Starting phenix.real_space_refine on Sat Aug 10 07:13:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/08_2024/8u7m_41986.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/08_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_41986/08_2024/8u7m_41986.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/08_2024/8u7m_41986.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/08_2024/8u7m_41986.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7m_41986/08_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 15.13, per 1000 atoms: 0.53 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: 11.83 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: 4.35 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: 10.14 Time building geometry restraints manager: 12.33 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 3.120 nonbonded pdb=" OG1 THR D 180 " pdb=" NZ LYS F 205 " model vdw 2.206 3.120 nonbonded pdb=" OG SER B 275 " pdb=" NE2 GLN B 283 " model vdw 2.209 3.120 nonbonded pdb=" OG SER F 275 " pdb=" NE2 GLN F 283 " model vdw 2.209 3.120 nonbonded pdb=" OG SER G 275 " pdb=" NE2 GLN G 283 " model vdw 2.211 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 73.940 Find NCS groups from input model: 1.090 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:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.170 ------------------------------------------------------------------------------- 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 : 3.029 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: 0.3922 time to fit residues: 325.8570 Evaluate side-chains 425 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.090 ------------------------------------------------------------------------------- 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: 0.0050 chunk 272 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 145 optimal weight: 0.9990 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 171 optimal weight: 0.2980 chunk 210 optimal weight: 1.9990 chunk 326 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN A 372 HIS B 334 GLN B 372 HIS C 334 GLN C 372 HIS C 469 GLN D 334 GLN D 368 GLN D 372 HIS E 334 GLN E 372 HIS E 469 GLN F 334 GLN F 372 HIS G 334 GLN G 372 HIS H 334 GLN H 372 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28800 Z= 0.208 Angle : 0.656 7.310 39176 Z= 0.326 Chirality : 0.046 0.193 4600 Planarity : 0.005 0.064 4800 Dihedral : 20.894 155.564 4800 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.29 % Allowed : 15.78 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3528 helix: 0.36 (0.14), residues: 1360 sheet: -0.60 (0.32), residues: 240 loop : -0.96 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 93 PHE 0.021 0.002 PHE C 456 TYR 0.012 0.002 TYR E 289 ARG 0.007 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 540 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 473 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.5704 (ttt-90) cc_final: 0.5361 (ttt-90) REVERT: A 208 LYS cc_start: 0.4411 (mmmt) cc_final: 0.3747 (mttm) REVERT: A 353 TYR cc_start: 0.7124 (t80) cc_final: 0.6861 (t80) REVERT: A 450 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7252 (ttpt) REVERT: B 179 MET cc_start: 0.7473 (ptt) cc_final: 0.7106 (ptt) REVERT: B 208 LYS cc_start: 0.4413 (mmmt) cc_final: 0.3721 (mttm) REVERT: B 450 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7367 (ttpt) REVERT: C 94 ASN cc_start: 0.6904 (OUTLIER) cc_final: 0.6696 (m-40) REVERT: C 179 MET cc_start: 0.7489 (ptt) cc_final: 0.7098 (ptt) REVERT: C 450 LYS cc_start: 0.7611 (ttmm) cc_final: 0.7232 (ttpt) REVERT: D 105 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5630 (mpt-90) REVERT: D 179 MET cc_start: 0.7571 (ptt) cc_final: 0.7195 (ptt) REVERT: D 182 ARG cc_start: 0.5581 (ttt-90) cc_final: 0.5157 (ttt-90) REVERT: D 353 TYR cc_start: 0.7126 (t80) cc_final: 0.6859 (t80) REVERT: D 450 LYS cc_start: 0.7581 (ttmm) cc_final: 0.7126 (ttpt) REVERT: E 105 ARG cc_start: 0.5796 (OUTLIER) cc_final: 0.3815 (tpt-90) REVERT: E 179 MET cc_start: 0.7474 (ptt) cc_final: 0.7104 (ptt) REVERT: E 182 ARG cc_start: 0.5646 (ttt-90) cc_final: 0.5230 (ttt-90) REVERT: E 353 TYR cc_start: 0.7130 (t80) cc_final: 0.6864 (t80) REVERT: E 450 LYS cc_start: 0.7743 (ttmm) cc_final: 0.7265 (ttpt) REVERT: F 179 MET cc_start: 0.7407 (ptt) cc_final: 0.7042 (ptt) REVERT: F 353 TYR cc_start: 0.7125 (t80) cc_final: 0.6852 (t80) REVERT: F 450 LYS cc_start: 0.7612 (ttmm) cc_final: 0.7238 (ttpt) REVERT: G 94 ASN cc_start: 0.6892 (OUTLIER) cc_final: 0.6682 (m-40) REVERT: G 179 MET cc_start: 0.7449 (ptt) cc_final: 0.7121 (ptt) REVERT: G 450 LYS cc_start: 0.7610 (ttmm) cc_final: 0.7215 (ttpt) REVERT: H 179 MET cc_start: 0.7454 (ptt) cc_final: 0.7093 (ptt) REVERT: H 353 TYR cc_start: 0.7129 (t80) cc_final: 0.6858 (t80) REVERT: H 450 LYS cc_start: 0.7646 (ttmm) cc_final: 0.7150 (ttpt) outliers start: 67 outliers final: 31 residues processed: 517 average time/residue: 0.3704 time to fit residues: 308.9175 Evaluate side-chains 449 