Starting phenix.real_space_refine on Sun Mar 24 14:10:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/03_2024/5i68_8072_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/03_2024/5i68_8072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/03_2024/5i68_8072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/03_2024/5i68_8072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/03_2024/5i68_8072_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/03_2024/5i68_8072_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 208 5.16 5 C 26504 2.51 5 N 7272 2.21 5 O 8008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 241": "NH1" <-> "NH2" Residue "D PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 451": "NH1" <-> "NH2" Residue "D TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 451": "NH1" <-> "NH2" Residue "E TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ARG 214": "NH1" <-> "NH2" Residue "G ARG 241": "NH1" <-> "NH2" Residue "G PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 451": "NH1" <-> "NH2" Residue "G TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 57": "NH1" <-> "NH2" Residue "H ARG 81": "NH1" <-> "NH2" Residue "H ARG 134": "NH1" <-> "NH2" Residue "H ARG 214": "NH1" <-> "NH2" Residue "H ARG 241": "NH1" <-> "NH2" Residue "H PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 451": "NH1" <-> "NH2" Residue "H TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 42016 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5252 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'peptide': 662, 'undetermined': 2} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 616, None: 2} Not linked: pdbres="PHE A 663 " pdbres=" MG A 701 " Not linked: pdbres=" MG A 701 " pdbres="FAD A 702 " Chain: "B" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5252 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'peptide': 662, 'undetermined': 2} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 616, None: 2} Not linked: pdbres="PHE B 663 " pdbres=" MG B 701 " Not linked: pdbres=" MG B 701 " pdbres="FAD B 702 " Chain: "C" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5252 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'peptide': 662, 'undetermined': 2} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 616, None: 2} Not linked: pdbres="PHE C 663 " pdbres=" MG C 701 " Not linked: pdbres=" MG C 701 " pdbres="FAD C 702 " Chain: "D" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5252 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'peptide': 662, 'undetermined': 2} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 616, None: 2} Not linked: pdbres="PHE D 663 " pdbres=" MG D 701 " Not linked: pdbres=" MG D 701 " pdbres="FAD D 702 " Chain: "E" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5252 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'peptide': 662, 'undetermined': 2} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 616, None: 2} Not linked: pdbres="PHE E 663 " pdbres=" MG E 701 " Not linked: pdbres=" MG E 701 " pdbres="FAD E 702 " Chain: "F" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5252 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'peptide': 662, 'undetermined': 2} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 616, None: 2} Not linked: pdbres="PHE F 663 " pdbres=" MG F 701 " Not linked: pdbres=" MG F 701 " pdbres="FAD F 702 " Chain: "G" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5252 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'peptide': 662, 'undetermined': 2} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 616, None: 2} Not linked: pdbres="PHE G 663 " pdbres=" MG G 701 " Not linked: pdbres=" MG G 701 " pdbres="FAD G 702 " Chain: "H" Number of atoms: 5252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5252 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'peptide': 662, 'undetermined': 2} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 616, None: 2} Not linked: pdbres="PHE H 663 " pdbres=" MG H 701 " Not linked: pdbres=" MG H 701 " pdbres="FAD H 702 " Time building chain proxies: 22.00, per 1000 atoms: 0.52 Number of scatterers: 42016 At special positions: 0 Unit cell: (140.22, 140.22, 136.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 208 16.00 P 16 15.00 Mg 8 11.99 O 8008 8.00 N 7272 7.00 C 26504 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: 14.99 Conformation dependent library (CDL) restraints added in 7.2 seconds 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 208 helices and 48 sheets defined 27.8% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.67 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 removed outlier: 4.319A pdb=" N ASP A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 50 No H-bonds generated for 'chain 'A' and resid 47 through 50' Processing helix chain 'A' and resid 52 through 54 No H-bonds generated for 'chain 'A' and resid 52 through 54' Processing helix chain 'A' and resid 56 through 59 Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 92 through 95 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.668A pdb=" N ASP A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.732A pdb=" N SER A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.728A