Starting phenix.real_space_refine on Sun Mar 24 13:10:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y59_33613/03_2024/7y59_33613_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y59_33613/03_2024/7y59_33613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y59_33613/03_2024/7y59_33613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y59_33613/03_2024/7y59_33613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y59_33613/03_2024/7y59_33613_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y59_33613/03_2024/7y59_33613_updated.pdb" } resolution = 4.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.049 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 30 5.49 5 S 208 5.16 5 C 26100 2.51 5 N 7345 2.21 5 O 7881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 701": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41564 Number of models: 1 Model: "" Number of chains: 16 Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "X" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 13, 'TRANS': 211} Chain: "Y" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1144 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 13, 'TRANS': 211} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 794 Unresolved non-hydrogen angles: 1045 Unresolved non-hydrogen dihedrals: 708 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 15, 'ASN:plan1': 7, 'TRP:plan': 9, 'ASP:plan': 7, 'PHE:plan': 21, 'GLU:plan': 3, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 456 Chain: "Z" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1144 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 185} Link IDs: {'PTRANS': 13, 'TRANS': 211} Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 794 Unresolved non-hydrogen angles: 1045 Unresolved non-hydrogen dihedrals: 708 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 15, 'ASN:plan1': 7, 'TRP:plan': 9, 'ASP:plan': 7, 'PHE:plan': 21, 'GLU:plan': 3, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 456 Chain: "A" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "B" Number of atoms: 5846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5846 Classifications: {'peptide': 745} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 703} Chain: "C" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 744, 5835 Classifications: {'peptide': 744} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 38, 'TRANS': 702} Chain: "D" Number of atoms: 5829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5829 Classifications: {'peptide': 743} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 701} Chain: "E" Number of atoms: 5911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 753, 5911 Classifications: {'peptide': 753} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 710} Chain: "F" Number of atoms: 5921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5921 Classifications: {'peptide': 755} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 712} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.12, per 1000 atoms: 0.48 Number of scatterers: 41564 At special positions: 0 Unit cell: (172.7, 179.3, 189.2, 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 208 16.00 P 30 15.00 O 7881 8.00 N 7345 7.00 C 26100 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: 18.44 Conformation dependent library (CDL) restraints added in 7.6 seconds 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10024 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 251 helices and 33 sheets defined 45.1% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.32 Creating SS restraints... Processing helix chain 'W' and resid 3 through 9 Processing helix chain 'W' and resid 13 through 31 Proline residue: W 26 - end of helix Processing helix chain 'W' and resid 36 through 38 No H-bonds generated for 'chain 'W' and resid 36 through 38' Processing helix chain 'W' and resid 43 through 47 Processing helix chain 'W' and resid 52 through 54 No H-bonds generated for 'chain 'W' and resid 52 through 54' Processing helix chain 'W' and resid 69 through 87 removed outlier: 6.550A pdb=" N THR W 84 " --> pdb=" O TYR W 80 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG W 85 " --> pdb=" O GLN W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 115 Processing helix chain 'W' and resid 123 through 137 removed outlier: 3.796A pdb=" N ASN W 137 " --> pdb=" O TRP W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 155 through 165 Processing helix chain 'W' and resid 171 through 193 removed outlier: 3.908A pdb=" N PHE W 188 " --> pdb=" O PHE W 184 " (cutoff:3.500A) Proline residue: W 191 - end of helix Processing helix chain 'W' and resid 205 through 209 Processing helix chain 'X' and resid 3 through 10 Processing helix chain 'X' and resid 13 through 31 Proline residue: X 26 - end of helix Processing helix chain 'X' and resid 36 through 38 No H-bonds generated for 'chain 'X' and resid 36 through 38' Processing helix chain 'X' and resid 43 through 48 Processing helix chain 'X' and resid 69 through 88 Processing helix chain 'X' and resid 95 through 115 Processing helix chain 'X' and resid 123 through 136 Processing helix chain 'X' and resid 155 through 165 Processing helix chain 'X' and resid 170 through 187 Processing helix chain 'X' and resid 189 through 193 Processing helix chain 'X' and resid 204 through 209 Processing helix chain 'Y' and resid 4 through 10 Processing helix chain 'Y' and resid 13 through 31 Proline residue: Y 26 - end of helix Processing helix chain 'Y' and resid 36 through 38 No H-bonds generated for 'chain 'Y' and resid 36 through 38' Processing helix chain 'Y' and resid 43 through 48 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 57 through 59 No H-bonds generated for 'chain 'Y' and resid 57 through 59' Processing helix chain 'Y' and resid 66 through 88 removed outlier: 3.753A pdb=" N GLY Y 69 " --> pdb=" O PRO Y 66 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N PHE Y 70 " --> pdb=" O GLY Y 67 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU Y 71 " --> pdb=" O THR Y 68 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR Y 72 " --> pdb=" O GLY Y 69 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER Y 83 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR Y 84 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR Y 88 " --> pdb=" O ARG Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 115 Processing helix chain 'Y' and resid 123 through 136 Processing helix chain 'Y' and resid 155 through 163 removed outlier: 3.870A pdb=" N ASN Y 163 " --> pdb=" O ILE Y 159 " (cutoff:3.500A) Processing helix chain 'Y' and resid 170 through 187 removed outlier: 3.726A pdb=" N MET Y 187 " --> pdb=" O TYR Y 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 190 through 193 No H-bonds generated for 'chain 'Y' and resid 190 through 193' Processing helix chain 'Z' and resid 4 through 9 Processing helix chain 'Z' and resid 13 through 31 Proline residue: Z 26 - end of helix removed outlier: 4.000A pdb=" N LEU Z 31 " --> pdb=" O LEU Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 43 through 48 Processing helix chain 'Z' and resid 52 through 54 No H-bonds generated for 'chain 'Z' and resid 52 through 54' Processing helix chain 'Z' and resid 57 through 60 Processing helix chain 'Z' and resid 69 through 88 removed outlier: 3.597A pdb=" N VAL Z 74 " --> pdb=" O PHE Z 70 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG Z 85 " --> pdb=" O GLN Z 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR Z 88 " --> pdb=" O THR Z 84 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 115 Processing helix chain 'Z' and resid 122 through 136 removed outlier: 4.190A pdb=" N LEU Z 136 " --> pdb=" O VAL Z 132 " (cutoff:3.500A) Processing helix chain 'Z' and resid 155 through 165 Processing helix chain 'Z' and resid 170 through 188 removed outlier: 3.680A pdb=" N PHE Z 188 " --> pdb=" O PHE Z 185 " (cutoff:3.500A) Processing helix chain 'Z' and resid 190 through 193 No H-bonds generated for 'chain 'Z' and resid 190 through 193' Processing helix chain 'Z' and resid 205 through 209 removed outlier: 4.172A pdb=" N TRP Z 209 " --> pdb=" O PHE Z 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 205 through 209' Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 135 through 138 No H-bonds generated for 'chain 'A' and resid 135 through 138' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 279 through 296 removed outlier: 4.325A pdb=" N LYS A 295 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN A 296 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.879A pdb=" N LYS A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.803A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 544 through 551 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 594 through 610 Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 715 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 765 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 3.667A pdb=" N GLU B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 320 through 335 removed outlier: 3.784A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.837A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 483 through 498 removed outlier: 4.291A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 544 through 551 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 579 through 586 removed outlier: 4.022A pdb=" N ALA B 585 " --> pdb=" O ILE B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 610 removed outlier: 3.527A pdb=" N ASP B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY B 610 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 651 through 661 Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 715 removed outlier: 3.903A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 749 through 765 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 121 through 123 No H-bonds generated for 'chain 'C' and resid 121 through 123' Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.570A pdb=" N MET C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 282 through 296 removed outlier: 3.543A pdb=" N LEU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 320 through 334 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.771A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 525 through 535 Processing helix chain 'C' and resid 544 through 551 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 579 through 586 removed outlier: 3.808A pdb=" N ILE C 582 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG C 586 " --> pdb=" O ALA C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 609 removed outlier: 4.246A pdb=" N ILE C 601 " --> pdb=" O ALA C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 651 through 660 Processing helix chain 'C' and resid 674 through 677 No H-bonds generated for 'chain 'C' and resid 674 through 677' Processing helix chain 'C' and resid 684 through 715 Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'D' and resid 43 through 49 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 193 through 199 removed outlier: 3.781A pdb=" N SER D 197 " --> pdb=" O GLU D 194 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN D 199 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.719A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 272 through 275 No H-bonds generated for 'chain 'D' and resid 272 through 275' Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 320 through 335 removed outlier: 3.691A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 426 Processing helix chain 'D' and resid 438 through 442 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 476 through 479 No H-bonds generated for 'chain 'D' and resid 476 through 479' Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.730A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 524 through 535 Processing helix chain 'D' and resid 544 through 551 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 581 through 586 Processing helix chain 'D' and resid 594 through 609 Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 651 through 660 Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 715 Processing helix chain 'D' and resid 733 through 742 removed outlier: 5.015A pdb=" N PHE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 762 Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.693A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 Processing helix chain 'E' and resid 306 through 308 No H-bonds generated for 'chain 'E' and resid 306 through 308' Processing helix chain 'E' and resid 320 through 333 Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 426 removed outlier: 4.326A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 498 removed outlier: 3.784A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 524 through 535 Processing helix chain 'E' and resid 544 through 551 Processing helix chain 'E' and resid 556 through 568 Processing helix chain 'E' and resid 579 through 586 removed outlier: 3.561A pdb=" N ILE E 582 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 585 " --> pdb=" O ILE E 582 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 586 " --> pdb=" O ALA E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 610 Processing helix chain 'E' and resid 651 through 661 removed outlier: 4.473A pdb=" N VAL E 654 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 713 Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 749 through 766 Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 120 through 122 No H-bonds generated for 'chain 'F' and resid 120 through 122' Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 218 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 279 through 294 removed outlier: 4.202A pdb=" N GLU F 294 " --> pdb=" O GLU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 334 Processing helix chain 'F' and resid 375 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 424 Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.519A pdb=" N SER F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 4.392A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 544 through 551 Processing helix chain 'F' and resid 557 through 568 Processing helix chain 'F' and resid 579 through 586 Processing helix chain 'F' and resid 594 through 610 Processing helix chain 'F' and resid 631 through 