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 414 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN 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 B residue 94 ASN Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain D residue 94 ASN 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 94 ASN 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 F residue 94 ASN Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 283 GLN 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 94 ASN 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: 0.5980 chunk 272 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 90 optimal weight: 0.0980 chunk 327 optimal weight: 0.4980 chunk 353 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 324 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 469 GLN D 368 GLN E 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28800 Z= 0.316 Angle : 0.695 6.561 39176 Z= 0.350 Chirality : 0.048 0.198 4600 Planarity : 0.005 0.054 4800 Dihedral : 19.468 149.916 4800 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.83 % Allowed : 15.74 % Favored : 80.43 % 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: 0.10 (0.14), residues: 1352 sheet: -0.95 (0.32), residues: 224 loop : -1.16 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 288 PHE 0.015 0.003 PHE B 456 TYR 0.016 0.002 TYR B 459 ARG 0.006 0.001 ARG C 105 *********************** 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 574 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 462 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4983 (mmmt) cc_final: 0.3953 (mttm) REVERT: A 450 LYS cc_start: 0.7716 (ttmm) cc_final: 0.7436 (ttpt) REVERT: A 459 TYR cc_start: 0.6651 (t80) cc_final: 0.6423 (t80) REVERT: B 179 MET cc_start: 0.7563 (ptt) cc_final: 0.7148 (ptt) REVERT: B 208 LYS cc_start: 0.4889 (mmmt) cc_final: 0.3983 (mttm) REVERT: B 459 TYR cc_start: 0.6811 (t80) cc_final: 0.6563 (t80) REVERT: C 179 MET cc_start: 0.7566 (ptt) cc_final: 0.7173 (ptt) REVERT: C 182 ARG cc_start: 0.5757 (ttt-90) cc_final: 0.5490 (ttt-90) REVERT: C 208 LYS cc_start: 0.4979 (mmmt) cc_final: 0.3915 (mttm) REVERT: D 179 MET cc_start: 0.7692 (ptt) cc_final: 0.7241 (ptt) REVERT: D 208 LYS cc_start: 0.5019 (mmmt) cc_final: 0.3941 (mttm) REVERT: D 459 TYR cc_start: 0.6813 (t80) cc_final: 0.6534 (t80) REVERT: E 179 MET cc_start: 0.7564 (ptt) cc_final: 0.7173 (ptt) REVERT: E 208 LYS cc_start: 0.4988 (mmmt) cc_final: 0.3926 (mttm) REVERT: E 450 LYS cc_start: 0.7768 (ttmm) cc_final: 0.7472 (ttpt) REVERT: E 459 TYR cc_start: 0.6625 (t80) cc_final: 0.6396 (t80) REVERT: F 179 MET cc_start: 0.7541 (ptt) cc_final: 0.7114 (ptt) REVERT: F 182 ARG cc_start: 0.5754 (ttt-90) cc_final: 0.5504 (ttt-90) REVERT: F 208 LYS cc_start: 0.4978 (mmmt) cc_final: 0.3925 (mttm) REVERT: G 179 MET cc_start: 0.7592 (ptt) cc_final: 0.7223 (ptt) REVERT: G 182 ARG cc_start: 0.5735 (ttt-90) cc_final: 0.5484 (ttt-90) REVERT: H 179 MET cc_start: 0.7547 (ptt) cc_final: 0.7151 (ptt) outliers start: 112 outliers final: 72 residues processed: 545 average time/residue: 0.3605 time to fit residues: 322.8498 Evaluate side-chains 504 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 432 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 283 GLN 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 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 453 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 142 ILE 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 283 GLN 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 D residue 45 ILE 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 333 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 45 ILE 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 283 GLN 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 453 ILE Chi-restraints excluded: chain F residue 45 ILE 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 333 THR 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 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 283 GLN 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 37 ILE 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 333 THR 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: 0.9980 chunk 246 optimal weight: 2.9990 chunk 169 optimal weight: 0.0030 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 328 optimal weight: 0.8980 chunk 347 optimal weight: 0.4980 chunk 171 optimal weight: 0.7980 chunk 311 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN D 368 GLN E 368 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 28800 Z= 0.193 Angle : 0.588 7.141 39176 Z= 0.293 Chirality : 0.044 0.172 4600 Planarity : 0.004 0.051 4800 Dihedral : 18.772 160.136 4800 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.72 % Allowed : 16.77 % Favored : 79.51 % 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: -0.48 (0.14), residues: 3528 helix: 0.55 (0.14), residues: 1352 sheet: -0.48 (0.30), residues: 240 loop : -0.90 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 288 PHE 0.016 0.001 PHE