pdb=" N ARG A 214 " --> pdb=" O HIS A 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 210 through 215' Processing helix chain 'A' and resid 269 through 279 Proline residue: A 274 - end of helix Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 335 through 345 removed outlier: 3.725A pdb=" N TRP A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 352 No H-bonds generated for 'chain 'A' and resid 350 through 352' Processing helix chain 'A' and resid 366 through 369 No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 374 through 383 removed outlier: 3.659A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 454 through 467 removed outlier: 3.641A pdb=" N GLU A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.771A pdb=" N ALA A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 608 No H-bonds generated for 'chain 'A' and resid 606 through 608' Processing helix chain 'A' and resid 618 through 635 Processing helix chain 'B' and resid 16 through 29 removed outlier: 4.319A pdb=" N ASP B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 No H-bonds generated for 'chain 'B' and resid 47 through 50' Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 56 through 59 Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 92 through 95 Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.668A pdb=" N ASP B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.732A pdb=" N SER B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.728A pdb=" N ARG B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 210 through 215' Processing helix chain 'B' and resid 269 through 279 Proline residue: B 274 - end of helix Processing helix chain 'B' and resid 285 through 289 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 335 through 345 removed outlier: 3.725A pdb=" N TRP B 343 " --> pdb=" O VAL B 339 " (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 366 through 369 No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 374 through 383 removed outlier: 3.659A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 454 through 467 removed outlier: 3.641A pdb=" N GLU B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 497 through 504 Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.771A pdb=" N ALA B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 608 No H-bonds generated for 'chain 'B' and resid 606 through 608' Processing helix chain 'B' and resid 618 through 635 Processing helix chain 'C' and resid 16 through 29 removed outlier: 4.319A pdb=" N ASP C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 50 No H-bonds generated for 'chain 'C' and resid 47 through 50' Processing helix chain 'C' and resid 52 through 54 No H-bonds generated for 'chain 'C' and resid 52 through 54' Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 92 through 95 Processing helix chain 'C' and resid 106 through 112 removed outlier: 3.668A pdb=" N ASP C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.732A pdb=" N SER C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 208 Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.728A pdb=" N ARG C 214 " --> pdb=" O HIS C 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 210 through 215' Processing helix chain 'C' and resid 269 through 279 Proline residue: C 274 - end of helix Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 335 through 345 removed outlier: 3.725A pdb=" N TRP C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) 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 366 through 369 No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 374 through 383 removed outlier: 3.659A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 454 through 467 removed outlier: 3.641A pdb=" N GLU C 465 " --> pdb=" O LYS C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.771A pdb=" N ALA C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 608 No H-bonds generated for 'chain 'C' and resid 606 through 608' Processing helix chain 'C' and resid 618 through 635 Processing helix chain 'D' and resid 16 through 29 removed outlier: 4.319A pdb=" N ASP D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 50 No H-bonds generated for 'chain 'D' and resid 47 through 50' Processing helix chain 'D' and resid 52 through 54 No H-bonds generated for 'chain 'D' and resid 52 through 54' Processing helix chain 'D' and resid 56 through 59 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 92 through 95 Processing helix chain 'D' and resid 106 through 112 removed outlier: 3.668A pdb=" N ASP D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.732A pdb=" N SER D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 208 Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.728A pdb=" N ARG D 214 " --> pdb=" O HIS D 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 210 through 215' Processing helix chain 'D' and resid 269 through 279 Proline residue: D 274 - end of helix Processing helix chain 'D' and resid 285 through 289 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.725A pdb=" N TRP D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 366 through 369 No H-bonds generated for 'chain 'D' and resid 366 through 369' Processing helix chain 'D' and resid 374 through 