Starting phenix.real_space_refine on Thu Jul 25 07:35:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/07_2024/8u7m_41986.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/07_2024/8u7m_41986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/07_2024/8u7m_41986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/07_2024/8u7m_41986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/07_2024/8u7m_41986.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/07_2024/8u7m_41986.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 176 5.16 5 C 17576 2.51 5 N 4832 2.21 5 O 5656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 395": "OE1" <-> "OE2" Residue "A GLU 399": "OE1" <-> "OE2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C GLU 399": "OE1" <-> "OE2" Residue "D GLU 395": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "E GLU 487": "OE1" <-> "OE2" Residue "F GLU 111": "OE1" <-> "OE2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 399": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 395": "OE1" <-> "OE2" Residue "G GLU 399": "OE1" <-> "OE2" Residue "G GLU 487": "OE1" <-> "OE2" Residue "H GLU 111": "OE1" <-> "OE2" Residue "H GLU 395": "OE1" <-> "OE2" Residue "H GLU 399": "OE1" <-> "OE2" Residue "H GLU 487": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 28336 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "B" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "C" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "D" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "E" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "F" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "G" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "H" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3380 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 4 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Time building chain proxies: 16.92, per 1000 atoms: 0.60 Number of scatterers: 28336 At special positions: 0 Unit cell: (170.52, 170.52, 105.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 P 96 15.00 O 5656 8.00 N 4832 7.00 C 17576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.59 Conformation dependent library (CDL) restraints added in 5.2 seconds 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6512 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 40 sheets defined 46.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 96 through 110 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.562A pdb=" N THR A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.521A pdb=" N GLU A 177 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.667A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.687A pdb=" N GLN A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 removed outlier: 4.109A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.000A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 110 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.555A pdb=" N THR B 173 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.549A pdb=" N GLU B 177 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'B' and resid 193 through 203 Processing helix chain 'B' and resid 223 through 233 removed outlier: 4.248A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 265 removed outlier: 3.687A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP B 261 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.726A pdb=" N GLN B 292 " --> pdb=" O HIS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 316 removed outlier: 4.104A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.000A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 380 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 486 removed outlier: 3.648A pdb=" N ARG B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 501 Processing helix chain 'C' and resid 19 through 25 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 110 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.553A pdb=" N THR C 173 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.541A pdb=" N GLU C 177 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 185 Processing helix chain 'C' and resid 193 through 203 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 255 through 265 removed outlier: 3.730A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.712A pdb=" N GLN C 292 " --> pdb=" O HIS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 316 removed outlier: 4.134A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.002A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 380 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 494 through 501 Processing helix chain 'D' and resid 19 through 25 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 110 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 169 through 173 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.556A pdb=" N GLU D 177 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 185 Processing helix chain 'D' and resid 193 through 203 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 255 through 265 removed outlier: 3.685A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.727A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 316 removed outlier: 4.141A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.022A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 380 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 486 removed outlier: 3.601A pdb=" N ARG D 480 " --> pdb=" O LEU D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 