B 456 TYR 0.009 0.001 TYR B 459 ARG 0.005 0.000 ARG E 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 544 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 435 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.5775 (ttt-90) cc_final: 0.5459 (tmt-80) REVERT: A 208 LYS cc_start: 0.4885 (mmmt) cc_final: 0.3902 (mttm) REVERT: A 283 GLN cc_start: 0.5949 (OUTLIER) cc_final: 0.5263 (tt0) REVERT: A 450 LYS cc_start: 0.7690 (ttmm) cc_final: 0.7467 (ttpt) REVERT: B 179 MET cc_start: 0.7429 (ptt) cc_final: 0.7216 (ptt) REVERT: B 208 LYS cc_start: 0.4809 (mmmt) cc_final: 0.3958 (mttm) REVERT: B 283 GLN cc_start: 0.6003 (OUTLIER) cc_final: 0.5263 (tt0) REVERT: B 377 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7187 (mm) REVERT: B 459 TYR cc_start: 0.6886 (t80) cc_final: 0.6622 (t80) REVERT: B 491 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5790 (tt0) REVERT: C 179 MET cc_start: 0.7446 (ptt) cc_final: 0.7237 (ptt) REVERT: C 182 ARG cc_start: 0.5833 (ttt-90) cc_final: 0.5424 (tmt-80) REVERT: C 208 LYS cc_start: 0.4845 (mmmt) cc_final: 0.3831 (mttm) REVERT: C 450 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7455 (ttpt) REVERT: C 491 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5925 (tt0) REVERT: D 182 ARG cc_start: 0.6026 (ttt-90) cc_final: 0.5452 (tmt-80) REVERT: D 208 LYS cc_start: 0.4869 (mmmt) cc_final: 0.3878 (mttm) REVERT: D 283 GLN cc_start: 0.6142 (OUTLIER) cc_final: 0.5407 (tt0) REVERT: D 450 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7428 (ttpt) REVERT: D 459 TYR cc_start: 0.6907 (t80) cc_final: 0.6672 (t80) REVERT: E 208 LYS cc_start: 0.4837 (mmmt) cc_final: 0.3858 (mttm) REVERT: E 283 GLN cc_start: 0.5942 (OUTLIER) cc_final: 0.5268 (tt0) REVERT: E 450 LYS cc_start: 0.7731 (ttmm) cc_final: 0.7505 (ttpt) REVERT: E 459 TYR cc_start: 0.6958 (t80) cc_final: 0.6756 (t80) REVERT: E 491 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6033 (tt0) REVERT: F 179 MET cc_start: 0.7451 (ptt) cc_final: 0.7215 (ptt) REVERT: F 182 ARG cc_start: 0.5831 (ttt-90) cc_final: 0.5447 (tmt-80) REVERT: F 208 LYS cc_start: 0.4894 (mmmt) cc_final: 0.3885 (mttm) REVERT: F 271 ILE cc_start: 0.7370 (pp) cc_final: 0.7112 (pp) REVERT: F 283 GLN cc_start: 0.5986 (OUTLIER) cc_final: 0.5267 (tt0) REVERT: F 377 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7204 (mm) REVERT: F 450 LYS cc_start: 0.7706 (ttmm) cc_final: 0.7441 (ttpt) REVERT: G 182 ARG cc_start: 0.5811 (ttt-90) cc_final: 0.5410 (tmt-80) REVERT: G 271 ILE cc_start: 0.7360 (pp) cc_final: 0.7088 (pp) REVERT: G 450 LYS cc_start: 0.7752 (ttmm) cc_final: 0.7471 (ttpt) REVERT: G 491 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6023 (tt0) REVERT: H 179 MET cc_start: 0.7462 (ptt) cc_final: 0.7192 (ptt) REVERT: H 212 VAL cc_start: 0.6248 (OUTLIER) cc_final: 0.5971 (m) REVERT: H 283 GLN cc_start: 0.6013 (OUTLIER) cc_final: 0.5303 (tt0) REVERT: H 450 LYS cc_start: 0.7644 (ttmm) cc_final: 0.7388 (ttpt) REVERT: H 491 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6012 (tt0) outliers start: 109 outliers final: 69 residues processed: 517 average time/residue: 0.3675 time to fit residues: 307.4207 Evaluate side-chains 495 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 412 time to evaluate : 3.019 ------------------------------------------------------------------------------- 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 282 TYR Chi-restraints excluded: chain A residue 283 GLN 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 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 94 ASN 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 283 GLN 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 142 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 319 ASP 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 282 TYR Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 319 ASP 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 491 GLU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN 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 491 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 94 ASN 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 327 CYS Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 453 ILE Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain H residue 208 LYS 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 370 VAL Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU 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: 0.7980 chunk 197 optimal weight: 0.0370 chunk 5 optimal weight: 0.0070 chunk 259 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 296 optimal weight: 0.9990 chunk 240 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.3046 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= 0.181 Angle : 0.569 6.727 39176 Z= 0.283 Chirality : 0.043 0.155 4600 Planarity : 0.004 0.049 4800 Dihedral : 18.203 177.635 4800 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.17 % Allowed : 17.96 % Favored : 77.87 % 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: -0.52 (0.14), residues: 3528 helix: 0.61 (0.14), residues: 1384 sheet: -0.74 (0.30), residues: 224 loop : -1.00 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 288 PHE 0.013 0.001 PHE B 456 TYR 0.009 0.001 TYR B 459 ARG 0.004 0.000 ARG E 182 *********************** 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 556 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 434 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ARG cc_start: 0.5977 (ttt-90) cc_final: 0.5723 (tmt-80) REVERT: A 208 LYS cc_start: 0.4748 (mmmt) cc_final: 0.3888 (mttm) REVERT: A 283 GLN cc_start: 0.5935 (OUTLIER) cc_final: 0.5257 (tt0) REVERT: A 450 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7456 (ttpt) REVERT: A 491 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6003 (tt0) REVERT: B 208 LYS cc_start: 0.4792 (mmmt) cc_final: 0.3929 (mttm) REVERT: B 271 ILE cc_start: 0.7401 (pp) cc_final: 0.7127 (pp) REVERT: B 283 GLN cc_start: 0.5980 (OUTLIER) cc_final: 0.5184 (tt0) REVERT: B 377 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7182 (mm) REVERT: B 491 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5904 (tt0) REVERT: C 182 ARG cc_start: 0.5809 (ttt-90) cc_final: 0.5604 (tmt-80) REVERT: C 208 LYS cc_start: 0.4698 (mmmt) cc_final: 0.3849 (mttm) REVERT: C 271 ILE cc_start: 0.7334 (pp) cc_final: 0.7064 (pp) REVERT: C 283 GLN cc_start: 0.6021 (OUTLIER) cc_final: 0.5349 (tt0) REVERT: C 450 LYS cc_start: 0.7736 (ttmm) cc_final: 0.7513 (ttpt) REVERT: C 491 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5954 (tt0) REVERT: D 182 ARG cc_start: 0.6036 (ttt-90) cc_final: 0.5727 (tmt-80) REVERT: D 208 LYS cc_start: 0.4852 (mmmt) cc_final: 0.3889 (mttm) REVERT: D 271 ILE cc_start: 0.7396 (pp) cc_final: 0.7136 (pp) REVERT: D 283 GLN cc_start: 0.5927 (OUTLIER) cc_final: 0.5202 (tt0) REVERT: D 450 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7495 (ttpt) REVERT: D 459 TYR cc_start: 0.6876 (t80) cc_final: 0.6662 (t80) REVERT: E 208 LYS cc_start: 0.4819 (mmmt) cc_final: 0.3878 (mttm) REVERT: E 271 ILE cc_start: 0.7417 (pp) cc_final: 0.7168 (pp) REVERT: E 283 GLN cc_start: 0.5947 (OUTLIER) cc_final: 0.5534 (mt0) REVERT: E 450 LYS cc_start: 0.7727 (ttmm) cc_final: 0.7485 (ttpt) REVERT: E 459 TYR cc_start: 0.6933 (t80) cc_final: 0.6731 (t80) REVERT: E 491 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5951 (tt0) REVERT: F 182 ARG cc_start: 0.6062 (ttt-90) cc_final: 0.5736 (tmt-80) REVERT: F 208 LYS cc_start: 0.4717 (mmmt) cc_final: 0.3872 (mttm) REVERT: F 271 ILE cc_start: 0.7400 (pp) cc_final: 0.7131 (pp) REVERT: F 283 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.5170 (tt0) REVERT: F 319 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6740 (m-30) REVERT: F 377 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7216 (mm) REVERT: F 450 LYS cc_start: 0.7745 (ttmm) cc_final: 0.7524 (ttpt) REVERT: G 182 ARG cc_start: 0.5779 (ttt-90) cc_final: 0.5572 (tmt-80) REVERT: G 271 ILE cc_start: 0.7377 (pp) cc_final: 0.7177 (pp) REVERT: G 283 GLN cc_start: 0.5931 (OUTLIER) cc_final: 0.5197 (tt0) REVERT: G 450 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7591 (ttpt) REVERT: G 491 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5949 (tt0) REVERT: H 271 ILE cc_start: 0.7405 (pp) cc_final: 0.7127 (pp) REVERT: H 283 GLN cc_start: 0.5962 (OUTLIER) cc_final: 0.5203 (tt0) REVERT: H 491 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5841 (tt0) outliers start: 122 outliers final: 78 residues processed: 534 average time/residue: 0.3612 time to fit residues: 316.1264 Evaluate side-chains 511 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 416 time to evaluate : 3.156 ------------------------------------------------------------------------------- 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 282 TYR Chi-restraints excluded: chain A residue 283 GLN 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 45 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 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 460 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 45 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 142 ILE 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 283 GLN 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 45 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 283 GLN 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 476 LEU 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 142 ILE Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 283 GLN 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 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 142 ILE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 319 ASP 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 37 ILE Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 94 ASN 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 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 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 453 ILE Chi-restraints excluded: chain H residue 476 LEU 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: 