383 removed outlier: 3.659A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 454 through 467 removed outlier: 3.641A pdb=" N GLU D 465 " --> pdb=" O LYS D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 497 through 504 Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.771A pdb=" N ALA D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 608 No H-bonds generated for 'chain 'D' and resid 606 through 608' Processing helix chain 'D' and resid 618 through 635 Processing helix chain 'E' and resid 16 through 29 removed outlier: 4.319A pdb=" N ASP E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 50 No H-bonds generated for 'chain 'E' and resid 47 through 50' Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 56 through 59 Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 92 through 95 Processing helix chain 'E' and resid 106 through 112 removed outlier: 3.668A pdb=" N ASP E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 127 Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.732A pdb=" N SER E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN E 170 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 208 Processing helix chain 'E' and resid 210 through 215 removed outlier: 3.728A pdb=" N ARG E 214 " --> pdb=" O HIS E 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 210 through 215' Processing helix chain 'E' and resid 269 through 279 Proline residue: E 274 - end of helix Processing helix chain 'E' and resid 285 through 289 Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing helix chain 'E' and resid 335 through 345 removed outlier: 3.725A pdb=" N TRP E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 366 through 369 No H-bonds generated for 'chain 'E' and resid 366 through 369' Processing helix chain 'E' and resid 374 through 383 removed outlier: 3.659A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 450 through 452 No H-bonds generated for 'chain 'E' and resid 450 through 452' Processing helix chain 'E' and resid 454 through 467 removed outlier: 3.641A pdb=" N GLU E 465 " --> pdb=" O LYS E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 480 No H-bonds generated for 'chain 'E' and resid 478 through 480' Processing helix chain 'E' and resid 497 through 504 Processing helix chain 'E' and resid 548 through 561 removed outlier: 3.771A pdb=" N ALA E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE E 554 " --> pdb=" O ASP E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 608 No H-bonds generated for 'chain 'E' and resid 606 through 608' Processing helix chain 'E' and resid 618 through 635 Processing helix chain 'F' and resid 16 through 29 removed outlier: 4.319A pdb=" N ASP F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 50 No H-bonds generated for 'chain 'F' and resid 47 through 50' Processing helix chain 'F' and resid 52 through 54 No H-bonds generated for 'chain 'F' and resid 52 through 54' Processing helix chain 'F' and resid 56 through 59 Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 92 through 95 Processing helix chain 'F' and resid 106 through 112 removed outlier: 3.668A pdb=" N ASP F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE F 112 " --> pdb=" O ASP F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 127 Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.732A pdb=" N SER F 169 " --> pdb=" O ARG F 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN F 170 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 208 Processing helix chain 'F' and resid 210 through 215 removed outlier: 3.728A pdb=" N ARG F 214 " --> pdb=" O HIS F 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 210 through 215' Processing helix chain 'F' and resid 269 through 279 Proline residue: F 274 - end of helix Processing helix chain 'F' and resid 285 through 289 Processing helix chain 'F' and resid 325 through 327 No H-bonds generated for 'chain 'F' and resid 325 through 327' Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.725A pdb=" N TRP F 343 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 352 No H-bonds generated for 'chain 'F' and resid 350 through 352' Processing helix chain 'F' and resid 366 through 369 No H-bonds generated for 'chain 'F' and resid 366 through 369' Processing helix chain 'F' and resid 374 through 383 removed outlier: 3.659A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 407 No H-bonds generated for 'chain 'F' and resid 405 through 407' Processing helix chain 'F' and resid 450 through 452 No H-bonds generated for 'chain 'F' and resid 450 through 452' Processing helix chain 'F' and resid 454 through 467 removed outlier: 3.641A pdb=" N GLU F 465 " --> pdb=" O LYS F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 480 No H-bonds generated for 'chain 'F' and resid 478 through 480' Processing helix chain 'F' and resid 497 through 504 Processing helix chain 'F' and resid 548 through 561 removed outlier: 3.771A pdb=" N ALA F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE F 554 " --> pdb=" O ASP F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 606 through 608 No H-bonds generated for 'chain 'F' and resid 606 through 608' Processing helix chain 'F' and resid 618 through 635 Processing helix chain 'G' and resid 16 through 