501 Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 110 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 169 through 173 removed outlier: 3.559A pdb=" N THR E 173 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.543A pdb=" N GLU E 177 " --> pdb=" O LEU E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 185 Processing helix chain 'E' and resid 193 through 203 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.671A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.689A pdb=" N GLN E 292 " --> pdb=" O HIS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 316 removed outlier: 4.109A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.003A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 380 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 486 removed outlier: 3.558A pdb=" N ARG E 480 " --> pdb=" O LEU E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 501 Processing helix chain 'F' and resid 19 through 25 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 110 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 159 through 164 Processing helix chain 'F' and resid 169 through 173 removed outlier: 3.559A pdb=" N THR F 173 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 178 removed outlier: 3.545A pdb=" N GLU F 177 " --> pdb=" O LEU F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 Processing helix chain 'F' and resid 193 through 203 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 255 through 265 removed outlier: 3.686A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP F 261 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.730A pdb=" N GLN F 292 " --> pdb=" O HIS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 316 removed outlier: 4.085A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.002A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 380 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 486 Processing helix chain 'F' and resid 494 through 501 Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 110 Processing helix chain 'G' and resid 126 through 138 Processing helix chain 'G' and resid 159 through 164 Processing helix chain 'G' and resid 169 through 173 removed outlier: 3.559A pdb=" N THR G 173 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 3.547A pdb=" N GLU G 177 " --> pdb=" O LEU G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 185 Processing helix chain 'G' and resid 193 through 203 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 255 through 265 removed outlier: 3.725A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.711A pdb=" N GLN G 292 " --> pdb=" O HIS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 316 removed outlier: 4.119A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.018A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 380 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 486 removed outlier: 3.601A pdb=" N ARG G 480 " --> pdb=" O LEU G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 501 Processing helix chain 'H' and resid 19 through 25 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 110 Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 159 through 164 Processing helix chain 'H' and resid 169 through 173 removed outlier: 3.558A pdb=" N THR H 173 " --> pdb=" O ASP H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 178 removed outlier: 3.551A pdb=" N GLU H 177 " --> pdb=" O LEU H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 185 Processing helix chain 'H' and resid 193 through 203 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 255 through 265 removed outlier: 3.687A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP H 261 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.728A pdb=" N GLN H 292 " --> pdb=" O HIS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 316 removed outlier: 4.139A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 removed outlier: 4.021A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 380 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 486 removed outlier: 3.615A pdb=" N ARG H 480 " --> pdb=" O LEU H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.503A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.603A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.952A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 5.980A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 222 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.493A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.194A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 144 removed outlier: 3.955A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 189 removed outlier: 5.978A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 222 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.494A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.228A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG C 322 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.965A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 189 removed outlier: 5.955A pdb=" N ALA C 188 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 222 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.495A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.611A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.952A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 188 through 189 removed outlier: 5.971A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 222 