (tttm) REVERT: K 364 GLU cc_start: 0.8714 (tp30) cc_final: 0.8342 (pt0) REVERT: L 47 MET cc_start: 0.6789 (mmm) cc_final: 0.5975 (mmm) REVERT: L 83 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7362 (tt0) REVERT: L 334 GLU cc_start: 0.7414 (pm20) cc_final: 0.7212 (pm20) REVERT: L 340 TRP cc_start: 0.8954 (t60) cc_final: 0.8468 (t60) REVERT: L 364 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8524 (tp30) REVERT: M 270 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8505 (tp30) REVERT: B 536 HIS cc_start: 0.7748 (m170) cc_final: 0.7392 (m-70) REVERT: B 663 GLU cc_start: 0.7565 (tp30) cc_final: 0.7244 (tt0) REVERT: B 665 TYR cc_start: 0.7305 (m-80) cc_final: 0.6953 (m-80) REVERT: C 537 SER cc_start: 0.8944 (t) cc_final: 0.8631 (t) REVERT: D 538 MET cc_start: 0.8112 (ttm) cc_final: 0.7904 (ttp) REVERT: A 640 ASP cc_start: 0.7522 (t0) cc_final: 0.6562 (p0) REVERT: A 648 ASP cc_start: 0.8045 (m-30) cc_final: 0.7691 (m-30) REVERT: A 675 ILE cc_start: 0.8660 (mm) cc_final: 0.8097 (mm) outliers start: 53 outliers final: 38 residues processed: 370 average time/residue: 0.3364 time to fit residues: 206.1693 Evaluate side-chains 362 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 319 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 270 GLU Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 598 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 247 optimal weight: 0.9980 chunk 286 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS K 280 ASN ** M 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 645 ASN ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 GLN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26476 Z= 0.263 Angle : 0.581 10.085 35905 Z= 0.281 Chirality : 0.045 0.144 3993 Planarity : 0.004 0.036 4597 Dihedral : 6.945 147.950 3662 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.37 % Allowed : 13.89 % Favored : 83.74 % 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 (0.15), residues: 3242 helix: 1.27 (0.15), residues: 1378 sheet: -0.10 (0.23), residues: 469 loop : 0.05 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 656 HIS 0.005 0.001 HIS J 161 PHE 0.010 0.001 PHE I 31 TYR 0.037 0.001 TYR C 641 ARG 0.004 0.000 ARG D 551 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 322 time to evaluate : 2.941 Fit side-chains REVERT: F 216 LEU cc_start: 0.8254 (mt) cc_final: 0.7916 (mp) REVERT: F 222 ASP cc_start: 0.8079 (t0) cc_final: 0.7589 (t0) REVERT: F 227 MET cc_start: 0.8226 (mmm) cc_final: 0.7858 (mmm) REVERT: H 221 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8663 (tt) REVERT: H 227 MET cc_start: 0.8118 (tpp) cc_final: 0.7800 (tpp) REVERT: H 286 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: I 72 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: I 269 MET cc_start: 0.8818 (mtm) cc_final: 0.8517 (mtm) REVERT: I 358 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8428 (m) REVERT: I 374 CYS cc_start: 0.7222 (m) cc_final: 0.6945 (m) REVERT: J 291 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8123 (tptt) REVERT: K 82 MET cc_start: 0.8307 (tpt) cc_final: 0.7752 (tpt) REVERT: K 126 THR cc_start: 0.8820 (m) cc_final: 0.8441 (p) REVERT: K 328 LYS cc_start: 0.8439 (mttp) cc_final: 0.7754 (tttp) REVERT: K 364 GLU cc_start: 0.8718 (tp30) cc_final: 0.8351 (pt0) REVERT: L 83 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7393 (tt0) REVERT: L 334 GLU cc_start: 0.7392 (pm20) cc_final: 0.7185 (pm20) REVERT: L 340 TRP cc_start: 0.9007 (t60) cc_final: 0.8501 (t60) REVERT: L 364 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8554 (tp30) REVERT: M 270 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8537 (tp30) REVERT: B 536 HIS cc_start: 0.7741 (m170) cc_final: 0.7386 (m-70) REVERT: B 663 GLU cc_start: 0.7676 (tp30) cc_final: 0.7306 (tt0) REVERT: B 665 TYR cc_start: 0.7389 (m-80) cc_final: 0.7041 (m-80) REVERT: C 537 SER cc_start: 0.8960 (t) cc_final: 0.8654 (t) REVERT: A 640 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.6595 (p0) REVERT: A 648 ASP cc_start: 0.8109 (m-30) cc_final: 0.7724 (m-30) REVERT: A 675 ILE cc_start: 0.8669 (mm) cc_final: 0.8119 (mm) outliers start: 66 outliers final: 56 residues processed: 366 average time/residue: 0.3669 time to fit residues: 225.1189 Evaluate side-chains 376 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 314 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 286 ASP Chi-restraints excluded: chain H residue 305 MET Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 324 THR Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 270 GLU Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 248 ILE Chi-restraints excluded: chain K residue 278 THR Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 190 MET Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 598 GLU Chi-restraints excluded: chain A residue 640 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 176 optimal weight: 0.0770 chunk 127 optimal weight: 0.0000 chunk 230 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 265 optimal weight: 10.0000 chunk 277 optimal weight: 5.9990 chunk 292 optimal weight: 0.0970 chunk 192 optimal weight: 3.