633 No H-bonds generated for 'chain 'F' and resid 631 through 633' Processing helix chain 'F' and resid 651 through 663 removed outlier: 4.396A pdb=" N LYS F 663 " --> pdb=" O ALA F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 715 Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.881A pdb=" N PHE F 742 " --> pdb=" O GLU F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 765 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 83 removed outlier: 8.123A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 5.915A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 365 through 369 removed outlier: 6.899A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 641 through 645 removed outlier: 9.308A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLY A 518 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR A 623 " --> pdb=" O GLY A 518 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 81 through 83 removed outlier: 7.636A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 38 through 41 removed outlier: 5.891A pdb=" N ILE B 70 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 41 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 72 " --> pdb=" O LEU B 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.519A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= I, first strand: chain 'B' and resid 365 through 369 removed outlier: 6.989A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLY B 245 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N THR B 347 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.630A pdb=" N VAL B 514 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 518 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU B 515 " --> pdb=" O ASP B 640 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU B 642 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N TYR B 517 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N TYR B 644 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 27 through 29 Processing sheet with id= L, first strand: chain 'C' and resid 38 through 42 removed outlier: 8.426A pdb=" N VAL C 39 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 70 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU C 41 " --> pdb=" O ILE C 70 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 72 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 181 through 183 removed outlier: 3.540A pdb=" N ARG C 113 " --> pdb=" O ASP C 169 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU C 167 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= O, first strand: chain 'C' and resid 365 through 369 removed outlier: 3.629A pdb=" N ILE C 241 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.727A pdb=" N GLY C 518 " --> pdb=" O THR C 623 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.788A pdb=" N ILE D 100 " --> pdb=" O LEU D 26 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 38 through 41 removed outlier: 8.419A pdb=" N VAL D 39 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.353A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 365 through 369 removed outlier: 6.584A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N GLY D 245 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N THR D 347 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.897A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.897A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 27 through 29 Processing sheet with id= W, first strand: chain 'E' and resid 38 through 40 removed outlier: 8.496A pdb=" N VAL E 39 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE E 70 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 58 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= Y, first strand: chain 'E' and resid 151 through 155 removed outlier: 4.328A pdb=" N LYS E 164 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU E 117 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 166 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 267 through 270 removed outlier: 6.818A pdb=" N ILE E 342 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE E 303 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET E 344 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE E 241 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU E 242 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLU E 366 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N TYR E 244 " --> pdb=" O GLU E 366 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP E 368 " --> pdb=" O TYR E 244 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.210A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.631A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 39 through 41 Processing sheet with id= AD, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.713A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AF, first strand: chain 'F' and resid 267 through 270 removed outlier: 3.741A pdb=" N ASP F 304 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE F 342 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE F 303 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET F 344 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU F 242 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU F 366 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR F 244 " --> pdb=" O GLU F 366 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP F 368 " --> pdb=" O TYR F 244 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 538 through 542 removed outlier: 3.545A pdb=" N PHE F 618 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY F 518 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU F 515 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU F 642 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR F 517 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR F 644 " --> pdb=" O TYR F 517 " (cutoff:3.500A) 1598 hydrogen bonds defined for protein. 4404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.19 Time building geometry restraints manager: 19.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14228 1.34 - 1.46: 8246 1.46 - 1.58: 19465 1.58 - 1.70: 35 1.70 - 1.81: 340 Bond restraints: 42314 Sorted by residual: bond pdb=" C LEU X 155 " pdb=" N PRO X 156 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.65e+00 bond pdb=" CA PRO A 246 " pdb=" C PRO A 246 " ideal model delta sigma weight residual 1.514 1.523 -0.008 5.50e-03 3.31e+04 2.35e+00 bond pdb=" C ASP E 726 " pdb=" O ASP E 726 " ideal model delta sigma weight residual 1.235 1.228 0.006 4.70e-03 4.53e+04 1.89e+00 bond pdb=" CG ARG C 711 " pdb=" CD ARG C 711 " ideal model delta sigma weight residual 1.520 1.484 0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" CA GLU C 554 " pdb=" CB GLU C 554 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.32e-02 5.74e+03 1.44e+00 ... (remaining 42309 not shown) Histogram of bond angle deviations from ideal: 97.05 - 105.62: 1104 105.62 - 114.18: 24795 114.18 - 122.75: 27329 122.75 - 131.31: 4046 131.31 - 139.88: 78 Bond angle restraints: 57352 Sorted by residual: angle pdb=" C GLU B 712 " pdb=" N ARG B 713 " pdb=" CA ARG B 713 " ideal model delta sigma weight residual 122.38 111.87 10.51 1.81e+00 3.05e-01 3.37e+01 angle pdb=" N VAL D 123 " pdb=" CA VAL D 123 " pdb=" C VAL D 123 " ideal model delta sigma weight residual 111.91 108.51 3.40 8.90e-01 1.26e+00 1.46e+01 angle pdb=" C PHE W 100 " pdb=" N MET W 101 " pdb=" CA MET W 101 " ideal model delta sigma weight residual 121.58 114.19 7.39 1.95e+00 2.63e-01 1.44e+01 angle pdb=" C LEU Z 186 " pdb=" N MET Z 187 " pdb=" CA MET Z 187 " ideal model delta sigma weight residual 122.23 116.33 5.90 1.57e+00 4.06e-01 1.41e+01 angle pdb=" N ILE F 309 " pdb=" CA ILE F 309 " pdb=" C ILE F 309 " ideal model delta sigma weight residual 113.53 109.99 3.54 9.80e-01 1.04e+00 1.30e+01 ... (remaining 57347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 25476 35.55 - 71.10: 485 71.10 - 106.65: 53 106.65 - 142.20: 5 142.20 - 177.76: 2 Dihedral angle restraints: 26021 sinusoidal: 10526 harmonic: 15495 Sorted by residual: dihedral pdb=" O2A ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PA ADP A 902 " pdb=" PB ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 117.76 -177.76 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP A 902 " pdb=" O5' ADP A 902 " pdb=" PA ADP A 902 " pdb=" O2A ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 97.03 -157.03 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O2A ADP C 902 " pdb=" O3A ADP C 902 " pdb=" PA ADP C 902 " pdb=" PB ADP C 902 " ideal model delta sinusoidal sigma weight residual -60.00 69.57 -129.57 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 26018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 4280 0.035 - 0.070: 1346 0.070 - 0.105: 616 0.105 - 0.140: 172 0.140 - 0.175: 18 Chirality restraints: 6432 Sorted by residual: chirality pdb=" CA ASP W 139 " pdb=" N ASP W 139 " pdb=" C ASP W 139 " pdb=" CB ASP W 139 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" C2' ADP E 902 " pdb=" C1' ADP E 902 " pdb=" C3' ADP E 902 " pdb=" O2' ADP E 902 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA GLU B 195 " pdb=" N GLU B 195 " pdb=" C GLU B 195 " pdb=" CB GLU B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 6429 not shown) Planarity restraints: 7554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 297 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO C 298 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 298 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 298 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 297 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO B 298 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 298 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 298 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 544 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.12e+00 pdb=" N PRO C 545 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 545 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 545 " 0.032 5.00e-02 4.00e+02 ... (remaining 7551 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 1040 2.67 - 3.23: 43987 3.23 - 3.79: 68477 3.79 - 4.34: 86970 4.34 - 4.90: 135115 Nonbonded interactions: 335589 Sorted by model distance: nonbonded pdb=" OG1 THR B 127 " pdb=" OG1 THR B 436 " model vdw 2.117 2.440 nonbonded pdb=" OG SER F 748 " pdb=" OD1 ASN F 750 " model vdw 2.127 2.440 nonbonded pdb=" O TRP A 454 " pdb=" OG SER A 457 " model vdw 2.179 2.440 nonbonded pdb=" NH1 ARG B 147 " pdb=" O LYS B 148 " model vdw 2.185 2.520 nonbonded pdb=" OD1 ASN F 624 " pdb=" OH TYR F 755 " model vdw 2.189 2.440 ... (remaining 335584 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 764 or resid 901 through 902)) selection = (chain 'B' and (resid 23 through 764 or resid 901 through 902)) selection = (chain 'C' and (resid 23 through 764 or resid 901 through 902)) selection = (chain 'D' and (resid 23 through 764 or resid 901 through 902)) selection = (chain 'E' and (resid 23 through 764 or resid 901 through 902)) selection = (chain 'F' and (resid 23 through 764 or resid 901 through 902)) } ncs_group { reference = (chain 'W' and ((resid 1 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 through 28 and (name N or name CA or name C o \ r name O or name CB )) or resid 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 or (resid 33 through 64 and (nam \ e N or name CA or name C or name O or name CB )) or resid 65 or (resid 66 and (n \ ame N or name CA or name C or name O or name CB )) or resid 67 or (resid 68 and \ (name N or name CA or name C or name O or name CB )) or resid 69 or (resid 70 th \ rough 88 and (name N or name CA or name C or name O or name CB )) or (resid 89 t \ hrough 92 and (name N or name CA or name C or name O or name CB )) or resid 93 o \ r (resid 94 through 112 and (name N or name CA or name C or name O or name CB )) \ or resid 113 or (resid 114 through 146 and (name N or name CA or name C or name \ O or name CB )) or resid 147 or (resid 148 through 160 and (name N or name CA o \ r name C or name O or name CB )) or resid 161 or (resid 162 through 166 and (nam \ e N or name CA or name C or name O or name CB )) or resid 167 through 168 or (re \ sid 169 through 175 and (name N or name CA or name C or name O or name CB )) or \ resid 176 or (resid 177 through 179 and (name N or name CA or name C or name O o \ r name CB )) or resid 180 or (resid 181 through 194 and (name N or name CA or na \ me C or name O or name CB )) or resid 195 through 196 or (resid 197 through 214 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 25 \ 0)) selection = (chain 'X' and ((resid 1 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 or (resid 6 through 28 and (name N or name CA or name C o \ r name O or name CB )) or resid 29 or (resid 30 through 31 and (name N or name C \ A or name C or name O or name CB )) or resid 32 or (resid 33 through 64 and (nam \ e N or name CA or name C or name O or name CB )) or resid 65 or (resid 66 and (n \ ame N or name CA or name C or name O or name CB )) or resid 67 or (resid 68 and \ (name N or name CA or name C or name O or name CB )) or resid 69 or (resid 70 th \ rough 88 and (name N or name CA or name C or name O or name CB )) or (resid 89 t \ hrough 92 and (name N or name CA or name C or name O or name CB )) or resid 93 o \ r (resid 94 through 112 and (name N or name CA or name C or name O or name CB )) \ or resid 113 or (resid 114 through 146 and (name N or name CA or name C or name \ O or name CB )) or resid 147 or (resid 148 through 160 and (name N or name CA o \ r name C or name O or name CB )) or resid 161 or (resid 162 through 166 and (nam \ e N or name CA or name C or name O or name CB )) or resid 167 through 168 or (re \ sid 169 through 175 and (name N or name CA or name C or name O or name CB )) or \ resid 176 or (resid 177 through 179 and (name N or name CA or name C or name O o \ r name CB )) or resid 180 or (resid 181 through 194 and (name N or name CA or na \ me C or name O or name CB )) or resid 195 through 196 or (resid 197 through 214 \ and (name N or name CA or name C or name O or name CB )) or resid 240 through 25 \ 0)) selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.630 Check model and map are aligned: 0.670 Set scattering table: 0.360 Process input model: 