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.502A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.598A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 142 through 144 removed outlier: 3.959A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.566A pdb=" N ILE E 222 " --> pdb=" O LEU E 209 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.494A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.724A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 142 through 144 removed outlier: 3.960A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 188 through 189 removed outlier: 5.975A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE F 222 " --> pdb=" O LEU F 209 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AD5, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.494A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.243A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 142 through 144 removed outlier: 3.956A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 208 through 210 removed outlier: 3.523A pdb=" N ILE G 222 " --> pdb=" O LEU G 209 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE1, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.495A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.241A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 142 through 144 removed outlier: 3.957A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 189 removed outlier: 5.895A pdb=" N ALA H 188 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE H 222 " --> pdb=" O LEU H 209 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3114 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: 10.18 Time building geometry restraints manager: 12.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4680 1.31 - 1.43: 6900 1.43 - 1.56: 16753 1.56 - 1.69: 171 1.69 - 1.81: 296 Bond restraints: 28800 Sorted by residual: bond pdb=" C5 IMP F 604 " pdb=" C6 IMP F 604 " ideal model delta sigma weight residual 1.390 1.532 -0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" C5 IMP G 604 " pdb=" C6 IMP G 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C5 IMP D 604 " pdb=" C6 IMP D 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C5 IMP B 604 " pdb=" C6 IMP B 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" C5 IMP H 604 " pdb=" C6 IMP H 604 " ideal model delta sigma weight residual 1.390 1.531 -0.141 2.00e-02 2.50e+03 4.98e+01 ... (remaining 28795 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.39: 777 105.39 - 112.42: 15218 112.42 - 119.45: 9456 119.45 - 126.49: 13318 126.49 - 133.52: 407 Bond angle restraints: 39176 Sorted by residual: angle pdb=" PB ATP A 603 " pdb=" O3B ATP A 603 " pdb=" PG ATP A 603 " ideal model delta sigma weight residual 139.87 122.69 17.18 1.00e+00 1.00e+00 2.95e+02 angle pdb=" PB ATP D 603 " pdb=" O3B ATP D 603 " pdb=" PG ATP D 603 " ideal model delta sigma weight residual 139.87 122.81 17.06 1.00e+00 1.00e+00 2.91e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PB ATP C 603 " pdb=" O3B ATP C 603 " pdb=" PG ATP C 603 " ideal model delta sigma weight residual 139.87 122.87 17.00 1.00e+00 1.00e+00 2.89e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 123.09 16.78 1.00e+00 1.00e+00 2.82e+02 ... (remaining 39171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 16912 35.57 - 71.14: 588 71.14 - 106.71: 97 106.71 - 142.28: 39 142.28 - 177.84: 12 Dihedral angle restraints: 17648 sinusoidal: 7488 harmonic: 10160 Sorted by residual: dihedral pdb=" C5' IMP A 604 " pdb=" O5' IMP A 604 " pdb=" P IMP A 604 " pdb=" O2P IMP A 604 " ideal model delta sinusoidal sigma weight residual 191.93 14.09 177.84 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP D 604 " pdb=" O5' IMP D 604 " pdb=" P IMP D 604 " pdb=" O2P IMP D 604 " ideal model delta sinusoidal sigma weight residual 191.93 14.31 177.62 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP B 604 " pdb=" O5' IMP B 604 " pdb=" P IMP B 604 " pdb=" O2P IMP B 604 " ideal model delta sinusoidal sigma weight residual 191.93 14.43 177.50 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 17645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 4568 0.340 - 0.680: 24 0.680 - 1.019: 0 1.019 - 1.359: 0 1.359 - 1.699: 8 Chirality restraints: 4600 Sorted by residual: chirality pdb=" C2' ATP A 603 " pdb=" C1' ATP A 603 " pdb=" C3' ATP A 603 " pdb=" O2' ATP A 603 " both_signs ideal model delta sigma weight residual False -2.68 -0.98 -1.70 2.00e-01 2.50e+01 7.21e+01 chirality pdb=" C2' ATP B 603 " pdb=" C1' ATP B 603 " pdb=" C3' ATP B 603 " pdb=" O2' ATP B 603 " both_signs ideal model delta sigma weight residual False -2.68 -0.98 -1.70 2.00e-01 2.50e+01 7.19e+01 chirality pdb=" C2' ATP C 603 " pdb=" C1' ATP C 603 " pdb=" C3' ATP C 603 " pdb=" O2' ATP C 603 " both_signs ideal model delta sigma weight residual False -2.68 -0.98 -1.70 2.00e-01 2.50e+01 7.19e+01 ... (remaining 4597 not shown) Planarity restraints: 4800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 63 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 64 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 63 " -0.064 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO C 64 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 63 " 0.063 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO E 64 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " 0.052 5.00e-02 4.00e+02 ... (remaining 4797 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2973 2.74 - 3.28: 29351 3.28 - 3.82: 46133 3.82 - 4.36: 57269 4.36 - 4.90: 98535 Nonbonded interactions: 234261 Sorted by model distance: nonbonded pdb=" NZ LYS A 205 " pdb=" OG1 THR E 180 " model vdw 2.203 2.520 nonbonded pdb=" OG1 THR D 180 " pdb=" NZ LYS F 205 " model vdw 2.206 2.520 nonbonded pdb=" OG SER B 275 " pdb=" NE2 GLN B 283 " model vdw 2.209 2.520 nonbonded pdb=" OG SER F 275 " pdb=" NE2 GLN F 283 " model vdw 2.209 2.520 nonbonded pdb=" OG SER G 275 " pdb=" NE2 GLN G 283 " model vdw 2.211 2.520 ... (remaining 234256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 4.