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS L 59 GLN M 101 HIS ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 684 GLN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26476 Z= 0.170 Angle : 0.545 11.273 35905 Z= 0.260 Chirality : 0.043 0.143 3993 Planarity : 0.004 0.036 4597 Dihedral : 6.752 144.149 3662 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.94 % Allowed : 14.57 % Favored : 83.48 % 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: 0.93 (0.15), residues: 3242 helix: 1.41 (0.15), residues: 1378 sheet: -0.02 (0.23), residues: 469 loop : 0.18 (0.17), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 656 HIS 0.006 0.001 HIS M 101 PHE 0.017 0.001 PHE B 540 TYR 0.037 0.001 TYR C 641 ARG 0.004 0.000 ARG D 551 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 329 time to evaluate : 3.032 Fit side-chains REVERT: F 216 LEU cc_start: 0.8215 (mt) cc_final: 0.7853 (mp) REVERT: F 222 ASP cc_start: 0.8035 (t0) cc_final: 0.7546 (t0) REVERT: F 227 MET cc_start: 0.8177 (mmm) cc_final: 0.7781 (mmm) REVERT: F 269 MET cc_start: 0.8841 (mtp) cc_final: 0.8607 (ttm) REVERT: H 221 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8609 (tt) REVERT: H 227 MET cc_start: 0.8063 (tpp) cc_final: 0.7786 (tpp) REVERT: H 237 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8344 (mt-10) REVERT: I 72 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: I 269 MET cc_start: 0.8778 (mtm) cc_final: 0.8489 (mtm) REVERT: I 358 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8346 (m) REVERT: I 374 CYS cc_start: 0.7317 (m) cc_final: 0.6990 (m) REVERT: J 119 MET cc_start: 0.8585 (mtp) cc_final: 0.8366 (mtm) REVERT: J 291 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8108 (tptt) REVERT: K 77 THR cc_start: 0.8981 (m) cc_final: 0.8648 (p) REVERT: K 82 MET cc_start: 0.8271 (tpt) cc_final: 0.7729 (tpt) REVERT: K 123 MET cc_start: 0.8966 (mmt) cc_final: 0.8736 (mmm) REVERT: K 227 MET cc_start: 0.7929 (mmm) cc_final: 0.7405 (mmm) REVERT: K 328 LYS cc_start: 0.8460 (mttp) cc_final: 0.7789 (tttp) REVERT: K 364 GLU cc_start: 0.8674 (tp30) cc_final: 0.8348 (pt0) REVERT: L 334 GLU cc_start: 0.7410 (pm20) cc_final: 0.7149 (pm20) REVERT: L 340 TRP cc_start: 0.8971 (t60) cc_final: 0.8487 (t60) REVERT: L 364 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8578 (tp30) REVERT: M 270 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8532 (tp30) REVERT: B 535 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8102 (ttm) REVERT: B 536 HIS cc_start: 0.7804 (m170) cc_final: 0.7446 (m-70) REVERT: B 663 GLU cc_start: 0.7576 (tp30) cc_final: 0.7273 (tt0) REVERT: B 665 TYR cc_start: 0.7322 (m-80) cc_final: 0.6968 (m-80) REVERT: C 537 SER cc_start: 0.8948 (t) cc_final: 0.8645 (t) REVERT: A 640 ASP cc_start: 0.7582 (t0) cc_final: 0.6639 (p0) REVERT: A 648 ASP cc_start: 0.8078 (m-30) cc_final: 0.7697 (m-30) REVERT: A 675 ILE cc_start: 0.8665 (mm) cc_final: 0.8122 (mm) outliers start: 54 outliers final: 45 residues processed: 365 average time/residue: 0.3246 time to fit residues: 196.4018 Evaluate side-chains 370 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 320 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain H residue 349 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 270 GLU Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 122 ILE Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain M residue 354 GLN Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 651 ILE Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 598 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 325 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 200 optimal weight: 0.0770 chunk 159 optimal weight: 0.8980 chunk 206 optimal weight: 0.5980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN K 101 HIS L 128 ASN ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26476 Z= 0.156 Angle : 0.538 12.510 35905 Z= 0.254 Chirality : 0.042 0.142 3993 Planarity : 0.004 0.038 4597 Dihedral : 6.528 136.896 3662 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.87 % Allowed : 14.68 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3242 helix: 1.47 (0.15), residues: 1385 sheet: 0.02 (0.23), residues: 469 loop : 0.32 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 656 HIS 0.008 0.001 HIS M 101 PHE 0.015 0.001 PHE B 540 TYR 0.037 0.001 TYR C 641 ARG 0.004 0.000 ARG D 551 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6484 Ramachandran restraints generated. 