0.9990 chunk 313 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 348 optimal weight: 2.9990 chunk 289 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN D 230 ASN E 230 ASN ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN G 230 ASN H 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 28800 Z= 0.235 Angle : 0.605 6.873 39176 Z= 0.303 Chirality : 0.044 0.170 4600 Planarity : 0.004 0.052 4800 Dihedral : 17.937 179.706 4800 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.37 % Allowed : 19.30 % Favored : 76.33 % 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: -0.47 (0.14), residues: 3528 helix: 0.61 (0.14), residues: 1360 sheet: -0.60 (0.29), residues: 240 loop : -0.93 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 93 PHE 0.013 0.002 PHE B 456 TYR 0.009 0.001 TYR C 459 ARG 0.004 0.000 ARG E 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 567 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 439 time to evaluate : 3.365 Fit side-chains revert: symmetry clash REVERT: A 208 LYS cc_start: 0.4790 (mmmt) cc_final: 0.3921 (mttm) REVERT: A 450 LYS cc_start: 0.7724 (ttmm) cc_final: 0.7497 (ttpt) REVERT: B 208 LYS cc_start: 0.4855 (mmmt) cc_final: 0.3949 (mttm) REVERT: B 271 ILE cc_start: 0.7436 (pp) cc_final: 0.7192 (pp) REVERT: B 377 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7276 (mm) REVERT: B 491 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6071 (tt0) REVERT: C 450 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7522 (ttpt) REVERT: C 491 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6079 (tt0) REVERT: D 208 LYS cc_start: 0.4899 (mmmt) cc_final: 0.3880 (mttm) REVERT: D 271 ILE cc_start: 0.7430 (pp) cc_final: 0.7174 (pp) REVERT: D 450 LYS cc_start: 0.7741 (ttmm) cc_final: 0.7528 (ttpt) REVERT: D 459 TYR cc_start: 0.6893 (t80) cc_final: 0.6610 (t80) REVERT: E 208 LYS cc_start: 0.4885 (mmmt) cc_final: 0.3908 (mttm) REVERT: E 450 LYS cc_start: 0.7699 (ttmm) cc_final: 0.7477 (ttpt) REVERT: E 459 TYR cc_start: 0.7045 (t80) cc_final: 0.6822 (t80) REVERT: E 491 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6140 (tt0) REVERT: F 182 ARG cc_start: 0.5872 (ttt-90) cc_final: 0.5436 (tmt-80) REVERT: F 208 LYS cc_start: 0.4779 (mmmt) cc_final: 0.3901 (mttm) REVERT: F 271 ILE cc_start: 0.7417 (pp) cc_final: 0.7153 (pp) REVERT: F 377 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7275 (mm) REVERT: F 450 LYS cc_start: 0.7717 (ttmm) cc_final: 0.7516 (ttpt) REVERT: G 271 ILE cc_start: 0.7453 (pp) cc_final: 0.7236 (pp) REVERT: G 491 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6019 (tt0) REVERT: H 271 ILE cc_start: 0.7431 (pp) cc_final: 0.7160 (pp) REVERT: H 283 GLN cc_start: 0.6051 (OUTLIER) cc_final: 0.5395 (tt0) REVERT: H 491 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6096 (tt0) outliers start: 128 outliers final: 103 residues processed: 535 average time/residue: 0.3663 time to fit residues: 319.2806 Evaluate side-chains 526 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 415 time to evaluate : 3.041 ------------------------------------------------------------------------------- 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 290 ILE 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 142 ILE 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 283 GLN 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 37 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 94 ASN 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 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 476 LEU 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 142 ILE Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain E residue 290 ILE 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 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 283 GLN 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 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 209 LEU 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 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 94 ASN 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 209 LEU Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 283 GLN 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 476 LEU Chi-restraints excluded: chain H residue 491 GLU 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: 0.0270 chunk 198 optimal weight: 4.9990 chunk 254 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 293 optimal weight: 0.0370 chunk 194 optimal weight: 0.7980 chunk 346 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 28800 Z= 0.164 Angle : 0.577 7.703 39176 Z= 0.288 Chirality : 0.043 0.165 4600 Planarity : 0.004 0.056 4800 Dihedral : 17.457 177.862 4800 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.65 % Allowed : 20.80 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.14), residues: 3528 helix: 0.74 (0.14), residues: 1392 sheet: -0.67 (0.30), residues: 224 loop : -0.99 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 171 PHE 0.011 0.001 PHE B 456 TYR 0.009 0.001 TYR