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 76.910 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.160 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 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 : 0.007 0.142 28800 Z= 0.419 Angle : 1.135 19.362 39176 Z= 0.567 Chirality : 0.088 1.699 4600 Planarity : 0.006 0.104 4800 Dihedral : 20.220 177.844 11136 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.27 % Allowed : 14.96 % Favored : 84.77 % 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: -1.11 (0.14), residues: 3528 helix: 0.12 (0.14), residues: 1344 sheet: -0.50 (0.29), residues: 280 loop : -1.42 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 372 PHE 0.013 0.002 PHE G 456 TYR 0.013 0.001 TYR E 459 ARG 0.009 0.001 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 505 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 507 average time/residue: 0.4101 time to fit residues: 344.5004 Evaluate side-chains 425 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.0000 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 171 optimal weight: 0.3980 chunk 210 optimal weight: 0.9990 chunk 326 optimal weight: 0.5980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN A 372 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 372 HIS ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 372 HIS C 469 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 368 GLN D 372 HIS ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN E 372 HIS E 469 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 372 HIS ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN G 372 HIS ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN H 372 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28800 Z= 0.204 Angle : 0.636 7.397 39176 Z= 0.315 Chirality : 0.045 0.198 4600 Planarity : 0.005 0.063 4800 Dihedral : 20.903 148.698 4800 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.61 % Allowed : 16.22 % Favored : 82.17 % 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: -0.62 (0.14), residues: 3528 helix: 0.35 (0.14), residues: 1360 sheet: -0.43 (0.33), residues: 240 loop : -0.95 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 93 PHE 0.020 0.002 PHE F 456 TYR 0.013 0.001 TYR E 289 ARG 0.006 0.000 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 484 time to evaluate : 3.061 Fit side-chains REVERT: A 105 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.5593 (mpt-90) REVERT: A 182 ARG cc_start: 0.5751 (ttt-90) cc_final: 0.5543 (ttt-90) REVERT: A 198 ASN cc_start: 0.5550 (m-40) cc_final: 0.5283 (m-40) REVERT: A 353 TYR cc_start: 0.7137 (t80) cc_final: 0.6854 (t80) REVERT: A 450 LYS cc_start: 0.7696 (ttmm) cc_final: 0.7224 (ttpt) REVERT: B 105 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5639 (mpt-90) REVERT: B 179 MET cc_start: 0.7570 (ptt) cc_final: 0.7204 (ptt) REVERT: B 208 LYS cc_start: 0.4492 (mmmt) cc_final: 0.3841 (mttm) REVERT: C 94 ASN cc_start: 0.6776 (OUTLIER) cc_final: 0.6532 (m-40) REVERT: C 105 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5647 (mpt-90) REVERT: C 179 MET cc_start: 0.7561 (ptt) cc_final: 0.7184 (ptt) REVERT: C 182 ARG cc_start: 0.5720 (ttt-90) cc_final: 0.5470 (tmt-80) REVERT: C 198 ASN cc_start: 0.5609 (m-40) cc_final: 0.5330 (m-40) REVERT: C 450 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7420 (ttpt) REVERT: D 78 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7158 (ttm) REVERT: D 105 ARG cc_start: 0.5822 (OUTLIER) cc_final: 0.5600 (mpt-90) REVERT: D 179 MET cc_start: 0.7534 (ptt) cc_final: 0.7108 (ptt) REVERT: D 182 ARG cc_start: 0.5692 (ttt-90) cc_final: 0.5490 (ttt-90) REVERT: D 198 ASN cc_start: 0.5595 (m-40) cc_final: 0.5317 (m-40) REVERT: D 353 TYR cc_start: 0.7125 (t80) cc_final: 0.6836 (t80) REVERT: D 450 LYS cc_start: 0.7553 (ttmm) cc_final: 0.7285 (ttpt) REVERT: E 105 ARG cc_start: 0.5844 (OUTLIER) cc_final: 0.5629 (mpt-90) REVERT: E 179 MET cc_start: 0.7546 (ptt) cc_final: 0.7152 (ptt) REVERT: E 182 ARG cc_start: 0.5850 (ttt-90) cc_final: 0.5608 (ttt-90) REVERT: E 198 ASN cc_start: 0.5610 (m-40) cc_final: 0.5333 (m-40) REVERT: E 353 TYR cc_start: 0.7141 (t80) cc_final: 0.6854 (t80) REVERT: E 450 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7230 (ttpt) REVERT: F 105 ARG cc_start: 0.5876 (OUTLIER) cc_final: 0.5660 (mpt-90) REVERT: F 179 MET cc_start: 0.7473 (ptt) cc_final: 0.7117 (ptt) REVERT: F 182 ARG cc_start: 0.5721 (ttt-90) cc_final: 0.5472 (tmt-80) REVERT: F 353 TYR cc_start: 0.7146 (t80) cc_final: 0.6853 (t80) REVERT: F 450 LYS cc_start: 0.7564 (ttmm) cc_final: 0.7360 (ttpt) REVERT: G 94 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6523 (m-40) REVERT: G 179 MET cc_start: 0.7514 (ptt) cc_final: 0.7145 (ptt) REVERT: G 182 ARG cc_start: 0.5701 (ttt-90) cc_final: 0.5449 (tmt-80) REVERT: G 198 ASN cc_start: 0.5605 (m-40) cc_final: 0.5312 (m-40) REVERT: G 450 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7420 (ttpt) REVERT: H 105 ARG cc_start: 0.5830 (OUTLIER) cc_final: 0.5616 (mpt-90) REVERT: H 179 MET cc_start: 