120.240 Find NCS groups from input model: 4.030 Set up NCS constraints: 0.290 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: 0.020 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 : 0.003 0.036 42314 Z= 0.196 Angle : 0.642 10.509 57352 Z= 0.336 Chirality : 0.043 0.175 6432 Planarity : 0.004 0.066 7554 Dihedral : 14.918 177.755 15997 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.09 % Favored : 91.50 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.24 (0.12), residues: 5365 helix: 0.95 (0.11), residues: 2419 sheet: 0.06 (0.20), residues: 685 loop : -1.47 (0.14), residues: 2261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP W 209 HIS 0.007 0.001 HIS A 183 PHE 0.021 0.001 PHE E 742 TYR 0.011 0.001 TYR X 80 ARG 0.007 0.000 ARG E 653 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1531 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.5228 (ppp) cc_final: 0.4770 (ppp) REVERT: W 53 TRP cc_start: 0.3776 (t-100) cc_final: 0.3114 (t60) REVERT: W 106 TRP cc_start: 0.6228 (t60) cc_final: 0.5600 (t-100) REVERT: W 112 THR cc_start: 0.8563 (m) cc_final: 0.8260 (p) REVERT: W 192 MET cc_start: 0.7908 (ppp) cc_final: 0.7703 (ppp) REVERT: W 208 ARG cc_start: 0.6630 (mtt180) cc_final: 0.5649 (tmt-80) REVERT: X 110 VAL cc_start: 0.8514 (p) cc_final: 0.8200 (t) REVERT: A 36 ASN cc_start: 0.8899 (m-40) cc_final: 0.8497 (p0) REVERT: A 150 ASP cc_start: 0.8952 (t0) cc_final: 0.8702 (t70) REVERT: A 205 ASP cc_start: 0.9313 (m-30) cc_final: 0.8944 (m-30) REVERT: A 224 LEU cc_start: 0.8991 (mt) cc_final: 0.8590 (mt) REVERT: A 241 ILE cc_start: 0.9132 (mt) cc_final: 0.8711 (mm) REVERT: A 306 LEU cc_start: 0.8598 (mm) cc_final: 0.8318 (mm) REVERT: A 315 LYS cc_start: 0.9299 (mmtt) cc_final: 0.9084 (mmmt) REVERT: A 326 SER cc_start: 0.9362 (m) cc_final: 0.8920 (t) REVERT: A 368 ASP cc_start: 0.8893 (p0) cc_final: 0.8640 (p0) REVERT: A 369 ILE cc_start: 0.7179 (mm) cc_final: 0.6257 (mt) REVERT: A 415 CYS cc_start: 0.9321 (m) cc_final: 0.9104 (t) REVERT: A 494 GLN cc_start: 0.8608 (tp40) cc_final: 0.8002 (tp-100) REVERT: A 495 TYR cc_start: 0.9026 (m-10) cc_final: 0.8773 (m-80) REVERT: A 535 CYS cc_start: 0.8934 (t) cc_final: 0.8649 (p) REVERT: A 615 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8742 (mmtm) REVERT: A 620 ILE cc_start: 0.9221 (mt) cc_final: 0.9002 (tt) REVERT: A 657 LEU cc_start: 0.9712 (mt) cc_final: 0.9347 (mt) REVERT: A 687 LEU cc_start: 0.8988 (mm) cc_final: 0.8723 (tp) REVERT: A 697 LEU cc_start: 0.9108 (mm) cc_final: 0.8798 (tp) REVERT: A 701 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8790 (tt0) REVERT: A 760 GLN cc_start: 0.8964 (mm110) cc_final: 0.8471 (pp30) REVERT: B 96 LEU cc_start: 0.8697 (mt) cc_final: 0.8391 (mt) REVERT: B 200 GLU cc_start: 0.8605 (mm-30) cc_final: 0.7858 (mp0) REVERT: B 203 TYR cc_start: 0.8039 (m-80) cc_final: 0.7559 (m-10) REVERT: B 219 MET cc_start: 0.8531 (ppp) cc_final: 0.8130 (ppp) REVERT: B 277 LYS cc_start: 0.8512 (tppt) cc_final: 0.8209 (tttt) REVERT: B 278 LEU cc_start: 0.8966 (tp) cc_final: 0.8571 (tt) REVERT: B 291 GLU cc_start: 0.8624 (pp20) cc_final: 0.8404 (pp20) REVERT: B 321 GLU cc_start: 0.9369 (mp0) cc_final: 0.9074 (pm20) REVERT: B 331 LEU cc_start: 0.9147 (mt) cc_final: 0.8780 (mt) REVERT: B 336 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8611 (mmmt) REVERT: B 401 ASN cc_start: 0.8911 (m110) cc_final: 0.8682 (t0) REVERT: B 424 ARG cc_start: 0.8589 (ttm110) cc_final: 0.8133 (ttp80) REVERT: B 484 ASP cc_start: 0.8901 (m-30) cc_final: 0.8378 (p0) REVERT: B 563 PHE cc_start: 0.9319 (m-10) cc_final: 0.9079 (m-80) REVERT: B 578 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7939 (mt-10) REVERT: B 607 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8656 (tp30) REVERT: B 611 MET cc_start: 0.7744 (mmp) cc_final: 0.6904 (mmp) REVERT: B 686 ASP cc_start: 0.9200 (t70) cc_final: 0.8966 (m-30) REVERT: B 691 CYS cc_start: 0.9648 (m) cc_final: 0.9286 (m) REVERT: B 695 CYS cc_start: 0.9328 (m) cc_final: 0.9110 (m) REVERT: B 725 ASP cc_start: 0.6066 (p0) cc_final: 0.5325 (t0) REVERT: C 46 MET cc_start: 0.8530 (ppp) cc_final: 0.8295 (ppp) REVERT: C 162 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7801 (tm-30) REVERT: C 168 THR cc_start: 0.5633 (p) cc_final: 0.4915 (p) REVERT: C 325 VAL cc_start: 0.9543 (t) cc_final: 0.9296 (p) REVERT: C 331 LEU cc_start: 0.8993 (mt) cc_final: 0.8588 (mt) REVERT: C 340 HIS cc_start: 0.8138 (m-70) cc_final: 0.7373 (m-70) REVERT: C 341 VAL cc_start: 0.8667 (t) cc_final: 0.8177 (t) REVERT: C 388 MET cc_start: 0.7482 (mmp) cc_final: 0.7222 (tpt) REVERT: C 398 GLN cc_start: 0.8903 (tt0) cc_final: 0.8469 (tm-30) REVERT: C 401 ASN cc_start: 0.9335 (m110) cc_final: 0.9075 (p0) REVERT: C 421 GLN cc_start: 0.9380 (tp-100) cc_final: 0.8340 (tm-30) REVERT: C 438 ASP cc_start: 0.8179 (p0) cc_final: 0.7841 (p0) REVERT: C 450 ASP cc_start: 0.8816 (t70) cc_final: 0.8527 (t0) REVERT: C 488 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8872 (mt-10) REVERT: C 491 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 515 LEU cc_start: 0.9353 (mt) cc_final: 0.8733 (pp) REVERT: C 522 CYS cc_start: 0.7589 (m) cc_final: 0.6728 (p) REVERT: C 524 LYS cc_start: 0.8688 (mttm) cc_final: 0.8446 (mtmt) REVERT: C 565 LYS cc_start: 0.9365 (ttmt) cc_final: 0.9123 (tptp) REVERT: C 575 PHE cc_start: 0.8159 (t80) cc_final: 0.7468 (t80) REVERT: C 636 PRO cc_start: 0.9020 (Cg_exo) cc_final: 0.8694 (Cg_endo) REVERT: C 695 CYS cc_start: 0.9410 (m) cc_final: 0.9076 (t) REVERT: D 62 LYS cc_start: 0.8386 (mttt) cc_final: 0.8027 (mtmm) REVERT: D 273 GLU cc_start: 0.8099 (pm20) cc_final: 0.7688 (pp20) REVERT: D 326 SER cc_start: 0.9530 (m) cc_final: 0.8652 (t) REVERT: D 410 ASP cc_start: 0.8844 (m-30) cc_final: 0.8628 (t70) REVERT: D 491 GLU cc_start: 0.7840 (tt0) cc_final: 0.7366 (tt0) REVERT: D 495 TYR cc_start: 0.8692 (m-10) cc_final: 0.8398 (m-10) REVERT: D 517 TYR cc_start: 0.8932 (p90) cc_final: 0.8519 (p90) REVERT: D 527 LEU cc_start: 0.9278 (mm) cc_final: 0.9027 (tp) REVERT: D 560 ARG cc_start: 0.9222 (mtt90) cc_final: 0.8773 (ptp-110) REVERT: D 603 GLN cc_start: 0.8403 (mt0) cc_final: 0.7974 (mt0) REVERT: D 661 LEU cc_start: 0.9288 (mt) cc_final: 0.8849 (pp) REVERT: D 720 MET cc_start: 0.0906 (ppp) cc_final: 0.0431 (ppp) REVERT: E 84 MET cc_start: 0.5783 (tmm) cc_final: 0.5254 (tmm) REVERT: E 90 ASN cc_start: 0.8433 (m110) cc_final: 0.8182 (t0) REVERT: E 105 CYS cc_start: 0.6735 (t) cc_final: 0.6398 (m) REVERT: E 219 MET cc_start: 0.7484 (mpp) cc_final: 0.7191 (mpp) REVERT: E 231 LYS cc_start: 0.8294 (mmtt) cc_final: 0.8089 (tptt) REVERT: E 270 ASN cc_start: 0.7884 (m-40) cc_final: 0.7652 (t0) REVERT: E 302 PHE cc_start: 0.8694 (t80) cc_final: 0.8254 (t80) REVERT: E 469 VAL cc_start: 0.7850 (p) cc_final: 0.7617 (m) REVERT: E 488 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8046 (mm-30) REVERT: E 563 PHE cc_start: 0.9175 (m-80) cc_final: 0.8825 (m-80) REVERT: E 573 VAL cc_start: 0.8971 (t) cc_final: 0.8664 (m) REVERT: E 603 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8417 (mm110) REVERT: E 607 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8530 (mm-30) REVERT: E 720 MET cc_start: 0.4236 (mmm) cc_final: 0.3753 (ptt) REVERT: E 740 MET cc_start: 0.5035 (ppp) cc_final: 0.4492 (ppp) REVERT: F 84 MET cc_start: 0.5697 (tmm) cc_final: 0.5091 (tmm) REVERT: F 158 MET cc_start: 0.6241 (ptt) cc_final: 0.5944 (ptt) REVERT: F 194 GLU cc_start: 0.6472 (pm20) cc_final: 0.6109 (tp30) REVERT: F 203 TYR cc_start: 0.7150 (m-80) cc_final: 0.6290 (m-80) REVERT: F 283 GLU cc_start: 0.8788 (mt-10) cc_final: 0.7576 (mm-30) REVERT: F 305 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8660 (mt-10) REVERT: F 312 LYS cc_start: 0.9350 (tppp) cc_final: 0.9041 (tptp) REVERT: F 330 THR cc_start: 0.8927 (m) cc_final: 0.8560 (p) REVERT: F 331 LEU cc_start: 0.9486 (mt) cc_final: 0.9215 (mt) REVERT: F 362 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7216 (mmt90) REVERT: F 404 HIS cc_start: 0.8821 (p90) cc_final: 0.8310 (p-80) REVERT: F 411 LEU cc_start: 0.9578 (mt) cc_final: 0.9046 (mt) REVERT: F 417 GLU cc_start: 0.7518 (pt0) cc_final: 0.7268 (pt0) REVERT: F 442 MET cc_start: 0.8493 (ppp) cc_final: 0.7977 (ppp) REVERT: F 460 ASN cc_start: 0.9064 (t0) cc_final: 0.8806 (t0) REVERT: F 524 LYS cc_start: 0.8431 (mttp) cc_final: 0.7736 (mttt) REVERT: F 529 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8576 (ptpt) REVERT: F 551 TRP cc_start: 0.8387 (t60) cc_final: 0.8115 (t60) REVERT: F 611 MET cc_start: 0.8399 (mmp) cc_final: 0.8038 (tpt) REVERT: F 678 MET cc_start: 0.8115 (ptp) cc_final: 0.7881 (ptp) REVERT: F 736 PHE cc_start: 0.8899 (m-80) cc_final: 0.8361 (m-80) outliers start: 0 outliers final: 0 residues processed: 1531 average time/residue: 0.5647 time to fit residues: 1362.4440 Evaluate side-chains 899 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 899 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 450 optimal weight: 5.9990 chunk 404 optimal weight: 6.9990 chunk 224 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 chunk 418 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 311 optimal weight: 5.9990 chunk 484 optimal weight: 0.5980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 51 GLN X 181 HIS A 317 HIS A 384 HIS ** A 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN B 36 ASN B 401 ASN ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 ASN C 382 GLN C 384 HIS ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS ** E 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS F 458 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 42314 Z= 0.268 Angle : 0.674 9.196 57352 Z= 0.342 Chirality : 0.045 0.321 6432 Planarity : 0.005 0.071 7554 Dihedral : 9.550 164.333 6113 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.79 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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 (0.12), residues: 5365 helix: 0.70 (0.11), residues: 2442 sheet: 0.01 (0.20), residues: 666 loop : -1.55 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 551 HIS 0.007 0.001 HIS A 404 PHE 0.037 0.002 PHE F 674 TYR 0.024 0.002 TYR E 203 ARG 0.015 0.001 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1068 time to evaluate : 4.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.5225 (ppp) cc_final: 0.4799 (ppp) REVERT: W 53 TRP cc_start: 0.3642 (t-100) cc_final: 0.3186 (t60) REVERT: W 76 LEU cc_start: 0.8241 (tt) cc_final: 0.7704 (mm) REVERT: W 105 ASN cc_start: 0.1988 (m110) cc_final: 0.1585 (m110) REVERT: W 106 TRP cc_start: 0.5743 (t60) cc_final: 0.5543 (t60) REVERT: W 186 LEU cc_start: 0.7278 (tt) cc_final: 0.6924 (mm) REVERT: W 208 ARG cc_start: 0.6539 (mtt180) cc_final: 0.5617 (tmt-80) REVERT: X 99 LEU cc_start: 0.8884 (mm) cc_final: 0.8429 (tp) REVERT: X 181 HIS cc_start: 0.8554 (t70) cc_final: 0.8248 (t70) REVERT: Y 246 PHE cc_start: 0.8499 (m-80) cc_final: 0.8203 (m-80) REVERT: Y 247 ARG cc_start: 0.6947 (mmp80) cc_final: 0.6089 (mmm160) REVERT: A 36 ASN cc_start: 0.9076 (m-40) cc_final: 0.8516 (p0) REVERT: A 84 MET cc_start: 0.7813 (tmm) cc_final: 0.7169 (tmm) REVERT: A 150 ASP cc_start: 0.8815 (t0) cc_final: 0.8589 (t70) REVERT: A 198 LEU cc_start: 0.9433 (tt) cc_final: 0.9187 (tt) REVERT: A 204 ASP cc_start: 0.9329 (p0) cc_final: 0.9008 (p0) REVERT: A 205 ASP cc_start: 0.9097 (m-30) cc_final: 0.8859 (m-30) REVERT: A 241 ILE cc_start: 0.9114 (mt) cc_final: 0.8810 (mm) REVERT: A 326 SER cc_start: 0.9482 (m) cc_final: 0.9100 (p) REVERT: A 388 MET cc_start: 0.9115 (ptp) cc_final: 0.8907 (ptp) REVERT: A 410 ASP cc_start: 0.8871 (t0) cc_final: 0.8661 (t70) REVERT: A 491 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8056 (mm-30) REVERT: A 494 GLN cc_start: 0.8169 (tp40) cc_final: 0.7857 (tp-100) REVERT: A 495 TYR cc_start: 0.8896 (m-10) cc_final: 0.8093 (m-80) REVERT: A 561 GLU cc_start: 0.9289 (pm20) cc_final: 0.8970 (pm20) REVERT: A 564 ASP cc_start: 0.9307 (m-30) cc_final: 0.8880 (m-30) REVERT: A 608 MET cc_start: 0.9019 (tmm) cc_final: 0.8631 (tmm) REVERT: A 634 LEU cc_start: 0.9005 (mm) cc_final: 0.8098 (tt) REVERT: A 701 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8852 (tt0) REVERT: A 740 MET cc_start: 0.8037 (tmm) cc_final: 0.7701 (tmm) REVERT: A 749 ASP cc_start: 0.8669 (t0) cc_final: 0.8178 (t0) REVERT: A 760 GLN cc_start: 0.8970 (mm110) cc_final: 0.8445 (pp30) REVERT: B 120 ASP cc_start: 0.9114 (t70) cc_final: 0.8664 (p0) REVERT: B 121 ASP cc_start: 0.9141 (m-30) cc_final: 0.8925 (m-30) REVERT: B 162 GLU cc_start: 0.9171 (pt0) cc_final: 0.8918 (pm20) REVERT: B 200 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7901 (mp0) REVERT: B 219 MET cc_start: 0.8574 (ppp) cc_final: 0.8208 (ppp) REVERT: B 236 LYS cc_start: 0.9171 (tptm) cc_final: 0.8894 (tptm) REVERT: B 267 PHE cc_start: 0.8094 (t80) cc_final: 0.7488 (t80) REVERT: B 273 GLU cc_start: 0.9018 (pt0) cc_final: 0.8788 (pt0) REVERT: B 277 LYS cc_start: 0.8633 (tppt) cc_final: 0.8408 (tttt) REVERT: B 291 GLU cc_start: 0.8725 (pp20) cc_final: 0.8473 (pp20) REVERT: B 321 GLU cc_start: 0.9474 (mp0) cc_final: 0.9224 (pm20) REVERT: B 329 LEU cc_start: 0.9299 (tp) cc_final: 0.8887 (tp) REVERT: B 332 MET cc_start: 0.8998 (ttp) cc_final: 0.8599 (ppp) REVERT: B 401 ASN cc_start: 0.9061 (m-40) cc_final: 0.8780 (t0) REVERT: B 484 ASP cc_start: 0.9033 (m-30) cc_final: 0.8469 (p0) REVERT: B 563 PHE cc_start: 0.9335 (m-10) cc_final: 0.9074 (m-80) REVERT: B 577 ASP cc_start: 0.8321 (t0) cc_final: 0.7899 (t70) REVERT: B 602 ASN cc_start: 0.7940 (t0) cc_final: 0.7339 (t0) REVERT: B 607 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8611 (tp30) REVERT: B 611 MET cc_start: 0.8173 (mmp) cc_final: 0.7224 (mmp) REVERT: B 686 ASP cc_start: 0.9355 (t70) cc_final: 0.8919 (m-30) REVERT: B 725 ASP cc_start: 0.6060 (p0) cc_final: 0.5213 (t0) REVERT: B 740 MET cc_start: 0.7930 (tpp) cc_final: 0.7152 (tpt) REVERT: B 757 MET cc_start: 0.9416 (mmt) cc_final: 0.9211 (mmm) REVERT: C 46 MET cc_start: 0.8602 (ppp) cc_final: 0.8343 (ppp) REVERT: C 162 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7757 (tm-30) REVERT: C 218 GLU cc_start: 0.9067 (tp30) cc_final: 0.8805 (tp30) REVERT: C 331 LEU cc_start: 0.9217 (mt) cc_final: 0.8793 (mt) REVERT: C 388 MET cc_start: 0.7424 (mmp) cc_final: 0.7212 (tpp) REVERT: C 421 GLN cc_start: 0.9476 (tp-100) cc_final: 0.8541 (tm-30) REVERT: C 488 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8775 (mp0) REVERT: C 515 LEU cc_start: 0.9327 (mt) cc_final: 0.8630 (pp) REVERT: C 522 CYS cc_start: 0.7761 (m) cc_final: 0.7110 (p) REVERT: C 562 ILE cc_start: 0.9682 (mm) cc_final: 0.9474 (tp) REVERT: C 575 PHE cc_start: 0.8279 (t80) cc_final: 0.7884 (t80) REVERT: C 607 GLU cc_start: 0.9066 (tp30) cc_final: 0.8865 (tp30) REVERT: C 689 GLU cc_start: 0.9447 (mt-10) cc_final: 0.9116 (mt-10) REVERT: C 697 LEU cc_start: 0.9249 (tp) cc_final: 0.9036 (tt) REVERT: D 100 ILE cc_start: 0.8876 (mm) cc_final: 0.8629 (pt) REVERT: D 491 GLU cc_start: 0.8006 (tt0) cc_final: 0.7407 (tt0) REVERT: D 495 TYR cc_start: 0.8559 (m-10) cc_final: 0.8170 (m-10) REVERT: D 517 TYR cc_start: 0.9115 (p90) cc_final: 0.8483 (p90) REVERT: D 560 ARG cc_start: 0.9111 (mtt90) cc_final: 0.8839 (mtt90) REVERT: D 564 ASP cc_start: 0.8984 (m-30) cc_final: 0.8781 (m-30) REVERT: D 577 ASP cc_start: 0.8290 (t0) cc_final: 0.7906 (t0) REVERT: D 603 GLN cc_start: 0.8720 (mt0) cc_final: 0.7929 (mt0) REVERT: D 604 ILE cc_start: 0.9738 (mt) cc_final: 0.9526 (mt) REVERT: D 605 LEU cc_start: 0.9411 (mp) cc_final: 0.8971 (mt) REVERT: E 90 ASN cc_start: 0.8398 (m110) cc_final: 0.8038 (t0) REVERT: E 105 CYS cc_start: 0.7108 (t) cc_final: 0.6773 (m) REVERT: E 275 MET cc_start: 0.8725 (tmm) cc_final: 0.8231 (tmm) REVERT: E 294 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8226 (tm-30) REVERT: E 302 PHE cc_start: 0.8747 (t80) cc_final: 0.8349 (t80) REVERT: E 315 LYS cc_start: 0.9242 (mmpt) cc_final: 0.9013 (mmmt) REVERT: E 321 GLU cc_start: 0.9236 (mp0) cc_final: 0.8751 (pm20) REVERT: E 379 GLU cc_start: 0.9195 (mp0) cc_final: 0.8884 (mm-30) REVERT: E 563 PHE cc_start: 0.9147 (m-80) cc_final: 0.8872 (m-80) REVERT: E 573 VAL cc_start: 0.9071 (t) cc_final: 0.8787 (m) REVERT: E 603 GLN cc_start: 0.9522 (mm-40) cc_final: 0.8553 (mm-40) REVERT: E 607 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8658 (mm-30) REVERT: E 720 MET cc_start: 0.4256 (mmm) cc_final: 0.3768 (ptt) REVERT: F 218 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8521 (mm-30) REVERT: F 312 LYS cc_start: 0.9379 (tppp) cc_final: 0.9114 (tptp) REVERT: F 321 GLU cc_start: 0.8117 (pm20) cc_final: 0.7867 (pm20) REVERT: F 331 LEU cc_start: 0.9628 (mt) cc_final: 0.9394 (mt) REVERT: F 404 HIS cc_start: 0.8826 (p90) cc_final: 0.8365 (p-80) REVERT: F 411 LEU cc_start: 0.9407 (mt) cc_final: 0.8925 (tp) REVERT: F 442 MET cc_start: 0.8629 (ppp) cc_final: 0.8300 (ppp) REVERT: F 464 LEU cc_start: 0.9018 (mt) cc_final: 0.8775 (mt) REVERT: F 465 ARG cc_start: 0.8534 (ttp80) cc_final: 0.8277 (ttp80) REVERT: F 515 LEU cc_start: 0.8450 (tt) cc_final: 0.8209 (tt) REVERT: F 517 TYR cc_start: 0.9011 (p90) cc_final: 0.8679 (p90) REVERT: F 529 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8732 (ptpt) REVERT: F 611 MET cc_start: 0.8255 (mmp) cc_final: 0.7973 (tpt) REVERT: F 736 PHE cc_start: 0.8963 (m-80) cc_final: 0.8295 (m-80) outliers start: 0 outliers final: 0 residues processed: 1068 average time/residue: 0.5344 time to fit residues: 920.0499 Evaluate side-chains 770 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 770 time to evaluate : 4.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 269 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 403 optimal weight: 0.7980 chunk 330 optimal weight: 0.9980 chunk 133 optimal weight: 0.0670 chunk 485 optimal weight: 1.9990 chunk 524 optimal weight: 0.7980 chunk 432 optimal weight: 6.9990 chunk 481 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 389 optimal weight: 40.0000 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 384 HIS A 499 HIS A 536 GLN A 568 GLN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 HIS C 714 GLN D 327 GLN D 536 GLN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN E 384 HIS ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS F 764 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 42314 Z= 0.172 Angle : 0.642 9.886 57352 Z= 0.317 Chirality : 0.045 0.381 6432 Planarity : 0.005 0.101 7554 Dihedral : 9.216 153.055 6113 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.55 % Favored : 92.00 % Rotamer: Outliers : 0.05 % Allowed : 4.30 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.45 (0.12), residues: 5365 helix: 0.71 (0.11), residues: 2418 sheet: 0.11 (0.20), residues: 647 loop : -1.53 (0.13), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 476 HIS 0.007 0.001 HIS D 406 PHE 0.037 0.001 PHE F 674 TYR 0.017 0.001 TYR B 203 ARG 0.029 0.001 ARG F 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1021 time to evaluate : 5.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.4529 (ppp) cc_final: 0.4073 (ppp) REVERT: W 53 TRP cc_start: 0.3484 (t-100) cc_final: 0.3034 (t60) REVERT: W 75 ASN cc_start: 0.8034 (m110) cc_final: 0.7585 (m110) REVERT: W 76 LEU cc_start: 0.8279 (tt) cc_final: 0.7802 (mm) REVERT: W 116 MET cc_start: 0.6955 (mtm) cc_final: 0.6416 (ttt) REVERT: W 186 LEU cc_start: 0.7383 (tt) cc_final: 0.7123 (mm) REVERT: W 208 ARG cc_start: 0.6504 (mtt180) cc_final: 0.5638 (tmt-80) REVERT: X 1 MET cc_start: 0.2174 (mtt) cc_final: 0.1915 (mtt) REVERT: X 181 HIS cc_start: 0.8501 (t70) cc_final: 0.8169 (t70) REVERT: A 36 ASN cc_start: 0.8930 (m-40) cc_final: 0.8392 (p0) REVERT: A 150 ASP cc_start: 0.8732 (t0) cc_final: 0.8526 (t70) REVERT: A 198 LEU cc_start: 0.9429 (tt) cc_final: 0.9147 (tt) REVERT: A 204 ASP cc_start: 0.9314 (p0) cc_final: 0.9080 (p0) REVERT: A 326 SER cc_start: 0.9416 (m) cc_final: 0.9010 (t) REVERT: A 369 ILE cc_start: 0.7671 (mm) cc_final: 0.6813 (mt) REVERT: A 410 ASP cc_start: 0.8768 (t0) cc_final: 0.8541 (t70) REVERT: A 420 LEU cc_start: 0.9627 (tp) cc_final: 0.9314 (tt) REVERT: A 491 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8185 (mm-30) REVERT: A 494 GLN cc_start: 0.8315 (tp40) cc_final: 0.7871 (tp-100) REVERT: A 495 TYR cc_start: 0.8910 (m-10) cc_final: 0.7995 (m-80) REVERT: A 564 ASP cc_start: 0.9216 (m-30) cc_final: 0.8768 (m-30) REVERT: A 608 MET cc_start: 0.8977 (tmm) cc_final: 0.8043 (tmm) REVERT: A 634 LEU cc_start: 0.9006 (mm) cc_final: 0.8155 (tt) REVERT: A 701 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8908 (tt0) REVERT: A 740 MET cc_start: 0.7995 (tmm) cc_final: 0.7743 (tmm) REVERT: A 760 GLN cc_start: 0.8952 (mm110) cc_final: 0.8438 (pp30) REVERT: B 36 ASN cc_start: 0.9298 (m-40) cc_final: 0.8985 (p0) REVERT: B 200 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7902 (mp0) REVERT: B 219 MET cc_start: 0.8471 (ppp) cc_final: 0.8131 (ppp) REVERT: B 292 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8378 (mt-10) REVERT: B 321 GLU cc_start: 0.9547 (mp0) cc_final: 0.9227 (pm20) REVERT: B 329 LEU cc_start: 0.9476 (tp) cc_final: 0.8778 (tp) REVERT: B 332 MET cc_start: 0.8978 (ttp) cc_final: 0.8540 (ppp) REVERT: B 333 ASP cc_start: 0.8247 (m-30) cc_final: 0.7686 (m-30) REVERT: B 401 ASN cc_start: 0.9025 (m-40) cc_final: 0.8725 (t0) REVERT: B 484 ASP cc_start: 0.9055 (m-30) cc_final: 0.8464 (p0) REVERT: B 538 ASN cc_start: 0.8331 (m-40) cc_final: 0.7749 (t0) REVERT: B 577 ASP cc_start: 0.8374 (t0) cc_final: 0.8058 (t70) REVERT: B 686 ASP cc_start: 0.9337 (t70) cc_final: 0.8886 (m-30) REVERT: B 695 CYS cc_start: 0.9360 (m) cc_final: 0.9083 (m) REVERT: B 725 ASP cc_start: 0.6014 (p0) cc_final: 0.5254 (t0) REVERT: B 740 MET cc_start: 0.7784 (tpp) cc_final: 0.7569 (tpp) REVERT: C 46 MET cc_start: 0.8664 (ppp) cc_final: 0.8391 (ppp) REVERT: C 162 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7804 (tm-30) REVERT: C 218 GLU cc_start: 0.8984 (tp30) cc_final: 0.8713 (tp30) REVERT: C 331 LEU cc_start: 0.9195 (mt) cc_final: 0.8849 (mt) REVERT: C 421 GLN cc_start: 0.9514 (tp-100) cc_final: 0.9163 (tp40) REVERT: C 488 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8769 (mp0) REVERT: C 515 LEU cc_start: 0.9264 (mt) cc_final: 0.8623 (pp) REVERT: C 522 CYS cc_start: 0.7506 (m) cc_final: 0.6830 (p) REVERT: C 524 LYS cc_start: 0.8755 (mttm) cc_final: 0.8448 (mtpt) REVERT: C 562 ILE cc_start: 0.9698 (mm) cc_final: 0.9491 (tp) REVERT: C 575 PHE cc_start: 0.8235 (t80) cc_final: 0.7926 (t80) REVERT: C 607 GLU cc_start: 0.9065 (tp30) cc_final: 0.8834 (tp30) REVERT: C 689 GLU cc_start: 0.9460 (mt-10) cc_final: 0.9108 (mt-10) REVERT: D 89 ARG cc_start: 0.8851 (ttm170) cc_final: 0.8564 (ttm170) REVERT: D 139 PHE cc_start: 0.8470 (m-80) cc_final: 0.7918 (m-80) REVERT: D 204 ASP cc_start: 0.8272 (p0) cc_final: 0.8064 (p0) REVERT: D 305 GLU cc_start: 0.8373 (pm20) cc_final: 0.8032 (pm20) REVERT: D 491 GLU cc_start: 0.7978 (tt0) cc_final: 0.7377 (tt0) REVERT: D 495 TYR cc_start: 0.8570 (m-10) cc_final: 0.8186 (m-10) REVERT: D 517 TYR cc_start: 0.9037 (p90) cc_final: 0.8443 (p90) REVERT: D 603 GLN cc_start: 0.8833 (mt0) cc_final: 0.8056 (mt0) REVERT: D 604 ILE cc_start: 0.9738 (mt) cc_final: 0.9525 (mt) REVERT: D 605 LEU cc_start: 0.9482 (mp) cc_final: 0.9049 (mt) REVERT: E 90 ASN cc_start: 0.8350 (m110) cc_final: 0.8017 (t0) REVERT: E 275 MET cc_start: 0.8739 (tmm) cc_final: 0.8463 (tmm) REVERT: E 294 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8278 (tm-30) REVERT: E 306 LEU cc_start: 0.9215 (pp) cc_final: 0.9010 (pp) REVERT: E 314 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8238 (tm-30) REVERT: E 315 LYS cc_start: 0.9314 (mmpt) cc_final: 0.8821 (mmmt) REVERT: E 321 GLU cc_start: 0.9186 (mp0) cc_final: 0.8366 (pm20) REVERT: E 332 MET cc_start: 0.8777 (tmm) cc_final: 0.8510 (tmm) REVERT: E 402 GLU cc_start: 0.8967 (pm20) cc_final: 0.8649 (pm20) REVERT: E 548 LEU cc_start: 0.9250 (mt) cc_final: 0.9030 (tt) REVERT: E 551 TRP cc_start: 0.7083 (m-10) cc_final: 0.6435 (m100) REVERT: E 573 VAL cc_start: 0.9212 (t) cc_final: 0.8904 (m) REVERT: E 603 GLN cc_start: 0.9549 (mm-40) cc_final: 0.8583 (mm-40) REVERT: E 607 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8593 (mm-30) REVERT: E 720 MET cc_start: 0.4364 (mmm) cc_final: 0.3894 (ptt) REVERT: F 203 TYR cc_start: 0.6305 (m-80) cc_final: 0.5962 (m-80) REVERT: F 230 PHE cc_start: 0.8177 (p90) cc_final: 0.7974 (p90) REVERT: F 312 LYS cc_start: 0.9355 (tppp) cc_final: 0.9101 (tptp) REVERT: F 321 GLU cc_start: 0.8156 (pm20) cc_final: 0.7785 (pm20) REVERT: F 331 LEU cc_start: 0.9566 (mt) cc_final: 0.9302 (mt) REVERT: F 359 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7773 (mtt90) REVERT: F 364 ASP cc_start: 0.8927 (p0) cc_final: 0.8382 (m-30) REVERT: F 403 THR cc_start: 0.8746 (m) cc_final: 0.7294 (m) REVERT: F 404 HIS cc_start: 0.8682 (p90) cc_final: 0.8203 (p-80) REVERT: F 411 LEU cc_start: 0.9330 (mt) cc_final: 0.8924 (tp) REVERT: F 442 MET cc_start: 0.8547 (ppp) cc_final: 0.8230 (ppp) REVERT: F 464 LEU cc_start: 0.9015 (mt) cc_final: 0.8772 (mt) REVERT: F 517 TYR cc_start: 0.8970 (p90) cc_final: 0.8732 (p90) REVERT: F 529 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8640 (ptpt) REVERT: F 611 MET cc_start: 0.8111 (mmp) cc_final: 0.7891 (tpt) REVERT: F 640 ASP cc_start: 0.7035 (m-30) cc_final: 0.6630 (m-30) REVERT: F 663 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8496 (ptmt) REVERT: F 736 PHE cc_start: 0.8951 (m-80) cc_final: 0.8336 (m-80) outliers start: 2 outliers final: 1 residues processed: 1022 average time/residue: 0.5139 time to fit residues: 856.9945 Evaluate side-chains 778 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 777 time to evaluate : 4.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 479 optimal weight: 6.9990 chunk 365 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 326 optimal weight: 9.9990 chunk 487 optimal weight: 0.9980 chunk 516 optimal weight: 8.9990 chunk 254 optimal weight: 4.9990 chunk 462 optimal weight: 40.0000 chunk 139 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 398 GLN A 494 GLN A 568 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN B 401 ASN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 317 HIS C 406 HIS ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 384 HIS ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN ** D 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 HIS ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS ** F 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 42314 Z= 0.303 Angle : 0.702 8.445 57352 Z= 0.357 Chirality : 0.046 0.238 6432 Planarity : 0.005 0.084 7554 Dihedral : 9.036 133.982 6113 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.11 % Favored : 91.46 % Rotamer: Outliers : 0.02 % Allowed : 4.52 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.81 (0.11), residues: 5365 helix: 0.42 (0.10), residues: 2442 sheet: -0.08 (0.20), residues: 653 loop : -1.73 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 476 HIS 0.013 0.002 HIS E 499 PHE 0.037 0.002 PHE F 674 TYR 0.044 0.002 TYR E 138 ARG 0.019 0.001 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 921 time to evaluate : 4.