C 459 ARG 0.006 0.000 ARG C 182 *********************** 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 536 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 429 time to evaluate : 2.942 Fit side-chains REVERT: A 208 LYS cc_start: 0.4740 (mmmt) cc_final: 0.3903 (mttm) REVERT: A 450 LYS cc_start: 0.7778 (ttmm) cc_final: 0.7549 (ttpt) REVERT: A 459 TYR cc_start: 0.6823 (t80) cc_final: 0.6545 (t80) REVERT: B 208 LYS cc_start: 0.4763 (mmmt) cc_final: 0.3931 (mttm) REVERT: B 271 ILE cc_start: 0.7417 (pp) cc_final: 0.7164 (pp) REVERT: B 283 GLN cc_start: 0.5808 (OUTLIER) cc_final: 0.5062 (tt0) REVERT: B 377 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7136 (mm) REVERT: B 491 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6026 (tt0) REVERT: C 271 ILE cc_start: 0.7417 (pp) cc_final: 0.7200 (pp) REVERT: C 283 GLN cc_start: 0.5854 (OUTLIER) cc_final: 0.5179 (tt0) REVERT: C 491 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5948 (tt0) REVERT: D 208 LYS cc_start: 0.4830 (mmmt) cc_final: 0.3838 (mttm) REVERT: D 271 ILE cc_start: 0.7387 (pp) cc_final: 0.7156 (pp) REVERT: D 283 GLN cc_start: 0.5852 (OUTLIER) cc_final: 0.5122 (tt0) REVERT: D 450 LYS cc_start: 0.7736 (ttmm) cc_final: 0.7523 (ttpt) REVERT: D 459 TYR cc_start: 0.6871 (t80) cc_final: 0.6628 (t80) REVERT: E 208 LYS cc_start: 0.4862 (mmmt) cc_final: 0.3869 (mttm) REVERT: E 217 GLU cc_start: 0.4225 (mp0) cc_final: 0.3800 (mp0) REVERT: E 450 LYS cc_start: 0.7691 (ttmm) cc_final: 0.7452 (ttpt) REVERT: E 459 TYR cc_start: 0.7013 (t80) cc_final: 0.6786 (t80) REVERT: E 491 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6084 (tt0) REVERT: F 182 ARG cc_start: 0.6048 (ttt-90) cc_final: 0.5820 (tmt170) REVERT: F 208 LYS cc_start: 0.4728 (mmmt) cc_final: 0.3901 (mttm) REVERT: F 283 GLN cc_start: 0.5850 (OUTLIER) cc_final: 0.5135 (tt0) REVERT: F 377 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7135 (mm) REVERT: G 283 GLN cc_start: 0.5914 (OUTLIER) cc_final: 0.5191 (tt0) REVERT: G 491 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6033 (tt0) REVERT: H 271 ILE cc_start: 0.7391 (pp) cc_final: 0.7150 (pp) REVERT: H 283 GLN cc_start: 0.5882 (OUTLIER) cc_final: 0.5135 (tt0) REVERT: H 491 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6081 (tt0) outliers start: 107 outliers final: 82 residues processed: 518 average time/residue: 0.3573 time to fit residues: 305.3589 Evaluate side-chains 500 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 405 time to evaluate : 3.093 ------------------------------------------------------------------------------- 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 209 LEU 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 114 PHE 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 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 283 GLN 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 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 114 PHE 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 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 460 LEU Chi-restraints excluded: chain D residue 476 LEU 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 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 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 283 GLN 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 208 LYS Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 318 VAL 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 370 VAL Chi-restraints excluded: chain H residue 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU 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: 3.9990 chunk 138 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 236 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 272 optimal weight: 0.4980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28800 Z= 0.247 Angle : 0.623 9.125 39176 Z= 0.311 Chirality : 0.045 0.175 4600 Planarity : 0.005 0.056 4800 Dihedral : 17.215 178.005 4800 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.10 % Allowed : 20.73 % Favored : 75.17 % 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: -0.43 (0.14), residues: 3528 helix: 0.72 (0.15), residues: 1352 sheet: -0.76 (0.29), residues: 224 loop : -0.95 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 93 PHE 0.013 0.002 PHE B 456 TYR 0.008 0.001 TYR B 459 ARG 0.005 0.000 ARG C 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 553 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 433 time to evaluate : 3.330 Fit side-chains REVERT: A 450 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7508 (ttpt) REVERT: A 459 TYR cc_start: 0.6899 (t80) cc_final: 0.6590 (t80) REVERT: B 208 LYS cc_start: 0.4820 (mmmt) cc_final: 0.3908 (mttm) REVERT: B 377 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7369 (mm) REVERT: B 491 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6078 (tt0) REVERT: C 491 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6072 (tt0) REVERT: D 271 ILE cc_start: 0.7474 (pp) cc_final: 0.7238 (pp) REVERT: D 450 LYS cc_start: 