0.7494 (ptt) cc_final: 0.7103 (ptt) REVERT: H 182 ARG cc_start: 0.5704 (ttt-90) cc_final: 0.5431 (ttt-90) REVERT: H 198 ASN cc_start: 0.5549 (m-40) cc_final: 0.5262 (m-40) REVERT: H 353 TYR cc_start: 0.7130 (t80) cc_final: 0.6839 (t80) REVERT: H 450 LYS cc_start: 0.7637 (ttmm) cc_final: 0.7141 (ttpt) outliers start: 47 outliers final: 20 residues processed: 508 average time/residue: 0.3595 time to fit residues: 295.5345 Evaluate side-chains 473 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 443 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 327 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 272 optimal weight: 0.3980 chunk 222 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 327 optimal weight: 4.9990 chunk 353 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 262 optimal weight: 0.0050 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28800 Z= 0.231 Angle : 0.620 6.712 39176 Z= 0.308 Chirality : 0.045 0.178 4600 Planarity : 0.005 0.051 4800 Dihedral : 19.111 153.020 4800 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.17 % Allowed : 15.71 % Favored : 80.12 % 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: -0.63 (0.14), residues: 3528 helix: 0.39 (0.14), residues: 1352 sheet: -0.81 (0.32), residues: 224 loop : -0.93 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 466 PHE 0.018 0.002 PHE C 456 TYR 0.017 0.002 TYR B 459 ARG 0.005 0.000 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 465 time to evaluate : 3.190 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.5916 (OUTLIER) cc_final: 0.3961 (tpt-90) REVERT: A 208 LYS cc_start: 0.4745 (mmmt) cc_final: 0.3910 (mttm) REVERT: A 450 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7431 (ttpt) REVERT: B 105 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.3946 (tpt-90) REVERT: B 179 MET cc_start: 0.7394 (ptt) cc_final: 0.7016 (ptt) REVERT: B 208 LYS cc_start: 0.4585 (mmmt) cc_final: 0.3813 (mttm) REVERT: C 105 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.4007 (tpt-90) REVERT: C 179 MET cc_start: 0.7399 (ptt) cc_final: 0.7038 (ptt) REVERT: C 208 LYS cc_start: 0.4774 (mmmt) cc_final: 0.3967 (mttm) REVERT: D 105 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.3972 (tpt-90) REVERT: D 179 MET cc_start: 0.7429 (ptt) cc_final: 0.7056 (ptt) REVERT: D 182 ARG cc_start: 0.5869 (ttt-90) cc_final: 0.5649 (tmt-80) REVERT: D 208 LYS cc_start: 0.4853 (mmmt) cc_final: 0.3972 (mttm) REVERT: E 105 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.3963 (tpt-90) REVERT: E 179 MET cc_start: 0.7390 (ptt) cc_final: 0.7021 (ptt) REVERT: E 208 LYS cc_start: 0.4819 (mmmt) cc_final: 0.3936 (mttm) REVERT: E 450 LYS cc_start: 0.7712 (ttmm) cc_final: 0.7416 (ttpt) REVERT: F 105 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.4039 (tpt-90) REVERT: F 179 MET cc_start: 0.7416 (ptt) cc_final: 0.7073 (ptt) REVERT: F 208 LYS cc_start: 0.4747 (mmmt) cc_final: 0.3938 (mttm) REVERT: F 271 ILE cc_start: 0.7302 (pp) cc_final: 0.7032 (pp) REVERT: G 179 MET cc_start: 0.7386 (ptt) cc_final: 0.7047 (ptt) REVERT: G 271 ILE cc_start: 0.7275 (pp) cc_final: 0.7010 (pp) REVERT: H 105 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.4032 (tpt-90) REVERT: H 179 MET cc_start: 0.7358 (ptt) cc_final: 0.7044 (ptt) REVERT: H 198 ASN cc_start: 0.5535 (m-40) cc_final: 0.5164 (m-40) REVERT: H 212 VAL cc_start: 0.6291 (OUTLIER) cc_final: 0.6071 (t) REVERT: H 450 LYS cc_start: 0.7697 (ttmm) cc_final: 0.7388 (ttpt) REVERT: H 459 TYR cc_start: 0.6364 (t80) cc_final: 0.6136 (t80) outliers start: 122 outliers final: 76 residues processed: 556 average time/residue: 0.3716 time to fit residues: 332.9190 Evaluate side-chains 516 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 432 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 367 ILE Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 367 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 367 ILE Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.5980 chunk 246 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 219 optimal weight: 0.9990 chunk 328 optimal weight: 3.9990 chunk 347 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 311 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 469 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN E 469 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28800 Z= 0.271 Angle : 0.622 6.725 39176 Z= 0.312 Chirality : 0.045 0.153 4600 Planarity : 0.005 0.046 4800 Dihedral : 18.563 171.929 4800 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.41 % Allowed : 17.11 % Favored : 78.48 % 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: -0.71 (0.14), residues: 3528 helix: 0.34 (0.14), residues: 1344 sheet: -0.72 (0.26), residues: 264 loop : -1.01 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 288 PHE 0.016 0.002 PHE F 456 TYR 0.016 0.002 TYR E 459 ARG 0.003 0.000 ARG D 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 438 time to evaluate : 3.099 Fit side-chains REVERT: A 105 ARG cc_start: 0.5976 (OUTLIER) cc_final: 0.4079 (tpt-90) REVERT: A 208 LYS cc_start: 0.4846 (mmmt) cc_final: 0.3963 (mttm) REVERT: A 450 LYS cc_start: 0.7672 (ttmm) cc_final: 0.7425 (ttpt) REVERT: B 105 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.4072 (tpt-90) REVERT: B 208 LYS cc_start: 0.4921 (mmmt) cc_final: 0.4011 (mttm) REVERT: B 491 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.6177 (tt0) REVERT: C 105 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.5725 (mpt-90) REVERT: C 208 LYS cc_start: 0.4928 (mmmt) cc_final: 0.4021 (mttm) REVERT: C 491 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6074 (tt0) REVERT: D 105 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.4081 (tpt-90) REVERT: D 208 LYS cc_start: 0.4950 (mmmt) cc_final: 0.4078 (mttm) REVERT: E 105 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.4125 (tpt-90) REVERT: E 208 LYS cc_start: 0.4913 (mmmt) cc_final: 0.4048 (mttm) REVERT: E 450 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7417 (ttpt) REVERT: F 105 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.4088 (tpt-90) REVERT: F 208 LYS cc_start: 0.4860 (mmmt) cc_final: 0.3986 (mttm) REVERT: F 377 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7351 (mm) REVERT: H 105 ARG cc_start: 0.6007 (OUTLIER) cc_final: 0.4075 (tpt-90) REVERT: H 450 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7474 (ttpt) REVERT: H 491 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5967 (tt0) outliers start: 129 outliers final: 76 residues processed: 534 average time/residue: 0.3593 time to fit residues: 312.5080 Evaluate side-chains 500 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 413 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 296 optimal weight: 0.6980 chunk 240 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 230 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS D 230 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS E 230 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN G 230 ASN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 466 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 28800 Z= 0.401 Angle : 0.736 7.778 39176 Z= 0.370 Chirality : 0.049 0.172 4600 Planarity : 0.006 0.048 4800 Dihedral : 18.254 173.776 4800 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.19 % Allowed : 18.51 % Favored : 76.30 % 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: -1.37 (0.13), residues: 3528 helix: -0.26 (0.14), residues: 1336 sheet: -1.20 (0.28), residues: 232 loop : -1.33 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 288 PHE 0.015 0.003 PHE C 90 TYR 0.009 0.002 TYR G 459 ARG 0.004 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 467 time to evaluate : 3.282 Fit side-chains REVERT: A 254 GLU cc_start: 0.7067 (tp30) cc_final: 0.6803 (tp30) REVERT: A 327 CYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7515 (p) REVERT: A 450 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7584 (ttpt) REVERT: B 377 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7446 (mm) REVERT: B 491 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6205 (tt0) REVERT: C 491 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6245 (tt0) REVERT: D 327 CYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7433 (p) REVERT: E 254 GLU cc_start: 0.6998 (tp30) cc_final: 0.6730 (tp30) REVERT: E 327 CYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7528 (p) REVERT: E 450 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7589 (ttpt) REVERT: E 459 TYR cc_start: 0.6847 (t80) cc_final: 0.6511 (t80) REVERT: E 491 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6290 (tt0) REVERT: F 327 CYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7493 (p) REVERT: F 377 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7459 (mm) REVERT: G 327 CYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7527 (p) REVERT: G 491 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6230 (tt0) REVERT: H 327 CYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7596 (p) REVERT: H 491 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6015 (tt0) outliers start: 152 outliers final: 89 residues processed: 589 average time/residue: 0.3562 time to fit residues: 343.6029 Evaluate side-chains 531 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 429 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.5980 chunk 313 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 204 optimal weight: 0.8980 chunk 85 optimal weight: 0.0370 chunk 348 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28800 Z= 0.172 Angle : 0.597 7.641 39176 Z= 0.297 Chirality : 0.044 0.174 4600 Planarity : 0.004 0.056 4800 Dihedral : 17.422 179.331 4800 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.35 % Allowed : 22.64 % Favored : 74.01 % 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 (0.14), residues: 3528 helix: 0.25 (0.14), residues: 1384 sheet: -0.76 (0.28), residues: 240 loop : -1.15 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 92 PHE 0.014 0.001 PHE B 35 TYR 0.010 0.001 TYR B 289 ARG 0.003 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 465 time to evaluate : 3.293 Fit side-chains REVERT: A 208 LYS cc_start: 0.4849 (mmmt) cc_final: 0.3867 (mttm) REVERT: A 450 LYS cc_start: 0.7868 (ttmm) cc_final: 0.7569 (ttpt) REVERT: A 491 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6361 (tt0) REVERT: B 208 LYS cc_start: 0.4830 (mmmt) cc_final: 0.3888 (mttm) REVERT: B 377 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7154 (mm) REVERT: C 208 LYS cc_start: 0.4777 (mmmt) cc_final: 0.3875 (mttm) REVERT: C 283 GLN cc_start: 0.6042 (OUTLIER) cc_final: 0.5611 (tt0) REVERT: D 208 LYS cc_start: 0.4946 (mmmt) cc_final: 0.3950 (mttm) REVERT: D 327 CYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7465 (p) REVERT: D 456 PHE cc_start: 0.7722 (t80) cc_final: 0.7500 (t80) REVERT: E 208 LYS cc_start: 0.4854 (mmmt) cc_final: 0.3860 (mttm) REVERT: E 450 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7564 (ttpt) REVERT: E 491 