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 1 MET cc_start: 0.4610 (ppp) cc_final: 0.3984 (ppp) REVERT: W 53 TRP cc_start: 0.3480 (t-100) cc_final: 0.3082 (t60) REVERT: W 75 ASN cc_start: 0.8018 (m110) cc_final: 0.7570 (m110) REVERT: W 76 LEU cc_start: 0.8226 (tt) cc_final: 0.7682 (mm) REVERT: W 186 LEU cc_start: 0.7440 (tt) cc_final: 0.7174 (mm) REVERT: W 208 ARG cc_start: 0.6464 (mtt180) cc_final: 0.5484 (tmt-80) REVERT: X 99 LEU cc_start: 0.8939 (mm) cc_final: 0.8466 (tp) REVERT: X 103 LEU cc_start: 0.9266 (mm) cc_final: 0.9039 (mm) REVERT: X 181 HIS cc_start: 0.8569 (t70) cc_final: 0.8237 (t70) REVERT: Y 246 PHE cc_start: 0.8709 (m-10) cc_final: 0.8400 (m-80) REVERT: Y 247 ARG cc_start: 0.6759 (mmp80) cc_final: 0.6135 (mmm160) REVERT: A 198 LEU cc_start: 0.9468 (tt) cc_final: 0.9218 (tt) REVERT: A 204 ASP cc_start: 0.9484 (p0) cc_final: 0.9033 (p0) REVERT: A 205 ASP cc_start: 0.9216 (m-30) cc_final: 0.8985 (m-30) REVERT: A 326 SER cc_start: 0.9448 (m) cc_final: 0.9068 (p) REVERT: A 410 ASP cc_start: 0.8931 (t0) cc_final: 0.8675 (t70) REVERT: A 494 GLN cc_start: 0.8316 (tp-100) cc_final: 0.7759 (tp-100) REVERT: A 495 TYR cc_start: 0.8966 (m-10) cc_final: 0.8660 (m-80) REVERT: A 508 MET cc_start: 0.8345 (ppp) cc_final: 0.7614 (ppp) REVERT: A 564 ASP cc_start: 0.9286 (m-30) cc_final: 0.8877 (m-30) REVERT: A 608 MET cc_start: 0.9098 (tmm) cc_final: 0.8284 (tmm) REVERT: A 634 LEU cc_start: 0.8949 (mm) cc_final: 0.7964 (tt) REVERT: A 701 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8824 (tt0) REVERT: A 740 MET cc_start: 0.8052 (tmm) cc_final: 0.7656 (tmm) REVERT: B 96 LEU cc_start: 0.8741 (mt) cc_final: 0.8520 (tt) REVERT: B 120 ASP cc_start: 0.9133 (t70) cc_final: 0.8792 (p0) REVERT: B 121 ASP cc_start: 0.9119 (m-30) cc_final: 0.8865 (m-30) REVERT: B 134 TYR cc_start: 0.9013 (m-80) cc_final: 0.8673 (m-80) REVERT: B 200 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8054 (mp0) REVERT: B 219 MET cc_start: 0.8690 (ppp) cc_final: 0.8479 (ppp) REVERT: B 236 LYS cc_start: 0.9334 (tptm) cc_final: 0.9114 (tptm) REVERT: B 273 GLU cc_start: 0.8905 (pt0) cc_final: 0.8686 (pt0) REVERT: B 275 MET cc_start: 0.9036 (tmm) cc_final: 0.8686 (tmm) REVERT: B 292 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8324 (mt-10) REVERT: B 333 ASP cc_start: 0.8467 (m-30) cc_final: 0.7875 (m-30) REVERT: B 401 ASN cc_start: 0.9012 (m110) cc_final: 0.8805 (t0) REVERT: B 465 ARG cc_start: 0.7467 (ptp-170) cc_final: 0.7025 (ptp-170) REVERT: B 484 ASP cc_start: 0.9136 (m-30) cc_final: 0.8458 (p0) REVERT: B 542 ILE cc_start: 0.8748 (mm) cc_final: 0.8372 (mt) REVERT: B 546 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9234 (tp30) REVERT: B 686 ASP cc_start: 0.9350 (t70) cc_final: 0.8845 (m-30) REVERT: B 691 CYS cc_start: 0.9344 (m) cc_final: 0.9102 (m) REVERT: C 46 MET cc_start: 0.8778 (ppp) cc_final: 0.8499 (ppp) REVERT: C 162 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7858 (tm-30) REVERT: C 218 GLU cc_start: 0.9142 (tp30) cc_final: 0.8850 (tp30) REVERT: C 221 GLU cc_start: 0.8411 (mp0) cc_final: 0.8147 (mp0) REVERT: C 266 PHE cc_start: 0.9473 (t80) cc_final: 0.9264 (t80) REVERT: C 292 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8514 (mp0) REVERT: C 329 LEU cc_start: 0.9069 (mt) cc_final: 0.8798 (mt) REVERT: C 331 LEU cc_start: 0.9288 (mt) cc_final: 0.8965 (mt) REVERT: C 421 GLN cc_start: 0.9550 (tp-100) cc_final: 0.8552 (tm-30) REVERT: C 485 VAL cc_start: 0.8923 (t) cc_final: 0.8689 (t) REVERT: C 488 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8697 (mp0) REVERT: C 522 CYS cc_start: 0.7631 (m) cc_final: 0.7073 (p) REVERT: C 524 LYS cc_start: 0.8962 (mttm) cc_final: 0.8685 (mtpt) REVERT: C 602 ASN cc_start: 0.9564 (m110) cc_final: 0.9193 (m-40) REVERT: C 607 GLU cc_start: 0.9098 (tp30) cc_final: 0.8859 (tp30) REVERT: C 689 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9135 (mt-10) REVERT: D 158 MET cc_start: 0.8716 (pmm) cc_final: 0.8504 (pmm) REVERT: D 182 ILE cc_start: 0.9027 (pt) cc_final: 0.8657 (tp) REVERT: D 225 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7522 (tpp80) REVERT: D 326 SER cc_start: 0.9498 (m) cc_final: 0.8632 (t) REVERT: D 366 GLU cc_start: 0.7086 (mp0) cc_final: 0.6880 (mp0) REVERT: D 491 GLU cc_start: 0.8115 (tt0) cc_final: 0.7395 (tt0) REVERT: D 495 TYR cc_start: 0.8572 (m-10) cc_final: 0.8149 (m-10) REVERT: D 517 TYR cc_start: 0.9146 (p90) cc_final: 0.8547 (p90) REVERT: D 560 ARG cc_start: 0.9163 (mtt90) cc_final: 0.8636 (ttm-80) REVERT: D 564 ASP cc_start: 0.8788 (m-30) cc_final: 0.8587 (m-30) REVERT: D 603 GLN cc_start: 0.8877 (mt0) cc_final: 0.8240 (mt0) REVERT: D 604 ILE cc_start: 0.9779 (mt) cc_final: 0.9530 (mt) REVERT: D 605 LEU cc_start: 0.9544 (mp) cc_final: 0.9204 (mt) REVERT: E 90 ASN cc_start: 0.8395 (m110) cc_final: 0.8066 (t0) REVERT: E 158 MET cc_start: 0.6388 (mtp) cc_final: 0.6151 (mtp) REVERT: E 274 ILE cc_start: 0.9476 (tp) cc_final: 0.9169 (tp) REVERT: E 275 MET cc_start: 0.8918 (tmm) cc_final: 0.8495 (tmm) REVERT: E 302 PHE cc_start: 0.8785 (t80) cc_final: 0.8349 (t80) REVERT: E 315 LYS cc_start: 0.9354 (mmpt) cc_final: 0.8829 (mmmt) REVERT: E 321 GLU cc_start: 0.9253 (mp0) cc_final: 0.8786 (pm20) REVERT: E 326 SER cc_start: 0.9465 (m) cc_final: 0.9127 (p) REVERT: E 332 MET cc_start: 0.8750 (tmm) cc_final: 0.8281 (tmm) REVERT: E 548 LEU cc_start: 0.9217 (mt) cc_final: 0.8965 (tt) REVERT: E 551 TRP cc_start: 0.7050 (m-10) cc_final: 0.6255 (m100) REVERT: E 573 VAL cc_start: 0.9224 (t) cc_final: 0.8930 (m) REVERT: E 603 GLN cc_start: 0.9636 (mm-40) cc_final: 0.8826 (mm110) REVERT: E 607 GLU cc_start: 0.9322 (mm-30) cc_final: 0.8713 (mm-30) REVERT: E 720 MET cc_start: 0.4464 (mmm) cc_final: 0.3910 (ptt) REVERT: E 740 MET cc_start: 0.6869 (ptt) cc_final: 0.6540 (ptt) REVERT: F 273 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8710 (mt-10) REVERT: F 321 GLU cc_start: 0.8235 (pm20) cc_final: 0.7915 (pm20) REVERT: F 331 LEU cc_start: 0.9648 (mt) cc_final: 0.9368 (mt) REVERT: F 442 MET cc_start: 0.8618 (ppp) cc_final: 0.8323 (ppp) REVERT: F 492 LEU cc_start: 0.9194 (mt) cc_final: 0.8958 (mt) REVERT: F 529 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8800 (ptpt) REVERT: F 611 MET cc_start: 0.8306 (mmp) cc_final: 0.8042 (tpt) REVERT: F 736 PHE cc_start: 0.9015 (m-80) cc_final: 0.8375 (m-80) outliers start: 1 outliers final: 1 residues processed: 922 average time/residue: 0.5517 time to fit residues: 840.0690 Evaluate side-chains 705 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 704 time to evaluate : 4.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 429 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 384 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 440 optimal weight: 9.9990 chunk 356 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 463 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 260 ASN A 337 GLN A 340 HIS A 398 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 HIS ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 HIS ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 421 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 42314 Z= 0.212 Angle : 0.640 9.219 57352 Z= 0.322 Chirality : 0.045 0.192 6432 Planarity : 0.005 0.070 7554 Dihedral : 8.807 127.796 6113 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.85 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.72 (0.11), residues: 5365 helix: 0.54 (0.11), residues: 2431 sheet: -0.05 (0.20), residues: 651 loop : -1.74 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP W 133 HIS 0.012 0.001 HIS C 340 PHE 0.035 0.001 PHE F 674 TYR 0.031 0.001 TYR B 203 ARG 0.009 0.001 ARG C 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 902 time to evaluate : 4.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 53 TRP cc_start: 0.3679 (t-100) cc_final: 0.3018 (t60) REVERT: W 75 ASN cc_start: 0.7980 (m110) cc_final: 0.7533 (m110) REVERT: W 76 LEU cc_start: 0.8213 (tt) cc_final: 0.7662 (mm) REVERT: W 116 MET cc_start: 0.6905 (mtm) cc_final: 0.6539 (ttt) REVERT: W 186 LEU cc_start: 0.7427 (tt) cc_final: 0.7180 (mm) REVERT: X 181 HIS cc_start: 0.8531 (t70) cc_final: 0.8168 (t70) REVERT: Y 246 PHE cc_start: 0.8735 (m-10) cc_final: 0.8533 (m-80) REVERT: Y 247 ARG cc_start: 0.6797 (mmp80) cc_final: 0.6492 (mmm160) REVERT: A 84 MET cc_start: 0.8068 (tmm) cc_final: 0.7687 (tmm) REVERT: A 173 TYR cc_start: 0.8402 (m-80) cc_final: 0.7989 (m-80) REVERT: A 198 LEU cc_start: 0.9343 (tt) cc_final: 0.9098 (tt) REVERT: A 204 ASP cc_start: 0.9458 (p0) cc_final: 0.9088 (p0) REVERT: A 326 SER cc_start: 0.9413 (m) cc_final: 0.8956 (p) REVERT: A 420 LEU cc_start: 0.9725 (tp) cc_final: 0.9430 (tt) REVERT: A 494 GLN cc_start: 0.8306 (tp-100) cc_final: 0.7818 (tp-100) REVERT: A 495 TYR cc_start: 0.8833 (m-10) cc_final: 0.8592 (m-80) REVERT: A 564 ASP cc_start: 0.9244 (m-30) cc_final: 0.8860 (m-30) REVERT: A 608 MET cc_start: 0.9189 (tmm) cc_final: 0.8326 (tmm) REVERT: A 634 LEU cc_start: 0.8929 (mm) cc_final: 0.8016 (tt) REVERT: A 701 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8752 (tt0) REVERT: A 740 MET cc_start: 0.7890 (tmm) cc_final: 0.7514 (tmm) REVERT: B 120 ASP cc_start: 0.9086 (t70) cc_final: 0.8749 (p0) REVERT: B 134 TYR cc_start: 0.9003 (m-80) cc_final: 0.8794 (m-80) REVERT: B 200 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7997 (mp0) REVERT: B 219 MET cc_start: 0.8656 (ppp) cc_final: 0.8046 (ptm) REVERT: B 275 MET cc_start: 0.9057 (tmm) cc_final: 0.8667 (tmm) REVERT: B 283 GLU cc_start: 0.9189 (pp20) cc_final: 0.8870 (pp20) REVERT: B 292 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 329 LEU cc_start: 0.9076 (tp) cc_final: 0.8718 (tt) REVERT: B 398 GLN cc_start: 0.8955 (tt0) cc_final: 0.8625 (tp-100) REVERT: B 401 ASN cc_start: 0.8991 (m110) cc_final: 0.8613 (t0) REVERT: B 449 MET cc_start: 0.8378 (ttt) cc_final: 0.7471 (ttt) REVERT: B 484 ASP cc_start: 0.9176 (m-30) cc_final: 0.8472 (p0) REVERT: B 542 ILE cc_start: 0.8794 (mm) cc_final: 0.8506 (mt) REVERT: B 546 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9203 (tp30) REVERT: B 686 ASP cc_start: 0.9354 (t70) cc_final: 0.8857 (m-30) REVERT: C 46 MET cc_start: 0.8724 (ppp) cc_final: 0.8410 (ppp) REVERT: C 162 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7924 (tm-30) REVERT: C 218 GLU cc_start: 0.9111 (tp30) cc_final: 0.8878 (tp30) REVERT: C 221 GLU cc_start: 0.8371 (mp0) cc_final: 0.8039 (mp0) REVERT: C 266 PHE cc_start: 0.9458 (t80) cc_final: 0.9195 (t80) REVERT: C 278 LEU cc_start: 0.9171 (tp) cc_final: 0.8869 (tp) REVERT: C 331 LEU cc_start: 0.9297 (mt) cc_final: 0.9022 (mt) REVERT: C 385 THR cc_start: 0.9222 (p) cc_final: 0.8903 (t) REVERT: C 410 ASP cc_start: 0.8694 (m-30) cc_final: 0.8275 (m-30) REVERT: C 421 GLN cc_start: 0.9560 (tp-100) cc_final: 0.9088 (tp40) REVERT: C 488 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8688 (mp0) REVERT: C 522 CYS cc_start: 0.7469 (m) cc_final: 0.6980 (p) REVERT: C 524 LYS cc_start: 0.8944 (mttm) cc_final: 0.8744 (mtpt) REVERT: C 602 ASN cc_start: 0.9506 (m110) cc_final: 0.9121 (m-40) REVERT: C 607 GLU cc_start: 0.9073 (tp30) cc_final: 0.8707 (tp30) REVERT: C 689 GLU cc_start: 0.9460 (mt-10) cc_final: 0.9029 (mt-10) REVERT: D 98 ASP cc_start: 0.7580 (m-30) cc_final: 0.7262 (m-30) REVERT: D 139 PHE cc_start: 0.8519 (m-80) cc_final: 0.8070 (m-80) REVERT: D 262 THR cc_start: 0.9280 (t) cc_final: 0.9015 (t) REVERT: D 326 SER cc_start: 0.9575 (m) cc_final: 0.8557 (t) REVERT: D 460 ASN cc_start: 0.9342 (t0) cc_final: 0.9024 (p0) REVERT: D 491 GLU cc_start: 0.8080 (tt0) cc_final: 0.7344 (tt0) REVERT: D 495 TYR cc_start: 0.8532 (m-10) cc_final: 0.8070 (m-10) REVERT: D 517 TYR cc_start: 0.9163 (p90) cc_final: 0.8643 (p90) REVERT: D 560 ARG cc_start: 0.9097 (mtt90) cc_final: 0.8808 (mmt90) REVERT: D 564 ASP cc_start: 0.8857 (m-30) cc_final: 0.8636 (m-30) REVERT: D 603 GLN cc_start: 0.8309 (mt0) cc_final: 0.7866 (mt0) REVERT: D 604 ILE cc_start: 0.9785 (mt) cc_final: 0.9530 (mt) REVERT: E 90 ASN cc_start: 0.8373 (m110) cc_final: 0.8063 (t0) REVERT: E 158 MET cc_start: 0.6435 (mtp) cc_final: 0.6211 (mtp) REVERT: E 274 ILE cc_start: 0.9524 (tp) cc_final: 0.9266 (tp) REVERT: E 275 MET cc_start: 0.8959 (tmm) cc_final: 0.8511 (tmm) REVERT: E 302 PHE cc_start: 0.8720 (t80) cc_final: 0.8301 (t80) REVERT: E 314 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8235 (tm-30) REVERT: E 315 LYS cc_start: 0.9344 (mmpt) cc_final: 0.8879 (mmmt) REVERT: E 321 GLU cc_start: 0.9247 (mp0) cc_final: 0.8771 (pm20) REVERT: E 326 SER cc_start: 0.9448 (m) cc_final: 0.9063 (p) REVERT: E 332 MET cc_start: 0.8683 (tmm) cc_final: 0.8396 (tmm) REVERT: E 499 HIS cc_start: 0.8281 (m90) cc_final: 0.8049 (m170) REVERT: E 548 LEU cc_start: 0.9306 (mt) cc_final: 0.9045 (tt) REVERT: E 551 TRP cc_start: 0.7135 (m-10) cc_final: 0.6259 (m100) REVERT: E 563 PHE cc_start: 0.9317 (m-10) cc_final: 0.9055 (m-10) REVERT: E 564 ASP cc_start: 0.9374 (m-30) cc_final: 0.9159 (m-30) REVERT: E 573 VAL cc_start: 0.9246 (t) cc_final: 0.8976 (m) REVERT: E 607 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8666 (mm-30) REVERT: E 673 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8455 (tp30) REVERT: E 720 MET cc_start: 0.4414 (mmm) cc_final: 0.3907 (ptt) REVERT: E 772 ARG cc_start: 0.5872 (ptt180) cc_final: 0.5629 (ptt180) REVERT: F 291 GLU cc_start: 0.9323 (pt0) cc_final: 0.9115 (pt0) REVERT: F 312 LYS cc_start: 0.9343 (tptp) cc_final: 0.9093 (tptp) REVERT: F 321 GLU cc_start: 0.8274 (pm20) cc_final: 0.7895 (pm20) REVERT: F 331 LEU cc_start: 0.9629 (mt) cc_final: 0.9356 (mt) REVERT: F 442 MET cc_start: 0.8641 (ppp) cc_final: 0.8325 (ppp) REVERT: F 492 LEU cc_start: 0.9200 (mt) cc_final: 0.8967 (mt) REVERT: F 529 LYS cc_start: 0.9000 (mtpp) cc_final: 0.8756 (ptpt) REVERT: F 640 ASP cc_start: 0.7116 (m-30) cc_final: 0.6650 (m-30) REVERT: F 736 PHE cc_start: 0.9009 (m-80) cc_final: 0.8411 (m-80) outliers start: 0 outliers final: 0 residues processed: 902 average time/residue: 0.5077 time to fit residues: 754.3968 Evaluate side-chains 700 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 700 time to evaluate : 4.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 173 optimal weight: 0.3980 chunk 464 optimal weight: 50.0000 chunk 102 optimal weight: 10.0000 chunk 303 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 516 optimal weight: 20.0000 chunk 428 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 271 optimal weight: 0.5980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 51 GLN A 36 ASN A 226 HIS A 340 HIS A 398 GLN A 538 ASN B 24 ASN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 602 ASN E 103 GLN E 340 HIS E 351 ASN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 GLN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 42314 Z= 0.228 Angle : 0.660 10.716 57352 Z= 0.332 Chirality : 0.045 0.237 6432 Planarity : 0.005 0.091 7554 Dihedral : 8.676 124.114 6113 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.09 % Favored : 91.50 % Rotamer: Outliers : 0.02 % Allowed : 2.39 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.75 (0.11), residues: 5365 helix: 0.51 (0.11), residues: 2424 sheet: -0.12 (0.20), residues: 654 loop : -1.71 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP W 133 HIS 0.011 0.001 HIS C 340 PHE 0.034 0.002 PHE F 674 TYR 0.036 0.002 TYR E 495 ARG 0.011 0.001 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 903 time to evaluate : 4.