29 removed outlier: 4.319A pdb=" N ASP G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 50 No H-bonds generated for 'chain 'G' and resid 47 through 50' Processing helix chain 'G' and resid 52 through 54 No H-bonds generated for 'chain 'G' and resid 52 through 54' Processing helix chain 'G' and resid 56 through 59 Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 92 through 95 Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.668A pdb=" N ASP G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE G 112 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 127 Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 159 through 170 removed outlier: 3.732A pdb=" N SER G 169 " --> pdb=" O ARG G 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN G 170 " --> pdb=" O ALA G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 208 Processing helix chain 'G' and resid 210 through 215 removed outlier: 3.728A pdb=" N ARG G 214 " --> pdb=" O HIS G 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN G 215 " --> pdb=" O SER G 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 210 through 215' Processing helix chain 'G' and resid 269 through 279 Proline residue: G 274 - end of helix Processing helix chain 'G' and resid 285 through 289 Processing helix chain 'G' and resid 325 through 327 No H-bonds generated for 'chain 'G' and resid 325 through 327' Processing helix chain 'G' and resid 335 through 345 removed outlier: 3.725A pdb=" N TRP G 343 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 352 No H-bonds generated for 'chain 'G' and resid 350 through 352' Processing helix chain 'G' and resid 366 through 369 No H-bonds generated for 'chain 'G' and resid 366 through 369' Processing helix chain 'G' and resid 374 through 383 removed outlier: 3.659A pdb=" N GLU G 382 " --> pdb=" O GLU G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 407 No H-bonds generated for 'chain 'G' and resid 405 through 407' Processing helix chain 'G' and resid 450 through 452 No H-bonds generated for 'chain 'G' and resid 450 through 452' Processing helix chain 'G' and resid 454 through 467 removed outlier: 3.641A pdb=" N GLU G 465 " --> pdb=" O LYS G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 480 No H-bonds generated for 'chain 'G' and resid 478 through 480' Processing helix chain 'G' and resid 497 through 504 Processing helix chain 'G' and resid 548 through 561 removed outlier: 3.771A pdb=" N ALA G 553 " --> pdb=" O GLU G 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE G 554 " --> pdb=" O ASP G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 608 No H-bonds generated for 'chain 'G' and resid 606 through 608' Processing helix chain 'G' and resid 618 through 635 Processing helix chain 'H' and resid 16 through 29 removed outlier: 4.319A pdb=" N ASP H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 50 No H-bonds generated for 'chain 'H' and resid 47 through 50' Processing helix chain 'H' and resid 52 through 54 No H-bonds generated for 'chain 'H' and resid 52 through 54' Processing helix chain 'H' and resid 56 through 59 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 92 through 95 Processing helix chain 'H' and resid 106 through 112 removed outlier: 3.668A pdb=" N ASP H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 112 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 127 Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 159 through 170 removed outlier: 3.732A pdb=" N SER H 169 " --> pdb=" O ARG H 165 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN H 170 " --> pdb=" O ALA H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.728A pdb=" N ARG H 214 " --> pdb=" O HIS H 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN H 215 " --> pdb=" O SER H 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 210 through 215' Processing helix chain 'H' and resid 269 through 279 Proline residue: H 274 - end of helix Processing helix chain 'H' and resid 285 through 289 Processing helix chain 'H' and resid 325 through 327 No H-bonds generated for 'chain 'H' and resid 325 through 327' Processing helix chain 'H' and resid 335 through 345 removed outlier: 3.725A pdb=" N TRP H 343 " --> pdb=" O VAL H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 366 through 369 No H-bonds generated for 'chain 'H' and resid 366 through 369' Processing helix chain 'H' and resid 374 through 383 removed outlier: 3.659A pdb=" N GLU H 382 " --> pdb=" O GLU H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 407 No H-bonds generated for 'chain 'H' and resid 405 through 407' Processing helix chain 'H' and resid 450 through 452 No H-bonds generated for 'chain 'H' and resid 450 through 452' Processing helix chain 'H' and resid 454 through 467 removed outlier: 3.641A pdb=" N GLU H 465 " --> pdb=" O LYS H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 478 through 480 No H-bonds generated for 'chain 'H' and resid 478 through 480' Processing helix chain 'H' and resid 497 through 504 Processing helix chain 'H' and resid 548 through 561 removed outlier: 3.771A pdb=" N ALA H 553 " --> pdb=" O GLU H 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE H 554 " --> pdb=" O ASP H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 