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6425 (tt0) REVERT: F 52 THR cc_start: 0.7734 (t) cc_final: 0.7479 (m) REVERT: F 208 LYS cc_start: 0.4869 (mmmt) cc_final: 0.3885 (mttm) REVERT: F 377 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7158 (mm) REVERT: G 491 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6336 (tt0) REVERT: H 327 CYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7567 (p) outliers start: 98 outliers final: 74 residues processed: 542 average time/residue: 0.3470 time to fit residues: 309.2550 Evaluate side-chains 532 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 450 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 293 optimal weight: 0.2980 chunk 194 optimal weight: 3.9990 chunk 346 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 28800 Z= 0.291 Angle : 0.665 8.042 39176 Z= 0.331 Chirality : 0.046 0.184 4600 Planarity : 0.005 0.053 4800 Dihedral : 17.181 173.450 4800 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.03 % Allowed : 22.40 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3528 helix: 0.13 (0.14), residues: 1352 sheet: -0.99 (0.24), residues: 280 loop : -1.18 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 288 PHE 0.015 0.002 PHE B 456 TYR 0.013 0.002 TYR C 459 ARG 0.004 0.000 ARG F 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 448 time to evaluate : 2.779 Fit side-chains REVERT: A 327 CYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7483 (p) REVERT: A 450 LYS cc_start: 0.7900 (ttmm) cc_final: 0.7508 (ttpt) REVERT: B 377 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7449 (mm) REVERT: B 491 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6262 (tt0) REVERT: D 327 CYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7469 (p) REVERT: E 327 CYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7438 (p) REVERT: E 450 LYS cc_start: 0.7902 (ttmm) cc_final: 0.7514 (ttpt) REVERT: F 52 THR cc_start: 0.7794 (t) cc_final: 0.7583 (m) REVERT: F 327 CYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7504 (p) REVERT: G 327 CYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7506 (p) REVERT: G 491 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6449 (tt0) REVERT: H 327 CYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7528 (p) REVERT: H 491 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6105 (tt0) outliers start: 118 outliers final: 95 residues processed: 539 average time/residue: 0.3397 time to fit residues: 305.0549 Evaluate side-chains 540 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 435 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 236 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 272 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 28800 Z= 0.233 Angle : 0.615 7.865 39176 Z= 0.306 Chirality : 0.044 0.155 4600 Planarity : 0.005 0.062 4800 Dihedral : 16.535 173.682 4800 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.72 % Allowed : 23.19 % Favored : 73.09 % 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: -0.85 (0.14), residues: 3528 helix: 0.25 (0.14), residues: 1344 sheet: -0.98 (0.25), residues: 272 loop : -1.08 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 288 PHE 0.014 0.002 PHE B 456 TYR 0.009 0.001 TYR C 459 ARG 0.002 0.000 ARG E 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 438 time to evaluate : 3.226 Fit side-chains REVERT: A 327 CYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7471 (p) REVERT: A 450 LYS cc_start: 0.7888 (ttmm) cc_final: 0.7490 (ttpt) REVERT: B 377 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7331 (mm) REVERT: B 491 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6320 (tt0) REVERT: C 491 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6353 (tt0) REVERT: E 450 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7502 (ttpt) REVERT: F 327 CYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7440 (p) REVERT: F 377 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7364 (mm) REVERT: G 327 CYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7493 (p) REVERT: G 491 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6346 (tt0) REVERT: H 491 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6182 (tt0) outliers start: 109 outliers final: 88 residues processed: 525 average time/residue: 0.3409 time to fit residues: 298.4060 Evaluate side-chains 523 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 426 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.3980 chunk 332 optimal weight: 0.9990 chunk 303 optimal weight: 2.9990 chunk 323 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 140 optimal weight: 0.0570 chunk 253 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 322 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.4447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 28800 Z= 0.198 Angle : 0.601 7.709 39176 Z= 0.297 Chirality : 0.043 0.185 4600 Planarity : 0.005 0.060 4800 Dihedral : 15.706 173.461 4800 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.62 % Allowed : 23.29 % Favored : 73.09 % 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: -0.87 (0.14), residues: 3528 helix: 0.25 (0.14), residues: 1392 sheet: -0.81 (0.25), residues: 272 loop : -1.16 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 288 PHE 0.015 0.001 PHE G 456 TYR 0.028 0.002 TYR G 459 ARG 0.003 0.000 ARG E 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 424 time to evaluate : 3.107 Fit side-chains REVERT: A 450 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7436 (ttpt) REVERT: B 