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 53 TRP cc_start: 0.3697 (t-100) cc_final: 0.3012 (t60) REVERT: W 75 ASN cc_start: 0.7984 (m110) cc_final: 0.7543 (m110) REVERT: W 76 LEU cc_start: 0.8198 (tt) cc_final: 0.7614 (mm) REVERT: W 116 MET cc_start: 0.7174 (mtm) cc_final: 0.6793 (ttt) REVERT: W 186 LEU cc_start: 0.7481 (tt) cc_final: 0.7257 (mm) REVERT: X 99 LEU cc_start: 0.8967 (mm) cc_final: 0.8469 (tp) REVERT: X 103 LEU cc_start: 0.9241 (mm) cc_final: 0.9001 (mm) REVERT: X 181 HIS cc_start: 0.8495 (t70) cc_final: 0.8128 (t70) REVERT: Y 246 PHE cc_start: 0.8731 (m-10) cc_final: 0.8516 (m-80) REVERT: Y 247 ARG cc_start: 0.6837 (mmp80) cc_final: 0.6535 (mmm160) REVERT: A 84 MET cc_start: 0.8170 (tmm) cc_final: 0.7817 (tmm) REVERT: A 173 TYR cc_start: 0.8380 (m-80) cc_final: 0.7988 (m-80) REVERT: A 198 LEU cc_start: 0.9391 (tt) cc_final: 0.9171 (tt) REVERT: A 204 ASP cc_start: 0.9461 (p0) cc_final: 0.9048 (p0) REVERT: A 205 ASP cc_start: 0.9402 (m-30) cc_final: 0.9121 (m-30) REVERT: A 265 PHE cc_start: 0.7875 (t80) cc_final: 0.7270 (t80) REVERT: A 302 PHE cc_start: 0.9234 (t80) cc_final: 0.9030 (t80) REVERT: A 326 SER cc_start: 0.9394 (m) cc_final: 0.8948 (p) REVERT: A 402 GLU cc_start: 0.8854 (pp20) cc_final: 0.8523 (pp20) REVERT: A 460 ASN cc_start: 0.8985 (p0) cc_final: 0.8778 (p0) REVERT: A 494 GLN cc_start: 0.8333 (tp-100) cc_final: 0.7824 (tp-100) REVERT: A 495 TYR cc_start: 0.8841 (m-10) cc_final: 0.8627 (m-80) REVERT: A 541 SER cc_start: 0.8047 (p) cc_final: 0.7775 (t) REVERT: A 561 GLU cc_start: 0.9273 (pm20) cc_final: 0.8913 (pm20) REVERT: A 564 ASP cc_start: 0.9308 (m-30) cc_final: 0.8905 (m-30) REVERT: A 602 ASN cc_start: 0.8025 (m110) cc_final: 0.7686 (m110) REVERT: A 608 MET cc_start: 0.9124 (tmm) cc_final: 0.8334 (tmm) REVERT: A 615 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8596 (mmtm) REVERT: A 634 LEU cc_start: 0.8884 (mm) cc_final: 0.7963 (tt) REVERT: A 701 GLU cc_start: 0.9215 (tp30) cc_final: 0.8932 (tt0) REVERT: A 740 MET cc_start: 0.7842 (tmm) cc_final: 0.7471 (tmm) REVERT: B 86 ARG cc_start: 0.8142 (ttt180) cc_final: 0.7669 (ttm170) REVERT: B 120 ASP cc_start: 0.9120 (t70) cc_final: 0.8817 (p0) REVERT: B 219 MET cc_start: 0.8519 (ppp) cc_final: 0.8219 (ttm) REVERT: B 275 MET cc_start: 0.9089 (tmm) cc_final: 0.8693 (tmm) REVERT: B 283 GLU cc_start: 0.9186 (pp20) cc_final: 0.8747 (pp20) REVERT: B 291 GLU cc_start: 0.8719 (pp20) cc_final: 0.8435 (pp20) REVERT: B 292 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8113 (mt-10) REVERT: B 329 LEU cc_start: 0.9167 (tp) cc_final: 0.8677 (tt) REVERT: B 398 GLN cc_start: 0.8983 (tt0) cc_final: 0.8592 (tp-100) REVERT: B 401 ASN cc_start: 0.8987 (m110) cc_final: 0.8613 (t0) REVERT: B 449 MET cc_start: 0.8417 (ttt) cc_final: 0.7434 (ttt) REVERT: B 466 GLU cc_start: 0.8188 (tp30) cc_final: 0.7940 (tp30) REVERT: B 484 ASP cc_start: 0.9009 (m-30) cc_final: 0.8326 (p0) REVERT: B 542 ILE cc_start: 0.8853 (mm) cc_final: 0.8544 (mt) REVERT: B 546 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9228 (tp30) REVERT: B 577 ASP cc_start: 0.8713 (t70) cc_final: 0.7916 (t70) REVERT: B 608 MET cc_start: 0.8584 (tmm) cc_final: 0.8033 (tmm) REVERT: B 611 MET cc_start: 0.8556 (mmp) cc_final: 0.8151 (mmp) REVERT: B 686 ASP cc_start: 0.9374 (t70) cc_final: 0.8839 (m-30) REVERT: C 46 MET cc_start: 0.8787 (ppp) cc_final: 0.8480 (ppp) REVERT: C 162 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7962 (tm-30) REVERT: C 218 GLU cc_start: 0.9120 (tp30) cc_final: 0.8785 (tp30) REVERT: C 221 GLU cc_start: 0.8369 (mp0) cc_final: 0.8145 (mp0) REVERT: C 266 PHE cc_start: 0.9445 (t80) cc_final: 0.9109 (t80) REVERT: C 281 GLU cc_start: 0.8220 (pm20) cc_final: 0.7943 (pm20) REVERT: C 291 GLU cc_start: 0.8666 (pm20) cc_final: 0.8448 (pm20) REVERT: C 331 LEU cc_start: 0.9268 (mt) cc_final: 0.8940 (mt) REVERT: C 338 ARG cc_start: 0.8788 (ttp80) cc_final: 0.8469 (tmm-80) REVERT: C 340 HIS cc_start: 0.7689 (m-70) cc_final: 0.7322 (m-70) REVERT: C 421 GLN cc_start: 0.9543 (tp-100) cc_final: 0.8587 (tm-30) REVERT: C 476 TRP cc_start: 0.7358 (m100) cc_final: 0.7004 (m100) REVERT: C 488 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8698 (mp0) REVERT: C 517 TYR cc_start: 0.8611 (p90) cc_final: 0.8395 (p90) REVERT: C 522 CYS cc_start: 0.7492 (m) cc_final: 0.6937 (p) REVERT: C 565 LYS cc_start: 0.9293 (tptp) cc_final: 0.8979 (tptp) REVERT: C 577 ASP cc_start: 0.8040 (m-30) cc_final: 0.7813 (m-30) REVERT: C 689 GLU cc_start: 0.9432 (mt-10) cc_final: 0.8994 (mt-10) REVERT: D 98 ASP cc_start: 0.7776 (m-30) cc_final: 0.7553 (m-30) REVERT: D 139 PHE cc_start: 0.8533 (m-80) cc_final: 0.8013 (m-80) REVERT: D 315 LYS cc_start: 0.9514 (mmmm) cc_final: 0.9192 (mmmm) REVERT: D 316 THR cc_start: 0.8174 (p) cc_final: 0.7819 (p) REVERT: D 326 SER cc_start: 0.9560 (m) cc_final: 0.9305 (m) REVERT: D 366 GLU cc_start: 0.7265 (mp0) cc_final: 0.6942 (mp0) REVERT: D 460 ASN cc_start: 0.9314 (t0) cc_final: 0.9015 (p0) REVERT: D 491 GLU cc_start: 0.8090 (tt0) cc_final: 0.7348 (tt0) REVERT: D 495 TYR cc_start: 0.8573 (m-10) cc_final: 0.8135 (m-10) REVERT: D 517 TYR cc_start: 0.9242 (p90) cc_final: 0.8827 (p90) REVERT: D 560 ARG cc_start: 0.9111 (mtt90) cc_final: 0.8804 (mmt90) REVERT: D 564 ASP cc_start: 0.8951 (m-30) cc_final: 0.8738 (m-30) REVERT: D 603 GLN cc_start: 0.8283 (mt0) cc_final: 0.7847 (mt0) REVERT: D 604 ILE cc_start: 0.9764 (mt) cc_final: 0.9540 (mt) REVERT: E 90 ASN cc_start: 0.8279 (m110) cc_final: 0.7971 (t0) REVERT: E 274 ILE cc_start: 0.9537 (tp) cc_final: 0.9272 (tp) REVERT: E 275 MET cc_start: 0.9028 (tmm) cc_final: 0.8583 (tmm) REVERT: E 302 PHE cc_start: 0.8746 (t80) cc_final: 0.8343 (t80) REVERT: E 314 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8275 (tm-30) REVERT: E 315 LYS cc_start: 0.9334 (mmpt) cc_final: 0.8847 (mmmt) REVERT: E 321 GLU cc_start: 0.9287 (mp0) cc_final: 0.8428 (pm20) REVERT: E 326 SER cc_start: 0.9460 (m) cc_final: 0.9082 (p) REVERT: E 332 MET cc_start: 0.8738 (tmm) cc_final: 0.8375 (tmm) REVERT: E 379 GLU cc_start: 0.9022 (mp0) cc_final: 0.8559 (mp0) REVERT: E 427 MET cc_start: 0.7265 (mmm) cc_final: 0.7035 (mmm) REVERT: E 499 HIS cc_start: 0.8482 (m90) cc_final: 0.8199 (m170) REVERT: E 548 LEU cc_start: 0.9258 (mt) cc_final: 0.9041 (mt) REVERT: E 551 TRP cc_start: 0.6987 (m-10) cc_final: 0.5996 (m100) REVERT: E 573 VAL cc_start: 0.9252 (t) cc_final: 0.8988 (m) REVERT: E 574 LEU cc_start: 0.9179 (tp) cc_final: 0.8972 (tp) REVERT: E 607 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8774 (mm-30) REVERT: E 720 MET cc_start: 0.4532 (mmm) cc_final: 0.4046 (ptt) REVERT: E 772 ARG cc_start: 0.6006 (ptt180) cc_final: 0.5735 (ptt180) REVERT: F 84 MET cc_start: 0.5409 (tmm) cc_final: 0.5128 (tmm) REVERT: F 198 LEU cc_start: 0.7809 (tp) cc_final: 0.7170 (tp) REVERT: F 312 LYS cc_start: 0.9341 (tptp) cc_final: 0.9098 (tptp) REVERT: F 317 HIS cc_start: 0.8141 (t-170) cc_final: 0.7924 (t70) REVERT: F 321 GLU cc_start: 0.8230 (pm20) cc_final: 0.7858 (pm20) REVERT: F 331 LEU cc_start: 0.9659 (mt) cc_final: 0.9393 (mt) REVERT: F 403 THR cc_start: 0.8337 (m) cc_final: 0.8001 (m) REVERT: F 410 ASP cc_start: 0.9341 (t70) cc_final: 0.9020 (t0) REVERT: F 442 MET cc_start: 0.8640 (ppp) cc_final: 0.8388 (ppp) REVERT: F 492 LEU cc_start: 0.9226 (mt) cc_final: 0.8993 (mt) REVERT: F 577 ASP cc_start: 0.9169 (t70) cc_final: 0.8918 (t70) REVERT: F 640 ASP cc_start: 0.7211 (m-30) cc_final: 0.6763 (m-30) REVERT: F 736 PHE cc_start: 0.9034 (m-80) cc_final: 0.8435 (m-80) outliers start: 1 outliers final: 0 residues processed: 904 average time/residue: 0.5518 time to fit residues: 825.2234 Evaluate side-chains 702 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 702 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 498 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 chunk 294 optimal weight: 10.0000 chunk 377 optimal weight: 2.9990 chunk 292 optimal weight: 0.9990 chunk 434 optimal weight: 6.9990 chunk 288 optimal weight: 1.9990 chunk 514 optimal weight: 0.9990 chunk 322 optimal weight: 0.6980 chunk 313 optimal weight: 30.0000 chunk 237 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 340 HIS A 348 ASN A 398 GLN ** A 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 602 ASN E 351 ASN E 384 HIS ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 42314 Z= 0.170 Angle : 0.636 10.794 57352 Z= 0.316 Chirality : 0.045 0.285 6432 Planarity : 0.005 0.064 7554 Dihedral : 8.444 122.470 6113 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.41 % Allowed : 7.44 % Favored : 92.15 % Rotamer: Outliers : 0.02 % Allowed : 1.28 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.60 (0.12), residues: 5365 helix: 0.63 (0.11), residues: 2427 sheet: 0.05 (0.20), residues: 632 loop : -1.65 (0.13), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP W 133 HIS 0.004 0.001 HIS C 340 PHE 0.032 0.001 PHE F 674 TYR 0.036 0.001 TYR E 495 ARG 0.010 0.000 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 922 time to evaluate : 4.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 53 TRP cc_start: 0.3623 (t-100) cc_final: 0.2972 (t60) REVERT: W 75 ASN cc_start: 0.7945 (m110) cc_final: 0.7501 (m110) REVERT: W 76 LEU cc_start: 0.8158 (tt) cc_final: 0.7590 (mm) REVERT: W 109 ILE cc_start: 0.4733 (tt) cc_final: 0.4323 (mt) REVERT: W 116 MET cc_start: 0.6999 (mtm) cc_final: 0.6638 (ttt) REVERT: W 186 LEU cc_start: 0.7547 (tt) cc_final: 0.7328 (mm) REVERT: X 181 HIS cc_start: 0.8499 (t70) cc_final: 0.8145 (t70) REVERT: X 183 TYR cc_start: 0.7485 (t80) cc_final: 0.7178 (t80) REVERT: Y 246 PHE cc_start: 0.8763 (m-10) cc_final: 0.8439 (m-80) REVERT: Y 247 ARG cc_start: 0.6790 (mmp80) cc_final: 0.5858 (tpp-160) REVERT: A 84 MET cc_start: 0.8117 (tmm) cc_final: 0.7807 (tmm) REVERT: A 173 TYR cc_start: 0.8328 (m-80) cc_final: 0.7925 (m-80) REVERT: A 198 LEU cc_start: 0.9411 (tt) cc_final: 0.9200 (tt) REVERT: A 204 ASP cc_start: 0.9439 (p0) cc_final: 0.8998 (p0) REVERT: A 205 ASP cc_start: 0.9374 (m-30) cc_final: 0.9062 (m-30) REVERT: A 265 PHE cc_start: 0.7870 (t80) cc_final: 0.7314 (t80) REVERT: A 302 PHE cc_start: 0.9259 (t80) cc_final: 0.9045 (t80) REVERT: A 326 SER cc_start: 0.9365 (m) cc_final: 0.8902 (p) REVERT: A 420 LEU cc_start: 0.9721 (tp) cc_final: 0.9425 (tt) REVERT: A 494 GLN cc_start: 0.8285 (tp-100) cc_final: 0.7767 (tp-100) REVERT: A 495 TYR cc_start: 0.8804 (m-10) cc_final: 0.8595 (m-80) REVERT: A 541 SER cc_start: 0.8078 (p) cc_final: 0.7783 (t) REVERT: A 561 GLU cc_start: 0.9289 (pm20) cc_final: 0.8959 (pm20) REVERT: A 564 ASP cc_start: 0.9292 (m-30) cc_final: 0.8885 (m-30) REVERT: A 608 MET cc_start: 0.9228 (tmm) cc_final: 0.8869 (tmm) REVERT: A 615 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8631 (mmtm) REVERT: A 634 LEU cc_start: 0.8875 (mm) cc_final: 0.7969 (tt) REVERT: A 740 MET cc_start: 0.7783 (tmm) cc_final: 0.7142 (tmm) REVERT: B 117 LEU cc_start: 0.9334 (mt) cc_final: 0.9006 (tp) REVERT: B 120 ASP cc_start: 0.9074 (t70) cc_final: 0.8751 (p0) REVERT: B 203 TYR cc_start: 0.8071 (m-10) cc_final: 0.7857 (m-10) REVERT: B 219 MET cc_start: 0.8505 (ppp) cc_final: 0.8106 (ttm) REVERT: B 275 MET cc_start: 0.9083 (tmm) cc_final: 0.8693 (tmm) REVERT: B 283 GLU cc_start: 0.9129 (pp20) cc_final: 0.8642 (pp20) REVERT: B 287 ARG cc_start: 0.8754 (mtm-85) cc_final: 0.8518 (mtm180) REVERT: B 291 GLU cc_start: 0.8779 (pp20) cc_final: 0.8524 (pp20) REVERT: B 292 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 329 LEU cc_start: 0.9235 (tp) cc_final: 0.8613 (tt) REVERT: B 333 ASP cc_start: 0.8440 (m-30) cc_final: 0.7634 (m-30) REVERT: B 398 GLN cc_start: 0.8961 (tt0) cc_final: 0.8557 (tp-100) REVERT: B 401 ASN cc_start: 0.8983 (m110) cc_final: 0.8609 (t0) REVERT: B 449 MET cc_start: 0.8470 (ttt) cc_final: 0.7569 (ttt) REVERT: B 484 ASP cc_start: 0.8994 (m-30) cc_final: 0.8305 (p0) REVERT: B 542 ILE cc_start: 0.8889 (mm) cc_final: 0.8612 (mt) REVERT: B 546 GLU cc_start: 0.9547 (mm-30) cc_final: 0.9203 (tp30) REVERT: B 608 MET cc_start: 0.8402 (tmm) cc_final: 0.7783 (tmm) REVERT: B 611 MET cc_start: 0.8571 (mmp) cc_final: 0.8201 (mmp) REVERT: B 686 ASP cc_start: 0.9340 (t70) cc_final: 0.8806 (m-30) REVERT: C 46 MET cc_start: 0.8793 (ppp) cc_final: 0.8475 (ppp) REVERT: C 162 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7933 (tm-30) REVERT: C 218 GLU cc_start: 0.9103 (tp30) cc_final: 0.8795 (tp30) REVERT: C 266 PHE cc_start: 0.9416 (t80) cc_final: 0.9066 (t80) REVERT: C 281 GLU cc_start: 0.8126 (pm20) cc_final: 0.7837 (pm20) REVERT: C 288 LYS cc_start: 0.9486 (ptmt) cc_final: 0.9171 (ptpp) REVERT: C 327 GLN cc_start: 0.9347 (tp-100) cc_final: 0.8850 (tp-100) REVERT: C 331 LEU cc_start: 0.9327 (mt) cc_final: 0.8676 (mt) REVERT: C 338 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8306 (tmm-80) REVERT: C 340 HIS cc_start: 0.7793 (m-70) cc_final: 0.7511 (p-80) REVERT: C 410 ASP cc_start: 0.8682 (m-30) cc_final: 0.8255 (m-30) REVERT: C 421 GLN cc_start: 0.9519 (tp-100) cc_final: 0.9077 (tp40) REVERT: C 476 TRP cc_start: 0.7262 (m100) cc_final: 0.6956 (m100) REVERT: C 485 VAL cc_start: 0.8910 (t) cc_final: 0.8708 (t) REVERT: C 488 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8716 (mp0) REVERT: C 517 TYR cc_start: 0.8550 (p90) cc_final: 0.8316 (p90) REVERT: C 522 CYS cc_start: 0.7512 (m) cc_final: 0.6936 (p) REVERT: C 564 ASP cc_start: 0.8779 (m-30) cc_final: 0.8532 (m-30) REVERT: C 565 LYS cc_start: 0.9244 (tptp) cc_final: 0.8947 (tptp) REVERT: C 577 ASP cc_start: 0.8130 (m-30) cc_final: 0.7856 (m-30) REVERT: C 611 MET cc_start: 0.8765 (mmp) cc_final: 0.8471 (mmp) REVERT: C 675 LEU cc_start: 0.8714 (tp) cc_final: 0.8496 (mp) REVERT: C 689 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9016 (mt-10) REVERT: D 315 LYS cc_start: 0.9480 (mmmm) cc_final: 0.9262 (mmmm) REVERT: D 316 THR cc_start: 0.8211 (p) cc_final: 0.7395 (p) REVERT: D 326 SER cc_start: 0.9520 (m) cc_final: 0.9283 (m) REVERT: D 366 GLU cc_start: 0.7252 (mp0) cc_final: 0.6969 (mp0) REVERT: D 460 ASN cc_start: 0.9311 (t0) cc_final: 0.8995 (p0) REVERT: D 491 GLU cc_start: 0.8103 (tt0) cc_final: 0.7411 (tt0) REVERT: D 495 TYR cc_start: 0.8749 (m-10) cc_final: 0.8303 (m-10) REVERT: D 517 TYR cc_start: 0.9208 (p90) cc_final: 0.8551 (p90) REVERT: D 560 ARG cc_start: 0.9090 (mtt90) cc_final: 0.8527 (mmt90) REVERT: D 603 GLN cc_start: 0.8317 (mt0) cc_final: 0.8057 (mt0) REVERT: D 609 ASP cc_start: 0.9007 (t0) cc_final: 0.8748 (t0) REVERT: E 90 ASN cc_start: 0.8313 (m110) cc_final: 0.7981 (t0) REVERT: E 274 ILE cc_start: 0.9503 (tp) cc_final: 0.9212 (tp) REVERT: E 275 MET cc_start: 0.9023 (tmm) cc_final: 0.8544 (tmm) REVERT: E 302 PHE cc_start: 0.8734 (t80) cc_final: 0.8343 (t80) REVERT: E 314 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8311 (tm-30) REVERT: E 315 LYS cc_start: 0.9301 (mmpt) cc_final: 0.8803 (mmmt) REVERT: E 321 GLU cc_start: 0.9292 (mp0) cc_final: 0.8419 (pm20) REVERT: E 326 SER cc_start: 0.9435 (m) cc_final: 0.9066 (p) REVERT: E 493 VAL cc_start: 0.9217 (t) cc_final: 0.8983 (m) REVERT: E 499 HIS cc_start: 0.8435 (m90) cc_final: 0.8175 (m170) REVERT: E 548 LEU cc_start: 0.9262 (mt) cc_final: 0.9030 (mt) REVERT: E 551 TRP cc_start: 0.6955 (m-10) cc_final: 0.5930 (m100) REVERT: E 563 PHE cc_start: 0.9377 (m-80) cc_final: 0.9057 (m-10) REVERT: E 564 ASP cc_start: 0.9272 (m-30) cc_final: 0.9071 (m-30) REVERT: E 573 VAL cc_start: 0.9258 (t) cc_final: 0.8979 (m) REVERT: E 574 LEU cc_start: 0.9210 (tp) cc_final: 0.8986 (tp) REVERT: E 720 MET cc_start: 0.4416 (mmm) cc_final: 0.3881 (ptt) REVERT: E 772 ARG cc_start: 0.6106 (ptt180) cc_final: 0.5836 (ptt180) REVERT: F 158 MET cc_start: 0.6218 (ptt) cc_final: 0.5738 (ppp) REVERT: F 203 TYR cc_start: 0.6385 (m-80) cc_final: 0.5993 (m-80) REVERT: F 312 LYS cc_start: 0.9333 (tptp) cc_final: 0.9076 (tptp) REVERT: F 321 GLU cc_start: 0.8241 (pm20) cc_final: 0.7916 (pm20) REVERT: F 331 LEU cc_start: 0.9668 (mt) cc_final: 0.9387 (mt) REVERT: F 442 MET cc_start: 0.8650 (ppp) cc_final: 0.8428 (ppp) REVERT: F 492 LEU cc_start: 0.9232 (mt) cc_final: 0.9002 (mt) REVERT: F 640 ASP cc_start: 0.7122 (m-30) cc_final: 0.6686 (m-30) REVERT: F 736 PHE cc_start: 0.8996 (m-80) cc_final: 0.8364 (m-80) REVERT: F 738 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8757 (tp30) outliers start: 1 outliers final: 0 residues processed: 923 average time/residue: 0.5073 time to fit residues: 768.9707 Evaluate side-chains 718 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 718 time to evaluate : 4.