606 through 608 No H-bonds generated for 'chain 'H' and resid 606 through 608' Processing helix chain 'H' and resid 618 through 635 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.718A pdb=" N ILE A 37 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 130 through 132 removed outlier: 6.114A pdb=" N ILE A 148 " --> pdb=" O THR A 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 225 through 227 removed outlier: 3.661A pdb=" N TYR A 258 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 264 through 266 Processing sheet with id= E, first strand: chain 'A' and resid 356 through 362 removed outlier: 6.850A pdb=" N ILE A 397 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY A 359 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR A 395 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS A 361 " --> pdb=" O MET A 393 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET A 393 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A 418 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 475 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 428 through 430 Processing sheet with id= G, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.718A pdb=" N ILE B 37 " --> pdb=" O VAL B 11 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 130 through 132 removed outlier: 6.114A pdb=" N ILE B 148 " --> pdb=" O THR B 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 225 through 227 removed outlier: 3.661A pdb=" N TYR B 258 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 264 through 266 Processing sheet with id= K, first strand: chain 'B' and resid 356 through 362 removed outlier: 6.850A pdb=" N ILE B 397 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY B 359 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR B 395 " --> pdb=" O GLY B 359 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS B 361 " --> pdb=" O MET B 393 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET B 393 " --> pdb=" O LYS B 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS B 418 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 475 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 428 through 430 Processing sheet with id= M, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.718A pdb=" N ILE C 37 " --> pdb=" O VAL C 11 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 130 through 132 removed outlier: 6.114A pdb=" N ILE C 148 " --> pdb=" O THR C 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 225 through 227 removed outlier: 3.661A pdb=" N TYR C 258 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 264 through 266 Processing sheet with id= Q, first strand: chain 'C' and resid 356 through 362 removed outlier: 6.850A pdb=" N ILE C 397 " --> pdb=" O GLU C 357 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY C 359 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR C 395 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS C 361 " --> pdb=" O MET C 393 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET C 393 " --> pdb=" O LYS C 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS C 418 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 475 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 428 through 430 Processing sheet with id= S, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.718A pdb=" N ILE D 37 " --> pdb=" O VAL D 11 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 130 through 132 removed outlier: 6.114A pdb=" N ILE D 148 " --> pdb=" O THR D 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 225 through 227 removed outlier: 3.661A pdb=" N TYR D 258 " --> pdb=" O VAL D 240 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 264 through 266 Processing sheet with id= W, first strand: chain 'D' and resid 356 through 362 removed outlier: 6.850A pdb=" N ILE D 397 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY D 359 " --> pdb=" O TYR D 395 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR D 395 " --> pdb=" O GLY D 359 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS D 361 " --> pdb=" O MET D 393 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET D 393 " --> pdb=" O LYS D 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS D 418 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 475 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 428 through 430 Processing sheet with id= Y, first strand: chain 'E' and resid 9 through 12 removed outlier: 3.718A pdb=" N ILE E 37 " --> pdb=" O VAL E 11 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 130 through 132 removed outlier: 6.114A pdb=" N ILE E 148 " --> pdb=" O THR E 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 225 through 227 removed outlier: 3.661A pdb=" N TYR E 258 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 264 through 266 Processing sheet with id= AC, first strand: chain 'E' and resid 356 through 362 removed outlier: 6.850A pdb=" N ILE E 397 " --> pdb=" O GLU E 357 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY E 359 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR E 395 " --> pdb=" O GLY E 359 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS E 361 " --> pdb=" O MET E 393 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET E 393 " --> pdb=" O LYS E 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS E 418 " --> pdb=" O PHE E 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY E 475 " --> pdb=" O ARG E 317 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 428 through 430 Processing sheet with id= AE, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.718A pdb=" N ILE F 37 " --> pdb=" O VAL F 11 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 130 through 132 removed outlier: 6.114A pdb=" N ILE F 148 " --> pdb=" O THR F 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'F' and resid 225 through 227 removed outlier: 3.661A pdb=" N TYR F 258 " --> pdb=" O VAL F 240 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 264 through 266 Processing sheet with id= AI, first strand: chain 'F' and resid 356 through 362 removed outlier: 6.850A pdb=" N ILE F 397 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY F 359 " --> pdb=" O TYR F 395 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR F 395 " --> pdb=" O GLY F 359 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS F 361 " --> pdb=" O MET F 393 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET F 393 " --> pdb=" O LYS F 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS F 418 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY F 475 " --> pdb=" O ARG F 317 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 428 through 430 Processing sheet with id= AK, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.718A pdb=" N ILE G 37 " --> pdb=" O VAL G 11 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 130 through 132 removed outlier: 6.114A pdb=" N ILE G 148 " --> pdb=" O THR G 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'G' and resid 225 through 227 removed outlier: 3.661A pdb=" N TYR G 258 " --> pdb=" O VAL G 240 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 264 through 266 Processing sheet with id= AO, first strand: chain 'G' and resid 356 through 362 removed outlier: 6.850A pdb=" N ILE G 397 " --> pdb=" O GLU G 357 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY G 359 " --> pdb=" O TYR G 395 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR G 395 " --> pdb=" O GLY G 359 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS G 361 " --> pdb=" O MET G 393 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET G 393 " --> pdb=" O LYS G 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS G 418 " --> pdb=" O PHE G 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY G 475 " --> pdb=" O ARG G 317 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 428 through 430 Processing sheet with id= AQ, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.718A pdb=" N ILE H 37 " --> pdb=" O VAL H 11 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'H' and resid 130 through 132 removed outlier: 6.114A pdb=" N ILE H 148 " --> pdb=" O THR H 131 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'H' and resid 225 through 227 removed outlier: 3.661A pdb=" N TYR H 258 " --> pdb=" O VAL H 240 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 264 through 266 Processing sheet with id= AU, first strand: chain 'H' and resid 356 through 362 removed outlier: 6.850A pdb=" N ILE H 397 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY H 359 " --> pdb=" O TYR H 395 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N TYR H 395 " --> pdb=" O GLY H 359 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS H 361 " --> pdb=" O MET H 393 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N MET H 393 " --> pdb=" O LYS H 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS H 418 " --> pdb=" O PHE H 312 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY H 475 " --> pdb=" O ARG H 317 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 428 through 430 808 hydrogen bonds defined for protein. 2328 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: 13.26 Time building geometry restraints manager: 16.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 7016 1.31 - 1.44: 12064 1.44 - 1.56: 23736 1.56 - 1.69: 40 1.69 - 1.81: 328 Bond restraints: 43184 Sorted by residual: bond pdb=" C ILE C 408 " pdb=" N PRO C 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 bond pdb=" C ILE G 408 " pdb=" N PRO G 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 bond pdb=" C ILE F 408 " pdb=" N PRO F 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 bond pdb=" C ILE D 408 " pdb=" N PRO D 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 bond pdb=" C ILE E 408 " pdb=" N PRO E 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 ... (remaining 43179 not shown) Histogram of bond angle deviations from ideal: 95.56 - 104.17: 1008 104.17 - 112.79: 21736 112.79 - 121.40: 25216 121.40 - 130.02: 10280 130.02 - 138.63: 432 Bond angle restraints: 58672 Sorted by residual: angle pdb=" C LEU G 51 " pdb=" N PRO G 52 " pdb=" CA PRO G 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 angle pdb=" C LEU H 51 " pdb=" N PRO H 52 " pdb=" CA PRO H 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 angle pdb=" C LEU E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 angle pdb=" C LEU F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 angle pdb=" C LEU