0.7711 (ttmm) cc_final: 0.7498 (ttpt) REVERT: E 208 LYS cc_start: 0.4962 (mmmt) cc_final: 0.3904 (mttm) REVERT: E 450 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7500 (ttpt) REVERT: E 459 TYR cc_start: 0.6989 (t80) cc_final: 0.6739 (t80) REVERT: F 182 ARG cc_start: 0.6277 (ttt-90) cc_final: 0.5931 (tmt170) REVERT: F 377 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7370 (mm) REVERT: G 491 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6085 (tt0) REVERT: H 271 ILE cc_start: 0.7465 (pp) cc_final: 0.7201 (pp) REVERT: H 283 GLN cc_start: 0.6147 (OUTLIER) cc_final: 0.5820 (mt0) REVERT: H 491 GLU cc_start: 0.6695 (OUTLIER) cc_final: 0.6127 (tt0) outliers start: 120 outliers final: 102 residues processed: 531 average time/residue: 0.3489 time to fit residues: 307.7217 Evaluate side-chains 531 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 422 time to evaluate : 2.892 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 290 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 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 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 114 PHE 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 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 476 LEU 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 290 ILE Chi-restraints excluded: chain E residue 327 CYS 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 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 283 GLN 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 209 LEU 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 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 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 333 THR 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 476 LEU 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: 0.0970 chunk 332 optimal weight: 0.3980 chunk 303 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 253 optimal weight: 0.0980 chunk 99 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 322 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28800 Z= 0.164 Angle : 0.578 7.586 39176 Z= 0.287 Chirality : 0.043 0.147 4600 Planarity : 0.004 0.061 4800 Dihedral : 16.584 179.706 4800 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.48 % Allowed : 21.96 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3528 helix: 0.84 (0.14), residues: 1392 sheet: -0.26 (0.27), residues: 264 loop : -0.98 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 171 PHE 0.010 0.001 PHE B 456 TYR 0.014 0.001 TYR D 459 ARG 0.005 0.000 ARG C 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 536 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 434 time to evaluate : 3.125 Fit side-chains revert: symmetry clash REVERT: A 450 LYS cc_start: 0.7823 (ttmm) cc_final: 0.7454 (ttpt) REVERT: A 459 TYR cc_start: 0.6921 (t80) cc_final: 0.6616 (t80) REVERT: B 208 LYS cc_start: 0.4740 (mmmt) cc_final: 0.3867 (mttm) REVERT: B 283 GLN cc_start: 0.5833 (OUTLIER) cc_final: 0.5094 (tt0) REVERT: B 377 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7141 (mm) REVERT: B 491 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5924 (tt0) REVERT: C 491 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5957 (tt0) REVERT: D 283 GLN cc_start: 0.5862 (OUTLIER) cc_final: 0.5157 (tt0) REVERT: D 459 TYR cc_start: 0.6636 (t80) cc_final: 0.6206 (t80) REVERT: E 208 LYS cc_start: 0.4847 (mmmt) cc_final: 0.3872 (mttm) REVERT: E 271 ILE cc_start: 0.7319 (pp) cc_final: 0.7086 (pp) REVERT: E 450 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7475 (ttpt) REVERT: E 459 TYR cc_start: 0.6957 (t80) cc_final: 0.6715 (t80) REVERT: F 208 LYS cc_start: 0.4833 (mmmt) cc_final: 0.3881 (mttm) REVERT: F 283 GLN cc_start: 0.5804 (OUTLIER) cc_final: 0.5075 (tt0) REVERT: F 377 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7139 (mm) REVERT: G 283 GLN cc_start: 0.5823 (OUTLIER) cc_final: 0.5116 (tt0) REVERT: G 491 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5985 (tt0) REVERT: H 283 GLN cc_start: 0.5870 (OUTLIER) cc_final: 0.5165 (tt0) REVERT: H 491 GLU cc_start: 0.6524 (OUTLIER) cc_final: 0.5965 (tt0) outliers start: 102 outliers final: 86 residues processed: 513 average time/residue: 0.3508 time to fit residues: 299.3097 Evaluate side-chains 509 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 412 time to evaluate : 3.072 ------------------------------------------------------------------------------- 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 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 114 PHE 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 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 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 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 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 476 LEU 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 327 CYS 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 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 283 GLN 