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 318 optimal weight: 20.0000 chunk 205 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 327 optimal weight: 0.0170 chunk 350 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 47 optimal weight: 40.0000 chunk 404 optimal weight: 0.7980 overall best weight: 1.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 340 HIS A 398 GLN A 538 ASN ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 602 ASN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 42314 Z= 0.193 Angle : 0.651 11.304 57352 Z= 0.325 Chirality : 0.045 0.200 6432 Planarity : 0.005 0.076 7554 Dihedral : 8.314 120.916 6113 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.70 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.65 (0.12), residues: 5365 helix: 0.61 (0.11), residues: 2425 sheet: -0.05 (0.20), residues: 635 loop : -1.69 (0.13), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP W 133 HIS 0.003 0.001 HIS W 240 PHE 0.031 0.001 PHE F 674 TYR 0.024 0.001 TYR E 495 ARG 0.010 0.001 ARG D 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 895 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 53 TRP cc_start: 0.3625 (t-100) cc_final: 0.2956 (t60) REVERT: W 75 ASN cc_start: 0.7970 (m110) cc_final: 0.7521 (m110) REVERT: W 76 LEU cc_start: 0.8165 (tt) cc_final: 0.7585 (mm) REVERT: W 101 MET cc_start: 0.8687 (pmm) cc_final: 0.8478 (pmm) REVERT: W 109 ILE cc_start: 0.4759 (tt) cc_final: 0.4338 (mt) REVERT: W 116 MET cc_start: 0.6999 (mtm) cc_final: 0.6644 (ttt) REVERT: X 99 LEU cc_start: 0.8921 (mm) cc_final: 0.8459 (tp) REVERT: X 103 LEU cc_start: 0.9252 (mm) cc_final: 0.9007 (mm) REVERT: X 181 HIS cc_start: 0.8450 (t70) cc_final: 0.8098 (t70) REVERT: Y 246 PHE cc_start: 0.8742 (m-10) cc_final: 0.8441 (m-80) REVERT: Y 247 ARG cc_start: 0.6803 (mmp80) cc_final: 0.5848 (tpp-160) REVERT: A 84 MET cc_start: 0.8145 (tmm) cc_final: 0.7087 (tmm) REVERT: A 173 TYR cc_start: 0.8372 (m-80) cc_final: 0.7974 (m-80) REVERT: A 204 ASP cc_start: 0.9461 (p0) cc_final: 0.9064 (p0) REVERT: A 205 ASP cc_start: 0.9363 (m-30) cc_final: 0.9078 (m-30) REVERT: A 253 LEU cc_start: 0.9532 (tt) cc_final: 0.9283 (tt) REVERT: A 265 PHE cc_start: 0.7906 (t80) cc_final: 0.7365 (t80) REVERT: A 326 SER cc_start: 0.9388 (m) cc_final: 0.8944 (p) REVERT: A 494 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7740 (tp-100) REVERT: A 495 TYR cc_start: 0.8846 (m-10) cc_final: 0.8622 (m-80) REVERT: A 541 SER cc_start: 0.8153 (p) cc_final: 0.7927 (t) REVERT: A 561 GLU cc_start: 0.9290 (pm20) cc_final: 0.8981 (pm20) REVERT: A 564 ASP cc_start: 0.9308 (m-30) cc_final: 0.8960 (m-30) REVERT: A 602 ASN cc_start: 0.7999 (m110) cc_final: 0.7747 (m110) REVERT: A 608 MET cc_start: 0.9222 (tmm) cc_final: 0.8858 (tmm) REVERT: A 615 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8665 (mmtm) REVERT: A 634 LEU cc_start: 0.8860 (mm) cc_final: 0.7972 (tt) REVERT: A 740 MET cc_start: 0.7718 (tmm) cc_final: 0.7074 (tmm) REVERT: B 117 LEU cc_start: 0.9337 (mt) cc_final: 0.8957 (tp) REVERT: B 203 TYR cc_start: 0.8117 (m-10) cc_final: 0.7852 (m-10) REVERT: B 219 MET cc_start: 0.8555 (ppp) cc_final: 0.8272 (ttm) REVERT: B 244 TYR cc_start: 0.8435 (p90) cc_final: 0.7911 (p90) REVERT: B 275 MET cc_start: 0.9092 (tmm) cc_final: 0.8752 (tmm) REVERT: B 283 GLU cc_start: 0.9089 (pp20) cc_final: 0.8845 (pm20) REVERT: B 292 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8049 (mt-10) REVERT: B 329 LEU cc_start: 0.9325 (tp) cc_final: 0.9022 (tp) REVERT: B 368 ASP cc_start: 0.8591 (p0) cc_final: 0.8320 (p0) REVERT: B 398 GLN cc_start: 0.8983 (tt0) cc_final: 0.8553 (tp-100) REVERT: B 401 ASN cc_start: 0.9014 (m110) cc_final: 0.8622 (t0) REVERT: B 449 MET cc_start: 0.8440 (ttt) cc_final: 0.7605 (ttt) REVERT: B 484 ASP cc_start: 0.9021 (m-30) cc_final: 0.8314 (p0) REVERT: B 525 THR cc_start: 0.8871 (p) cc_final: 0.8530 (p) REVERT: B 529 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9070 (mmtp) REVERT: B 542 ILE cc_start: 0.8920 (mm) cc_final: 0.8612 (mt) REVERT: B 546 GLU cc_start: 0.9555 (mm-30) cc_final: 0.9170 (tp30) REVERT: B 608 MET cc_start: 0.8418 (tmm) cc_final: 0.7893 (tmm) REVERT: B 611 MET cc_start: 0.8563 (mmp) cc_final: 0.7437 (mmp) REVERT: B 686 ASP cc_start: 0.9362 (t70) cc_final: 0.8689 (m-30) REVERT: B 725 ASP cc_start: 0.6121 (p0) cc_final: 0.5320 (t0) REVERT: C 46 MET cc_start: 0.8781 (ppp) cc_final: 0.8484 (ppp) REVERT: C 162 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8065 (tm-30) REVERT: C 218 GLU cc_start: 0.9143 (tp30) cc_final: 0.8826 (tp30) REVERT: C 221 GLU cc_start: 0.8522 (mp0) cc_final: 0.8130 (mp0) REVERT: C 275 MET cc_start: 0.9330 (tpp) cc_final: 0.9103 (tpp) REVERT: C 281 GLU cc_start: 0.8131 (pm20) cc_final: 0.7828 (pm20) REVERT: C 327 GLN cc_start: 0.9333 (tp-100) cc_final: 0.8865 (tp-100) REVERT: C 331 LEU cc_start: 0.9403 (mt) cc_final: 0.8864 (mt) REVERT: C 340 HIS cc_start: 0.7889 (m-70) cc_final: 0.7666 (p-80) REVERT: C 353 ILE cc_start: 0.9614 (pt) cc_final: 0.9255 (pt) REVERT: C 421 GLN cc_start: 0.9540 (tp-100) cc_final: 0.9066 (tp40) REVERT: C 449 MET cc_start: 0.8277 (tmm) cc_final: 0.8073 (tmm) REVERT: C 476 TRP cc_start: 0.7508 (m100) cc_final: 0.7201 (m100) REVERT: C 488 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8691 (mp0) REVERT: C 517 TYR cc_start: 0.8521 (p90) cc_final: 0.8315 (p90) REVERT: C 564 ASP cc_start: 0.8799 (m-30) cc_final: 0.8559 (m-30) REVERT: C 565 LYS cc_start: 0.9258 (tptp) cc_final: 0.8928 (tptp) REVERT: C 577 ASP cc_start: 0.8097 (m-30) cc_final: 0.7818 (m-30) REVERT: C 607 GLU cc_start: 0.9025 (tp30) cc_final: 0.8706 (tp30) REVERT: C 611 MET cc_start: 0.8894 (mmp) cc_final: 0.8086 (mmp) REVERT: C 689 GLU cc_start: 0.9447 (mt-10) cc_final: 0.9018 (mt-10) REVERT: D 315 LYS cc_start: 0.9533 (mmmm) cc_final: 0.9232 (mmmm) REVERT: D 326 SER cc_start: 0.9490 (m) cc_final: 0.9248 (m) REVERT: D 366 GLU cc_start: 0.7291 (mp0) cc_final: 0.7023 (mp0) REVERT: D 460 ASN cc_start: 0.9293 (t0) cc_final: 0.9010 (p0) REVERT: D 491 GLU cc_start: 0.8063 (tt0) cc_final: 0.7425 (tt0) REVERT: D 495 TYR cc_start: 0.8757 (m-10) cc_final: 0.8284 (m-10) REVERT: D 517 TYR cc_start: 0.9191 (p90) cc_final: 0.8221 (p90) REVERT: D 560 ARG cc_start: 0.9068 (mtt90) cc_final: 0.8790 (mmt90) REVERT: D 603 GLN cc_start: 0.8388 (mt0) cc_final: 0.7941 (mt0) REVERT: E 90 ASN cc_start: 0.8280 (m110) cc_final: 0.7991 (t0) REVERT: E 274 ILE cc_start: 0.9458 (tp) cc_final: 0.9156 (tp) REVERT: E 275 MET cc_start: 0.9047 (tmm) cc_final: 0.8590 (tmm) REVERT: E 314 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8252 (tm-30) REVERT: E 315 LYS cc_start: 0.9308 (mmpt) cc_final: 0.8846 (mmmt) REVERT: E 321 GLU cc_start: 0.9307 (mp0) cc_final: 0.8831 (pm20) REVERT: E 326 SER cc_start: 0.9423 (m) cc_final: 0.9060 (p) REVERT: E 495 TYR cc_start: 0.9025 (m-80) cc_final: 0.8417 (m-80) REVERT: E 499 HIS cc_start: 0.8630 (m90) cc_final: 0.8241 (m-70) REVERT: E 548 LEU cc_start: 0.9244 (mt) cc_final: 0.9033 (mt) REVERT: E 551 TRP cc_start: 0.6820 (m-10) cc_final: 0.5855 (m100) REVERT: E 561 GLU cc_start: 0.8943 (pp20) cc_final: 0.8725 (pp20) REVERT: E 564 ASP cc_start: 0.9315 (m-30) cc_final: 0.9062 (m-30) REVERT: E 573 VAL cc_start: 0.9212 (t) cc_final: 0.8959 (m) REVERT: E 574 LEU cc_start: 0.9233 (tp) cc_final: 0.9009 (tp) REVERT: E 608 MET cc_start: 0.8504 (tmm) cc_final: 0.8270 (tmm) REVERT: E 720 MET cc_start: 0.4485 (mmm) cc_final: 0.4034 (ptt) REVERT: E 772 ARG cc_start: 0.6124 (ptt180) cc_final: 0.5828 (ptt180) REVERT: F 158 MET cc_start: 0.6347 (ptt) cc_final: 0.5818 (ppp) REVERT: F 312 LYS cc_start: 0.9339 (tptp) cc_final: 0.9087 (tptp) REVERT: F 321 GLU cc_start: 0.8248 (pm20) cc_final: 0.7913 (pm20) REVERT: F 331 LEU cc_start: 0.9689 (mt) cc_final: 0.9409 (mt) REVERT: F 336 LYS cc_start: 0.8245 (tmmt) cc_final: 0.7960 (tmtt) REVERT: F 349 ARG cc_start: 0.8478 (mpp80) cc_final: 0.8219 (mpp80) REVERT: F 442 MET cc_start: 0.8705 (ppp) cc_final: 0.8369 (ppp) REVERT: F 492 LEU cc_start: 0.9239 (mt) cc_final: 0.9001 (mt) REVERT: F 640 ASP cc_start: 0.7139 (m-30) cc_final: 0.6719 (m-30) REVERT: F 736 PHE cc_start: 0.8985 (m-80) cc_final: 0.8364 (m-80) REVERT: F 738 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8793 (tp30) outliers start: 0 outliers final: 0 residues processed: 895 average time/residue: 0.5128 time to fit residues: 752.8346 Evaluate side-chains 704 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 704 time to evaluate : 4.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 468 optimal weight: 6.9990 chunk 493 optimal weight: 2.9990 chunk 449 optimal weight: 3.9990 chunk 479 optimal weight: 6.9990 chunk 492 optimal weight: 0.8980 chunk 288 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 376 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 433 optimal weight: 0.0980 chunk 453 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 340 HIS A 398 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 602 ASN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 42314 Z= 0.191 Angle : 0.664 11.680 57352 Z= 0.331 Chirality : 0.045 0.237 6432 Planarity : 0.005 0.092 7554 Dihedral : 8.202 119.879 6113 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.40 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.12), residues: 5365 helix: 0.63 (0.11), residues: 2420 sheet: -0.08 (0.20), residues: 636 loop : -1.70 (0.13), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP W 133 HIS 0.004 0.001 HIS C 340 PHE 0.060 0.002 PHE E 563 TYR 0.022 0.001 TYR E 138 ARG 0.021 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 885 time to evaluate : 5.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 53 TRP cc_start: 0.3619 (t-100) cc_final: 0.3012 (t60) REVERT: W 75 ASN cc_start: 0.7974 (m110) cc_final: 0.7524 (m110) REVERT: W 76 LEU cc_start: 0.8162 (tt) cc_final: 0.7580 (mm) REVERT: W 109 ILE cc_start: 0.4748 (tt) cc_final: 0.4335 (mt) REVERT: W 116 MET cc_start: 0.6988 (mtm) cc_final: 0.6628 (ttt) REVERT: Y 246 PHE cc_start: 0.8736 (m-10) cc_final: 0.8469 (m-80) REVERT: Y 247 ARG cc_start: 0.6792 (mmp80) cc_final: 0.5856 (tpp-160) REVERT: A 84 MET cc_start: 0.8180 (tmm) cc_final: 0.7110 (tmm) REVERT: A 173 TYR cc_start: 0.8371 (m-80) cc_final: 0.7962 (m-80) REVERT: A 198 LEU cc_start: 0.9402 (tt) cc_final: 0.9187 (tt) REVERT: A 204 ASP cc_start: 0.9462 (p0) cc_final: 0.9069 (p0) REVERT: A 205 ASP cc_start: 0.9338 (m-30) cc_final: 0.9047 (m-30) REVERT: A 253 LEU cc_start: 0.9528 (tt) cc_final: 0.9258 (tt) REVERT: A 265 PHE cc_start: 0.7936 (t80) cc_final: 0.7450 (t80) REVERT: A 326 SER cc_start: 0.9401 (m) cc_final: 0.8972 (p) REVERT: A 494 GLN cc_start: 0.8267 (tp-100) cc_final: 0.7755 (tp-100) REVERT: A 495 TYR cc_start: 0.8900 (m-10) cc_final: 0.8699 (m-80) REVERT: A 561 GLU cc_start: 0.9262 (pm20) cc_final: 0.8941 (pm20) REVERT: A 564 ASP cc_start: 0.9313 (m-30) cc_final: 0.8935 (m-30) REVERT: A 608 MET cc_start: 0.9248 (tmm) cc_final: 0.8813 (tmm) REVERT: A 634 LEU cc_start: 0.8853 (mm) cc_final: 0.7984 (tt) REVERT: A 740 MET cc_start: 0.7704 (tmm) cc_final: 0.7052 (tmm) REVERT: A 749 ASP cc_start: 0.8702 (t0) cc_final: 0.8500 (t0) REVERT: B 117 LEU cc_start: 0.9276 (mt) cc_final: 0.8884 (tp) REVERT: B 219 MET cc_start: 0.8556 (ppp) cc_final: 0.8263 (ttm) REVERT: B 244 TYR cc_start: 0.8413 (p90) cc_final: 0.7893 (p90) REVERT: B 275 MET cc_start: 0.9143 (tmm) cc_final: 0.8771 (tmm) REVERT: B 291 GLU cc_start: 0.8789 (pp20) cc_final: 0.8517 (pp20) REVERT: B 292 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8035 (mt-10) REVERT: B 329 LEU cc_start: 0.9210 (tp) cc_final: 0.9008 (tp) REVERT: B 331 LEU cc_start: 0.9527 (mm) cc_final: 0.9197 (mm) REVERT: B 368 ASP cc_start: 0.8554 (p0) cc_final: 0.8278 (p0) REVERT: B 398 GLN cc_start: 0.8985 (tt0) cc_final: 0.8545 (tp-100) REVERT: B 401 ASN cc_start: 0.9015 (m110) cc_final: 0.8651 (t0) REVERT: B 449 MET cc_start: 0.8399 (ttt) cc_final: 0.7616 (ttt) REVERT: B 466 GLU cc_start: 0.8202 (tp30) cc_final: 0.7817 (tp30) REVERT: B 484 ASP cc_start: 0.9019 (m-30) cc_final: 0.8310 (p0) REVERT: B 525 THR cc_start: 0.8934 (p) cc_final: 0.8592 (p) REVERT: B 529 LYS cc_start: 0.9319 (mmtm) cc_final: 0.9051 (mmtp) REVERT: B 542 ILE cc_start: 0.8908 (mm) cc_final: 0.8612 (mt) REVERT: B 546 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9192 (tp30) REVERT: B 572 CYS cc_start: 0.8621 (p) cc_final: 0.8049 (p) REVERT: B 577 ASP cc_start: 0.8451 (t70) cc_final: 0.7784 (t70) REVERT: B 608 MET cc_start: 0.8427 (tmm) cc_final: 0.7892 (tmm) REVERT: B 611 MET cc_start: 0.8444 (mmp) cc_final: 0.8035 (mmp) REVERT: B 686 ASP cc_start: 0.9354 (t70) cc_final: 0.8738 (m-30) REVERT: B 725 ASP cc_start: 0.6281 (p0) cc_final: 0.5540 (t0) REVERT: C 46 MET cc_start: 0.8785 (ppp) cc_final: 0.8472 (ppp) REVERT: C 162 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8094 (tm-30) REVERT: C 218 GLU cc_start: 0.9118 (tp30) cc_final: 0.8815 (tp30) REVERT: C 221 GLU cc_start: 0.8521 (mp0) cc_final: 0.8121 (mp0) REVERT: C 275 MET cc_start: 0.9319 (tpp) cc_final: 0.9104 (tpp) REVERT: C 281 GLU cc_start: 0.8135 (pm20) cc_final: 0.7821 (pm20) REVERT: C 326 SER cc_start: 0.9310 (m) cc_final: 0.8594 (t) REVERT: C 331 LEU cc_start: 0.9394 (mt) cc_final: 0.9183 (mt) REVERT: C 362 ARG cc_start: 0.7616 (mpt-90) cc_final: 0.7362 (mtt-85) REVERT: C 421 GLN cc_start: 0.9546 (tp-100) cc_final: 0.9082 (tp40) REVERT: C 438 ASP cc_start: 0.7960 (p0) cc_final: 0.7674 (p0) REVERT: C 449 MET cc_start: 0.8266 (tmm) cc_final: 0.8050 (tmm) REVERT: C 476 TRP cc_start: 0.7531 (m100) cc_final: 0.7224 (m100) REVERT: C 485 VAL cc_start: 0.8945 (t) cc_final: 0.8744 (t) REVERT: C 488 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8675 (mp0) REVERT: C 564 ASP cc_start: 0.8800 (m-30) cc_final: 0.8551 (m-30) REVERT: C 565 LYS cc_start: 0.9232 (tptp) cc_final: 0.8912 (tptp) REVERT: C 577 ASP cc_start: 0.8024 (m-30) cc_final: 0.7761 (m-30) REVERT: C 607 GLU cc_start: 0.9002 (tp30) cc_final: 0.8718 (tp30) REVERT: C 611 MET cc_start: 0.8906 (mmp) cc_final: 0.8218 (mmp) REVERT: C 689 GLU cc_start: 0.9452 (mt-10) cc_final: 0.9025 (mt-10) REVERT: D 98 ASP cc_start: 0.7752 (m-30) cc_final: 0.7307 (m-30) REVERT: D 304 ASP cc_start: 0.8426 (p0) cc_final: 0.8160 (p0) REVERT: D 305 GLU cc_start: 0.8698 (pm20) cc_final: 0.8241 (pm20) REVERT: D 315 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9278 (mmmm) REVERT: D 316 THR cc_start: 0.8150 (p) cc_final: 0.7878 (p) REVERT: D 326 SER cc_start: 0.9509 (m) cc_final: 0.9245 (m) REVERT: D 366 GLU cc_start: 0.7204 (mp0) cc_final: 0.6935 (mp0) REVERT: D 460 ASN cc_start: 0.9298 (t0) cc_final: 0.8991 (p0) REVERT: D 491 GLU cc_start: 0.8053 (tt0) cc_final: 0.7417 (tt0) REVERT: D 495 TYR cc_start: 0.8787 (m-10) cc_final: 0.8300 (m-10) REVERT: D 560 ARG cc_start: 0.9055 (mtt90) cc_final: 0.8545 (mmt90) REVERT: D 603 GLN cc_start: 0.8385 (mt0) cc_final: 0.8097 (mt0) REVERT: D 609 ASP cc_start: 0.9006 (t0) cc_final: 0.8788 (t0) REVERT: E 90 ASN cc_start: 0.8208 (m110) cc_final: 0.7915 (t0) REVERT: E 274 ILE cc_start: 0.9429 (tp) cc_final: 0.9122 (tp) REVERT: E 275 MET cc_start: 0.9065 (tmm) cc_final: 0.8711 (tmm) REVERT: E 302 PHE cc_start: 0.8768 (t80) cc_final: 0.8521 (t80) REVERT: E 314 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8265 (tm-30) REVERT: E 315 LYS cc_start: 0.9326 (mmpt) cc_final: 0.8853 (mmmt) REVERT: E 321 GLU cc_start: 0.9291 (mp0) cc_final: 0.8450 (pm20) REVERT: E 326 SER cc_start: 0.9418 (m) cc_final: 0.9057 (p) REVERT: E 379 GLU cc_start: 0.9053 (mp0) cc_final: 0.8641 (mp0) REVERT: E 495 TYR cc_start: 0.9011 (m-80) cc_final: 0.8409 (m-80) REVERT: E 499 HIS cc_start: 0.8619 (m90) cc_final: 0.8317 (m-70) REVERT: E 527 LEU cc_start: 0.9438 (mm) cc_final: 0.9192 (mp) REVERT: E 548 LEU cc_start: 0.9239 (mt) cc_final: 0.8996 (mt) REVERT: E 551 TRP cc_start: 0.6807 (m-10) cc_final: 0.5803 (m100) REVERT: E 564 ASP cc_start: 0.9294 (m-30) cc_final: 0.9082 (m-30) REVERT: E 573 VAL cc_start: 0.9273 (t) cc_final: 0.9031 (m) REVERT: E 574 LEU cc_start: 0.9179 (tp) cc_final: 0.8965 (tp) REVERT: E 720 MET cc_start: 0.4227 (mmm) cc_final: 0.3855 (ptt) REVERT: E 772 ARG cc_start: 0.6081 (ptt180) cc_final: 0.5813 (ptt180) REVERT: F 158 MET cc_start: 0.6333 (ptt) cc_final: 0.5746 (ppp) REVERT: F 312 LYS cc_start: 0.9307 (tptp) cc_final: 0.9049 (tptp) REVERT: F 321 GLU cc_start: 0.8259 (pm20) cc_final: 0.7928 (pm20) REVERT: F 331 LEU cc_start: 0.9689 (mt) cc_final: 0.9398 (mt) REVERT: F 349 ARG cc_start: 0.8490 (mpp80) cc_final: 0.8214 (mpp80) REVERT: F 403 THR cc_start: 0.8132 (m) cc_final: 0.7801 (m) REVERT: F 410 ASP cc_start: 0.9184 (t70) cc_final: 0.8956 (t0) REVERT: F 442 MET cc_start: 0.8719 (ppp) cc_final: 0.8368 (ppp) REVERT: F 492 LEU cc_start: 0.9263 (mt) cc_final: 0.9033 (mt) REVERT: F 529 LYS cc_start: 0.8769 (mmtm) cc_final: 0.8359 (mmmt) REVERT: F 561 GLU cc_start: 0.9369 (pm20) cc_final: 0.9154 (pm20) REVERT: F 640 ASP cc_start: 0.7142 (m-30) cc_final: 0.6702 (m-30) REVERT: F 736 PHE cc_start: 0.9038 (m-80) cc_final: 0.8434 (m-80) REVERT: F 738 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8819 (tp30) outliers start: 0 outliers final: 0 residues processed: 885 average time/residue: 0.5246 time to fit residues: 765.5238 Evaluate side-chains 707 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 707 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 477 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 chunk 507 optimal weight: 9.9990 chunk 309 optimal weight: 9.9990 chunk 240 optimal weight: 3.9990 chunk 352 optimal weight: 10.0000 chunk 532 optimal weight: 4.9990 chunk 489 optimal weight: 4.9990 chunk 423 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 105 ASN A 36 ASN A 340 HIS A 398 GLN B 499 HIS ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 384 HIS D 602 ASN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN E 351 ASN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 42314 Z= 0.267 Angle : 0.707 16.445 57352 Z= 0.358 Chirality : 0.045 0.208 6432 Planarity : 0.005 0.100 7554 Dihedral : 8.321 119.779 6113 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.29 % Favored : 91.31 % Rotamer: Outliers : 0.02 % Allowed : 0.31 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % 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: -0.88 (0.11), residues: 5365 helix: 0.43 (0.11), residues: 2412 sheet: -0.31 (0.20), residues: 632 loop : -1.74 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP W 133 HIS 0.009 0.001 HIS C 340 PHE 0.044 0.002 PHE X 100 TYR 0.034 0.002 TYR D 517 ARG 0.009 0.001 ARG C 338 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10730 Ramachandran restraints generated. 5365 Oldfield, 0 Emsley, 5365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 850 time to evaluate : 5.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 75 ASN cc_start: 0.8005 (m110) cc_final: 0.7641 (m110) REVERT: W 76 LEU cc_start: 0.8124 (tt) cc_final: 0.7482 (mm) REVERT: W 109 ILE cc_start: 0.4801 (tt) cc_final: 0.4353 (mt) REVERT: W 116 MET cc_start: 0.7029 (mtm) cc_final: 0.6611 (ttt) REVERT: X 183 TYR cc_start: 0.8153 (t80) cc_final: 0.7897 (t80) REVERT: Y 246 PHE cc_start: 0.8763 (m-10) cc_final: 0.8495 (m-80) REVERT: Y 247 ARG cc_start: 0.6798 (mmp80) cc_final: 0.5822 (tpp-160) REVERT: A 84 MET cc_start: 0.8253 (tmm) cc_final: 0.7097 (tmm) REVERT: A 173 TYR cc_start: 0.8485 (m-80) cc_final: 0.8042 (m-80) REVERT: A 198 LEU cc_start: 0.9423 (tt) cc_final: 0.9219 (tt) REVERT: A 265 PHE cc_start: 0.8030 (t80) cc_final: 0.7584 (t80) REVERT: A 326 SER cc_start: 0.9427 (m) cc_final: 0.9006 (p) REVERT: A 494 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7719 (tp-100) REVERT: A 495 TYR cc_start: 0.8966 (m-10) cc_final: 0.8709 (m-80) REVERT: A 561 GLU cc_start: 0.9239 (pm20) cc_final: 0.8928 (pm20) REVERT: A 564 ASP cc_start: 0.9312 (m-30) cc_final: 0.8907 (m-30) REVERT: A 602 ASN cc_start: 0.8110 (m110) cc_final: 0.7877 (m110) REVERT: A 608 MET cc_start: 0.9297 (tmm) cc_final: 0.8886 (tmm) REVERT: A 701 GLU cc_start: 0.9265 (tp30) cc_final: 0.8973 (tt0) REVERT: A 749 ASP cc_start: 0.8684 (t0) cc_final: 0.8478 (t0) REVERT: B 158 MET cc_start: 0.7840 (ttt) cc_final: 0.7590 (ttt) REVERT: B 203 TYR cc_start: 0.8087 (m-10) cc_final: 0.7787 (m-10) REVERT: B 219 MET cc_start: 0.8709 (ppp) cc_final: 0.8440 (ttm) REVERT: B 275 MET cc_start: 0.9225 (tmm) cc_final: 0.8859 (tmm) REVERT: B 291 GLU cc_start: 0.8803 (pp20) cc_final: 0.8571 (pp20) REVERT: B 292 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 329 LEU cc_start: 0.9137 (tp) cc_final: 0.8621 (tt) REVERT: B 368 ASP cc_start: 0.8479 (p0) cc_final: 0.8250 (p0) REVERT: B 398 GLN cc_start: 0.8997 (tt0) cc_final: 0.8566 (pp30) REVERT: B 401 ASN cc_start: 0.9047 (m110) cc_final: 0.8695 (t0) REVERT: B 449 MET cc_start: 0.8446 (ttt) cc_final: 0.7840 (ttt) REVERT: B 484 ASP cc_start: 0.9050 (m-30) cc_final: 0.8304 (p0) REVERT: B 525 THR cc_start: 0.8919 (p) cc_final: 0.8564 (p) REVERT: B 529 LYS cc_start: 0.9363 (mmtm) cc_final: 0.9095 (mmtp) REVERT: B 542 ILE cc_start: 0.9000 (mm) cc_final: 0.8716 (mt) REVERT: B 546 GLU cc_start: 0.9557 (mm-30) cc_final: 0.9195 (tp30) REVERT: B 572 CYS cc_start: 0.8707 (p) cc_final: 0.8240 (p) REVERT: B 607 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8570 (tm-30) REVERT: B 686 ASP cc_start: 0.9393 (t70) cc_final: 0.8778 (m-30) REVERT: B 720 MET cc_start: -0.0094 (mmt) cc_final: -0.0407 (tpp) REVERT: B 725 ASP cc_start: 0.6397 (p0) cc_final: 0.5605 (t0) REVERT: C 46 MET cc_start: 0.8750 (ppp) cc_final: 0.8436 (ppp) REVERT: C 162 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8099 (tm-30) REVERT: C 218 GLU cc_start: 0.9115 (tp30) cc_final: 0.8852 (tp30) REVERT: C 221 GLU cc_start: 0.8639 (mp0) cc_final: 0.8219 (mp0) REVERT: C 326 SER cc_start: 0.9367 (m) cc_final: 0.8723 (t) REVERT: C 331 LEU cc_start: 0.9415 (mt) cc_final: 0.9163 (mt) REVERT: C 421 GLN cc_start: 0.9579 (tp-100) cc_final: 0.8692 (tm-30) REVERT: C 488 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8654 (mp0) REVERT: C 564 ASP cc_start: 0.8837 (m-30) cc_final: 0.8588 (m-30) REVERT: C 565 LYS cc_start: 0.9270 (tptp) cc_final: 0.8939 (tptp) REVERT: C 577 ASP cc_start: 0.8114 (m-30) cc_final: 0.7879 (m-30) REVERT: C 607 GLU cc_start: 0.9064 (tp30) cc_final: 0.8748 (tp30) REVERT: C 611 MET cc_start: 0.9048 (mmp) cc_final: 0.8353 (mmp) REVERT: C 619 ILE cc_start: 0.8627 (mp) cc_final: 0.8409 (tp) REVERT: C 689 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9012 (mt-10) REVERT: D 98 ASP cc_start: 0.7505 (m-30) cc_final: 0.7293 (m-30) REVERT: D 304 ASP cc_start: 0.8462 (p0) cc_final: 0.8183 (p0) REVERT: D 305 GLU cc_start: 0.8750 (pm20) cc_final: 0.8324 (pm20) REVERT: D 312 LYS cc_start: 0.9101 (mttm) cc_final: 0.8711 (mmmt) REVERT: D 326 SER cc_start: 0.9527 (m) cc_final: 0.9247 (m) REVERT: D 327 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8241 (tp40) REVERT: D 351 ASN cc_start: 0.8542 (m110) cc_final: 0.8247 (t0) REVERT: D 460 ASN cc_start: 0.9223 (t0) cc_final: 0.8995 (p0) REVERT: D 491 GLU cc_start: 0.8027 (tt0) cc_final: 0.7416 (tt0) REVERT: D 495 TYR cc_start: 0.8808 (m-10) cc_final: 0.8309 (m-10) REVERT: D 517 TYR cc_start: 0.9148 (p90) cc_final: 0.7999 (p90) REVERT: D 543 LYS cc_start: 0.9418 (mmmt) cc_final: 0.9193 (mmmt) REVERT: D 603 GLN cc_start: 0.8368 (mt0) cc_final: 0.7960 (mt0) REVERT: D 604 ILE cc_start: 0.9793 (mt) cc_final: 0.9589 (mt) REVERT: D 689 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8552 (mt-10) REVERT: E 90 ASN cc_start: 0.8361 (m110) cc_final: 0.8071 (t0) REVERT: E 274 ILE cc_start: 0.9463 (tp) cc_final: 0.9186 (tp) REVERT: E 275 MET cc_start: 0.9110 (tmm) cc_final: 0.8776 (tmm) REVERT: E 302 PHE cc_start: 0.8821 (t80) cc_final: 0.8556 (t80) REVERT: E 314 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8322 (tm-30) REVERT: E 315 LYS cc_start: 0.9349 (mmpt) cc_final: 0.8949 (mmmt) REVERT: E 321 GLU cc_start: 0.9315 (mp0) cc_final: 0.8883 (pm20) REVERT: E 326 SER cc_start: 0.9424 (m) cc_final: 0.9091 (p) REVERT: E 379 GLU cc_start: 0.9024 (mp0) cc_final: 0.8634 (mp0) REVERT: E 449 MET cc_start: 0.8812 (tpp) cc_final: 0.8303 (tpp) REVERT: E 450 ASP cc_start: 0.8584 (t70) cc_final: 0.8349 (t0) REVERT: E 495 TYR cc_start: 0.9075 (m-80) cc_final: 0.8471 (m-80) REVERT: E 499 HIS cc_start: 0.8702 (m90) cc_final: 0.8357 (m-70) REVERT: E 548 LEU cc_start: 0.9277 (mt) cc_final: 0.9053 (mt) REVERT: E 551 TRP cc_start: 0.7137 (m-10) cc_final: 0.6140 (m100) REVERT: E 564 ASP cc_start: 0.9246 (m-30) cc_final: 0.9010 (m-30) REVERT: E 720 MET cc_start: 0.4608 (mmm) cc_final: 0.4271 (ptt) REVERT: E 772 ARG cc_start: 0.6093 (ptt180) cc_final: 0.5840 (ptt180) REVERT: F 158 MET cc_start: 0.6424 (ptt) cc_final: 0.5977 (ppp) REVERT: F 312 LYS cc_start: 0.9392 (tptp) cc_final: 0.9123 (tptp) REVERT: F 321 GLU cc_start: 0.8290 (pm20) cc_final: 0.7986 (pm20) REVERT: F 331 LEU cc_start: 0.9699 (mt) cc_final: 0.9436 (mt) REVERT: F 403 THR cc_start: 0.7937 (m) cc_final: 0.7711 (m) REVERT: F 410 ASP cc_start: 0.9267 (t70) cc_final: 0.8997 (t0) REVERT: F 442 MET cc_start: 0.8720 (ppp) cc_final: 0.8289 (ppp) REVERT: F 492 LEU cc_start: 0.9301 (mt) cc_final: 0.9068 (mt) REVERT: F 529 LYS cc_start: 0.8829 (mmtm) cc_final: 0.8447 (mmmt) REVERT: F 577 ASP cc_start: 0.9157 (t70) cc_final: 0.8091 (t70) REVERT: F 640 ASP cc_start: 0.7241 (m-30) cc_final: 0.6830 (m-30) REVERT: F 689 GLU cc_start: 0.9622 (tp30) cc_final: 0.9420 (tp30) REVERT: F 696 LYS cc_start: 0.9814 (mmmt) cc_final: 0.9595 (mmmt) REVERT: F 736 PHE cc_start: 0.9068 (m-80) cc_final: 0.8510 (m-80) outliers start: 1 outliers final: 0 residues processed: 851 average time/residue: 0.5039 time to fit residues: 706.5829 Evaluate side-chains 676 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 675 time to evaluate : 4.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 534 random chunks: chunk 259 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 451 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 424 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 435 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS A 398 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 ASN ** E 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 602 ASN E 603 GLN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.119703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081979 restraints weight = 145504.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.084666 restraints weight = 88277.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086449 restraints weight = 63300.054| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 42314 Z= 0.235 Angle : 0.698 13.227 57352 Z= 0.352 Chirality : 0.046 0.226 6432 Planarity : 0.005 0.081 7554 Dihedral : 8.277 119.888 6113 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.88 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.69 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.92 (0.11), residues: 5365 helix: 0.37 (0.11), residues: 2406 sheet: -0.31 (0.20), residues: 633 loop : -1.73 (0.13), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP W 133 HIS 0.004 0.001 HIS X 240 PHE 0.047 0.002 PHE X 100 TYR 0.021 0.002 TYR E 138 ARG 0.007 0.001 ARG D 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13048.73 seconds wall clock time: 232 minutes 9.60 seconds (13929.60 seconds total)