208 LYS cc_start: 0.4787 (mmmt) cc_final: 0.3800 (mttm) REVERT: B 271 ILE cc_start: 0.7435 (pp) cc_final: 0.7180 (pp) REVERT: B 283 GLN cc_start: 0.6151 (OUTLIER) cc_final: 0.5433 (tt0) REVERT: B 377 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7318 (mm) REVERT: B 456 PHE cc_start: 0.7943 (t80) cc_final: 0.7588 (t80) REVERT: C 491 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6498 (tt0) REVERT: D 283 GLN cc_start: 0.6158 (OUTLIER) cc_final: 0.5788 (tt0) REVERT: E 450 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7452 (ttpt) REVERT: F 377 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7306 (mm) REVERT: G 283 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5755 (tt0) REVERT: G 491 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6351 (tt0) REVERT: H 166 LEU cc_start: 0.6294 (mp) cc_final: 0.5354 (mp) REVERT: H 283 GLN cc_start: 0.6156 (OUTLIER) cc_final: 0.5799 (tt0) REVERT: H 491 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6166 (tt0) outliers start: 106 outliers final: 92 residues processed: 507 average time/residue: 0.3445 time to fit residues: 290.6492 Evaluate side-chains 513 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 412 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 327 CYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 0.5980 chunk 341 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 237 optimal weight: 0.5980 chunk 358 optimal weight: 0.9990 chunk 330 optimal weight: 0.1980 chunk 285 optimal weight: 0.0050 chunk 29 optimal weight: 0.6980 chunk 220 optimal weight: 0.6980 chunk 175 optimal weight: 3.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 28800 Z= 0.170 Angle : 0.588 7.655 39176 Z= 0.288 Chirality : 0.043 0.166 4600 Planarity : 0.004 0.063 4800 Dihedral : 15.202 176.616 4800 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.97 % Allowed : 23.77 % Favored : 73.26 % 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: -0.63 (0.14), residues: 3528 helix: 0.51 (0.14), residues: 1392 sheet: -0.67 (0.26), residues: 264 loop : -1.08 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 288 PHE 0.014 0.001 PHE G 456 TYR 0.021 0.001 TYR C 459 ARG 0.003 0.000 ARG H 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7056 Ramachandran restraints generated. 3528 Oldfield, 0 Emsley, 3528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 420 time to evaluate : 3.189 Fit side-chains REVERT: A 450 LYS cc_start: 0.7837 (ttmm) cc_final: 0.7421 (ttpt) REVERT: B 208 LYS cc_start: 0.4761 (mmmt) cc_final: 0.3786 (mttm) REVERT: B 377 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7215 (mm) REVERT: B 459 TYR cc_start: 0.6641 (t80) cc_final: 0.6284 (t80) REVERT: B 491 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6468 (tt0) REVERT: C 491 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6485 (tt0) REVERT: E 450 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7454 (ttpt) REVERT: F 377 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7202 (mm) REVERT: G 166 LEU cc_start: 0.6208 (mp) cc_final: 0.5272 (mp) REVERT: G 459 TYR cc_start: 0.6725 (t80) cc_final: 0.6367 (t80) REVERT: G 491 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6195 (tt0) REVERT: H 166 LEU cc_start: 0.6185 (mp) cc_final: 0.5232 (mp) REVERT: H 491 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6285 (tt0) outliers start: 87 outliers final: 73 residues processed: 482 average time/residue: 0.3483 time to fit residues: 279.0747 Evaluate side-chains 489 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 410 time to evaluate : 3.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 257 LYS Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 114 PHE Chi-restraints excluded: chain D residue 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 327 CYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain E residue 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 395 GLU Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 491 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 257 LYS Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 395 GLU Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 114 PHE Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 327 CYS Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 491 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 286 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 293 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.0370 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.189720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.162277 restraints weight = 32728.261| |-----------------------------------------------------------------------------| r_work (start): 0.4199 rms_B_bonded: 1.93 r_work: 0.4078 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3944 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28800 Z= 0.229 Angle : 0.624 7.629 39176 Z= 0.306 Chirality : 0.044 0.205 4600 Planarity : 0.005 0.060 4800 Dihedral : 15.070 175.515 4800 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.18 % Allowed : 23.63 % Favored : 73.19 % 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 (0.14), residues: 3528 helix: 0.59 (0.15), residues: 1352 sheet: -0.64 (0.26), residues: 272 loop : -1.00 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 93 PHE 0.015 0.002 PHE G 456 TYR 0.019 0.002 TYR D 459 ARG 0.002 0.000 ARG A 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6770.41 seconds wall clock time: 121 minutes 40.61 seconds (7300.61 seconds total)