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 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 283 GLN 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 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 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 395 GLU Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 476 LEU 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: 0.4980 chunk 341 optimal weight: 0.5980 chunk 208 optimal weight: 0.7980 chunk 162 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 358 optimal weight: 0.9990 chunk 330 optimal weight: 0.0030 chunk 285 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 chunk 175 optimal weight: 0.8980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28800 Z= 0.183 Angle : 0.591 8.166 39176 Z= 0.293 Chirality : 0.043 0.152 4600 Planarity : 0.005 0.061 4800 Dihedral : 15.891 179.601 4800 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.55 % Allowed : 22.17 % Favored : 74.28 % 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: -0.25 (0.14), residues: 3528 helix: 0.90 (0.14), residues: 1392 sheet: -0.18 (0.27), residues: 264 loop : -0.99 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 92 PHE 0.015 0.001 PHE B 456 TYR 0.014 0.001 TYR D 459 ARG 0.006 0.000 ARG C 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 531 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 427 time to evaluate : 3.060 Fit side-chains revert: symmetry clash REVERT: A 450 LYS cc_start: 0.7812 (ttmm) cc_final: 0.7445 (ttpt) REVERT: A 459 TYR cc_start: 0.6945 (t80) cc_final: 0.6643 (t80) REVERT: A 491 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5979 (tt0) REVERT: B 208 LYS cc_start: 0.4751 (mmmt) cc_final: 0.3876 (mttm) REVERT: B 283 GLN cc_start: 0.5864 (OUTLIER) cc_final: 0.5101 (tt0) REVERT: B 377 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7196 (mm) REVERT: B 491 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.5981 (tt0) REVERT: D 283 GLN cc_start: 0.5873 (OUTLIER) cc_final: 0.5154 (tt0) REVERT: D 459 TYR cc_start: 0.6573 (t80) cc_final: 0.6151 (t80) REVERT: E 208 LYS cc_start: 0.4849 (mmmt) cc_final: 0.3871 (mttm) REVERT: E 271 ILE cc_start: 0.7394 (pp) cc_final: 0.7191 (pp) REVERT: E 450 LYS cc_start: 0.7818 (ttmm) cc_final: 0.7505 (ttpt) REVERT: E 459 TYR cc_start: 0.6965 (t80) cc_final: 0.6715 (t80) REVERT: E 491 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5988 (tt0) REVERT: F 208 LYS cc_start: 0.4844 (mmmt) cc_final: 0.3883 (mttm) REVERT: F 283 GLN cc_start: 0.5797 (OUTLIER) cc_final: 0.5041 (tt0) REVERT: F 377 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7192 (mm) REVERT: G 283 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.5131 (tt0) REVERT: G 491 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6032 (tt0) REVERT: H 283 GLN cc_start: 0.5869 (OUTLIER) cc_final: 0.5160 (tt0) outliers start: 104 outliers final: 85 residues processed: 507 average time/residue: 0.3702 time to fit residues: 314.0193 Evaluate side-chains 505 residues out of total 2928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 409 time to evaluate : 3.109 ------------------------------------------------------------------------------- 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 209 LEU 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 114 PHE 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 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 114 PHE 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 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 476 LEU 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 327 CYS 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 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 283 GLN 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 209 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 283 GLN 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 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 476 LEU 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: 0.6980 chunk 87 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 293 optimal weight: 0.0030 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.190005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.163216 restraints weight = 33188.173| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 1.86 r_work: 0.4174 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28800 Z= 0.186 Angle : 0.599 8.048 39176 Z= 0.294 Chirality : 0.043 0.163 4600 Planarity : 0.005 0.062 4800 Dihedral : 15.504 179.633 4800 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.48 % Allowed : 22.58 % Favored : 73.94 % 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: -0.20 (0.14), residues: 3528 helix: 0.96 (0.15), residues: 1392 sheet: -0.16 (0.27), residues: 264 loop : -0.97 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 92 PHE 0.015 0.001 PHE B 456 TYR 0.014 0.001 TYR C 289 ARG 0.005 0.000 ARG C 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7022.30 seconds wall clock time: 126 minutes 33.86 seconds (7593.86 seconds total)