3242 Oldfield, 0 Emsley, 3242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 334 time to evaluate : 3.041 Fit side-chains REVERT: F 216 LEU cc_start: 0.8200 (mt) cc_final: 0.7843 (mp) REVERT: F 222 ASP cc_start: 0.8012 (t0) cc_final: 0.7521 (t0) REVERT: F 227 MET cc_start: 0.8146 (mmm) cc_final: 0.7746 (mmm) REVERT: F 269 MET cc_start: 0.8806 (mtp) cc_final: 0.8554 (ttm) REVERT: H 221 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8627 (tt) REVERT: H 227 MET cc_start: 0.8042 (tpp) cc_final: 0.7768 (tpp) REVERT: H 237 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8284 (mt-10) REVERT: I 72 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: I 269 MET cc_start: 0.8763 (mtm) cc_final: 0.8484 (mtm) REVERT: I 358 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8339 (m) REVERT: I 374 CYS cc_start: 0.7320 (m) cc_final: 0.7119 (m) REVERT: J 47 MET cc_start: 0.7633 (mmm) cc_final: 0.7177 (mmm) REVERT: J 291 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8103 (tptt) REVERT: K 77 THR cc_start: 0.8970 (m) cc_final: 0.8631 (p) REVERT: K 82 MET cc_start: 0.8253 (tpt) cc_final: 0.7711 (tpt) REVERT: K 123 MET cc_start: 0.8961 (mmt) cc_final: 0.8727 (mmm) REVERT: K 227 MET cc_start: 0.7887 (mmm) cc_final: 0.7346 (mmm) REVERT: K 328 LYS cc_start: 0.8464 (mttp) cc_final: 0.7808 (tttp) REVERT: K 364 GLU cc_start: 0.8634 (tp30) cc_final: 0.8331 (pt0) REVERT: L 83 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7452 (tt0) REVERT: L 334 GLU cc_start: 0.7400 (pm20) cc_final: 0.6983 (pp20) REVERT: L 340 TRP cc_start: 0.8974 (t60) cc_final: 0.8511 (t60) REVERT: L 364 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8590 (tp30) REVERT: M 270 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8536 (tp30) REVERT: B 536 HIS cc_start: 0.7839 (m170) cc_final: 0.7496 (m-70) REVERT: B 663 GLU cc_start: 0.7559 (tp30) cc_final: 0.7284 (tt0) REVERT: B 665 TYR cc_start: 0.7305 (m-80) cc_final: 0.6950 (m-80) REVERT: B 675 ILE cc_start: 0.8192 (mp) cc_final: 0.7934 (mt) REVERT: C 537 SER cc_start: 0.8948 (t) cc_final: 0.8651 (t) REVERT: A 640 ASP cc_start: 0.7591 (t0) cc_final: 0.6681 (p0) REVERT: A 648 ASP cc_start: 0.8081 (m-30) cc_final: 0.7682 (m-30) REVERT: A 675 ILE cc_start: 0.8661 (mm) cc_final: 0.8134 (mm) outliers start: 52 outliers final: 44 residues processed: 366 average time/residue: 0.3273 time to fit residues: 198.6052 Evaluate side-chains 367 residues out of total 2779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 319 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain H residue 85 ILE Chi-restraints excluded: chain H residue 221 LEU Chi-restraints excluded: chain H residue 320 LEU Chi-restraints excluded: chain I residue 12 ASN Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 72 GLU Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 145 SER Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 244 ASP Chi-restraints excluded: chain I residue 270 GLU Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 358 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 277 THR Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 190 MET Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain K residue 323 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 143 TYR Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 270 GLU Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain M residue 351 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain A residue 594 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 38 optimal weight: 0.0980 chunk 72 optimal weight: 4.9990 chunk 259 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 266 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 228 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 162 ASN K 101 HIS L 128 ASN M 40 HIS ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103442 restraints weight = 40695.372| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.47 r_work: 0.3143 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26476 Z= 0.225 Angle : 0.565 12.311 35905 Z= 0.270 Chirality : 0.044 0.143 3993 Planarity : 0.004 0.037 4597 Dihedral : 6.603 138.762 3662 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.02 % Allowed : 14.83 % Favored : 83.16 % 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: 0.98 (0.15), residues: 3242 helix: 1.42 (0.15), residues: 1385 sheet: -0.03 (0.23), residues: 469 loop : 0.25 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 656 HIS 0.005 0.001 HIS M 101 PHE 0.014 0.001 PHE B 540 TYR 0.035 0.001 TYR C 641 ARG 0.004 0.000 ARG D 551 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5267.13 seconds wall clock time: 94 minutes 58.62 seconds (5698.62 seconds total)