D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 ... (remaining 58667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 24368 16.40 - 32.79: 1152 32.79 - 49.19: 224 49.19 - 65.58: 16 65.58 - 81.98: 32 Dihedral angle restraints: 25792 sinusoidal: 10616 harmonic: 15176 Sorted by residual: dihedral pdb=" CA ARG D 662 " pdb=" C ARG D 662 " pdb=" N PHE D 663 " pdb=" CA PHE D 663 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ARG C 662 " pdb=" C ARG C 662 " pdb=" N PHE C 663 " pdb=" CA PHE C 663 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ARG G 662 " pdb=" C ARG G 662 " pdb=" N PHE G 663 " pdb=" CA PHE G 663 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 25789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 5352 0.096 - 0.192: 592 0.192 - 0.288: 112 0.288 - 0.383: 48 0.383 - 0.479: 16 Chirality restraints: 6120 Sorted by residual: chirality pdb=" CA TYR A 383 " pdb=" N TYR A 383 " pdb=" C TYR A 383 " pdb=" CB TYR A 383 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA TYR D 383 " pdb=" N TYR D 383 " pdb=" C TYR D 383 " pdb=" CB TYR D 383 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA TYR C 383 " pdb=" N TYR C 383 " pdb=" C TYR C 383 " pdb=" CB TYR C 383 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 ... (remaining 6117 not shown) Planarity restraints: 7672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD C 702 " -0.193 2.00e-02 2.50e+03 1.57e-01 1.17e+03 pdb=" C10 FAD C 702 " -0.112 2.00e-02 2.50e+03 pdb=" C2 FAD C 702 " 0.092 2.00e-02 2.50e+03 pdb=" C4 FAD C 702 " 0.081 2.00e-02 2.50e+03 pdb=" C4X FAD C 702 " -0.088 2.00e-02 2.50e+03 pdb=" C5X FAD C 702 " -0.184 2.00e-02 2.50e+03 pdb=" C6 FAD C 702 " -0.151 2.00e-02 2.50e+03 pdb=" C7 FAD C 702 " 0.023 2.00e-02 2.50e+03 pdb=" C7M FAD C 702 " -0.005 2.00e-02 2.50e+03 pdb=" C8 FAD C 702 " -0.045 2.00e-02 2.50e+03 pdb=" C8M FAD C 702 " 0.473 2.00e-02 2.50e+03 pdb=" C9 FAD C 702 " -0.004 2.00e-02 2.50e+03 pdb=" C9A FAD C 702 " -0.075 2.00e-02 2.50e+03 pdb=" N1 FAD C 702 " -0.108 2.00e-02 2.50e+03 pdb=" N10 FAD C 702 " 0.009 2.00e-02 2.50e+03 pdb=" N3 FAD C 702 " 0.217 2.00e-02 2.50e+03 pdb=" N5 FAD C 702 " -0.138 2.00e-02 2.50e+03 pdb=" O2 FAD C 702 " 0.045 2.00e-02 2.50e+03 pdb=" O4 FAD C 702 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD G 702 " 0.193 2.00e-02 2.50e+03 1.57e-01 1.17e+03 pdb=" C10 FAD G 702 " 0.112 2.00e-02 2.50e+03 pdb=" C2 FAD G 702 " -0.092 2.00e-02 2.50e+03 pdb=" C4 FAD G 702 " -0.081 2.00e-02 2.50e+03 pdb=" C4X FAD G 702 " 0.088 2.00e-02 2.50e+03 pdb=" C5X FAD G 702 " 0.184 2.00e-02 2.50e+03 pdb=" C6 FAD G 702 " 0.151 2.00e-02 2.50e+03 pdb=" C7 FAD G 702 " -0.023 2.00e-02 2.50e+03 pdb=" C7M FAD G 702 " 0.005 2.00e-02 2.50e+03 pdb=" C8 FAD G 702 " 0.045 2.00e-02 2.50e+03 pdb=" C8M FAD G 702 " -0.473 2.00e-02 2.50e+03 pdb=" C9 FAD G 702 " 0.004 2.00e-02 2.50e+03 pdb=" C9A FAD G 702 " 0.075 2.00e-02 2.50e+03 pdb=" N1 FAD G 702 " 0.108 2.00e-02 2.50e+03 pdb=" N10 FAD G 702 " -0.009 2.00e-02 2.50e+03 pdb=" N3 FAD G 702 " -0.217 2.00e-02 2.50e+03 pdb=" N5 FAD G 702 " 0.138 2.00e-02 2.50e+03 pdb=" O2 FAD G 702 " -0.045 2.00e-02 2.50e+03 pdb=" O4 FAD G 702 " -0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD A 702 " 0.193 2.00e-02 2.50e+03 1.57e-01 1.17e+03 pdb=" C10 FAD A 702 " 0.112 2.00e-02 2.50e+03 pdb=" C2 FAD A 702 " -0.092 2.00e-02 2.50e+03 pdb=" C4 FAD A 702 " -0.081 2.00e-02 2.50e+03 pdb=" C4X FAD A 702 " 0.088 2.00e-02 2.50e+03 pdb=" C5X FAD A 702 " 0.184 2.00e-02 2.50e+03 pdb=" C6 FAD A 702 " 0.151 2.00e-02 2.50e+03 pdb=" C7 FAD A 702 " -0.023 2.00e-02 2.50e+03 pdb=" C7M FAD A 702 " 0.005 2.00e-02 2.50e+03 pdb=" C8 FAD A 702 " 0.045 2.00e-02 2.50e+03 pdb=" C8M FAD A 702 " -0.473 2.00e-02 2.50e+03 pdb=" C9 FAD A 702 " 0.004 2.00e-02 2.50e+03 pdb=" C9A FAD A 702 " 0.075 2.00e-02 2.50e+03 pdb=" N1 FAD A 702 " 0.108 2.00e-02 2.50e+03 pdb=" N10 FAD A 702 " -0.009 2.00e-02 2.50e+03 pdb=" N3 FAD A 702 " -0.217 2.00e-02 2.50e+03 pdb=" N5 FAD A 702 " 0.138 2.00e-02 2.50e+03 pdb=" O2 FAD A 702 " -0.045 2.00e-02 2.50e+03 pdb=" O4 FAD A 702 " -0.162 2.00e-02 2.50e+03 ... (remaining 7669 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 40 2.12 - 2.81: 13464 2.81 - 3.51: 56896 3.51 - 4.20: 103888 4.20 - 4.90: 182112 Nonbonded interactions: 356400 Sorted by model distance: nonbonded pdb=" OH TYR A 486 " pdb=" OG SER A 517 " model vdw 1.419 2.440 nonbonded pdb=" OH TYR G 486 " pdb=" OG SER G 517 " model vdw 1.419 2.440 nonbonded pdb=" OH TYR D 486 " pdb=" OG SER D 517 " model vdw 1.419 2.440 nonbonded pdb=" OH TYR H 486 " pdb=" OG SER H 517 " model vdw 1.419 2.440 nonbonded pdb=" OH TYR F 486 " pdb=" OG SER F 517 " model vdw 1.419 2.440 ... (remaining 356395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.070 Extract box with map and model: 4.460 Check model and map are aligned: 0.590 Set scattering table: 0.370 Process input model: 101.400 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.009 0.098 43184 Z= 0.616 Angle : 1.466 13.629 58672 Z= 0.951 Chirality : 0.075 0.479 6120 Planarity : 0.007 0.157 7672 Dihedral : 10.476 81.980 16144 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.25 % Allowed : 3.04 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.41 (0.11), residues: 5280 helix: -1.75 (0.11), residues: 1264 sheet: -0.63 (0.24), residues: 488 loop : 0.52 (0.11), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 48 HIS 0.010 0.002 HIS D 418 PHE 0.025 0.003 PHE D 325 TYR 0.033 0.003 TYR A 50 ARG 0.009 0.001 ARG H 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1143 time to evaluate : 4.805 Fit side-chains REVERT: A 38 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: A 128 LYS cc_start: 0.7683 (ttpt) cc_final: 0.7404 (mtpt) REVERT: A 308 ASP cc_start: 0.6640 (m-30) cc_final: 0.6274 (m-30) REVERT: A 348 THR cc_start: 0.8509 (p) cc_final: 0.8276 (p) REVERT: A 515 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.6344 (m-70) REVERT: A 563 GLU cc_start: 0.7864 (pm20) cc_final: 0.6891 (pm20) REVERT: B 38 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: B 318 ILE cc_start: 0.8418 (tt) cc_final: 0.8211 (tt) REVERT: B 348 THR cc_start: 0.8438 (p) cc_final: 0.8238 (p) REVERT: B 563 GLU cc_start: 0.7838 (pm20) cc_final: 0.7049 (pm20) REVERT: C 38 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6672 (tm-30) REVERT: C 128 LYS cc_start: 0.7533 (ttpt) cc_final: 0.7285 (mtpt) REVERT: C 230 ILE cc_start: 0.8855 (mt) cc_final: 0.8649 (mt) REVERT: C 348 THR cc_start: 0.8430 (p) cc_final: 0.8214 (p) REVERT: C 354 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8278 (t0) REVERT: C 563 GLU cc_start: 0.7777 (pm20) cc_final: 0.7033 (pm20) REVERT: D 38 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6782 (tm-30) REVERT: D 128 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7375 (mtpt) REVERT: D 348 THR cc_start: 0.8504 (p) cc_final: 0.8257 (p) REVERT: D 354 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8297 (t0) REVERT: D 515 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.6364 (m-70) REVERT: D 563 GLU cc_start: 0.7910 (pm20) cc_final: 0.7015 (pm20) REVERT: E 38 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: E 128 LYS cc_start: 0.7546 (ttpt) cc_final: 0.7339 (mtpt) REVERT: E 308 ASP cc_start: 0.6578 (m-30) cc_final: 0.6112 (m-30) REVERT: E 563 GLU cc_start: 0.7894 (pm20) cc_final: 0.7088 (pm20) REVERT: F 38 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: F 286 ILE cc_start: 0.7979 (tp) cc_final: 0.7430 (mp) REVERT: F 354 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8268 (t0) REVERT: F 431 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7942 (tp) REVERT: F 563 GLU cc_start: 0.7799 (pm20) cc_final: 0.7124 (pm20) REVERT: G 38 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: G 230 ILE cc_start: 0.8872 (mt) cc_final: 0.8658 (mt) REVERT: G 286 ILE cc_start: 0.7889 (tp) cc_final: 0.7368 (mp) REVERT: G 308 ASP cc_start: 0.6598 (m-30) cc_final: 0.6121 (m-30) REVERT: G 348 THR cc_start: 0.8500 (p) cc_final: 0.8284 (p) REVERT: G 354 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8199 (t0) REVERT: G 515 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.6299 (m-70) REVERT: G 563 GLU cc_start: 0.7905 (pm20) cc_final: 0.6908 (pm20) REVERT: H 38 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6595 (tm-30) REVERT: H 128 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7381 (mtpt) REVERT: H 308 ASP cc_start: 0.6599 (m-30) cc_final: 0.6187 (m-30) REVERT: H 318 ILE cc_start: 0.8526 (tt) cc_final: 0.8282 (tt) REVERT: H 515 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.6331 (m-70) REVERT: H 563 GLU cc_start: 0.7974 (pm20) cc_final: 0.6951 (pm20) outliers start: 56 outliers final: 12 residues processed: 1191 average time/residue: 0.5876 time to fit residues: 1108.3225 Evaluate side-chains 671 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 642 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 515 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 4.9990 chunk 400 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 269 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 413 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 308 optimal weight: 5.9990 chunk 479 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 142 HIS ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 249 ASN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 541 HIS A 561 HIS ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 249 ASN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 HIS B 561 HIS B 594 ASN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN C 249 ASN ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 ASN C 541 HIS ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS D 218 ASN D 249 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN D 541 HIS D 561 HIS ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 249 ASN ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 HIS E 594 ASN F 142 HIS ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN F 249 ASN ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 ASN F 541 HIS G 142 HIS ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 249 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN G 541 HIS H 142 HIS ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 ASN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 508 ASN H 541 HIS H 594 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 43184 Z= 0.338 Angle : 0.742 9.462 58672 Z= 0.385 Chirality : 0.050 0.158 6120 Planarity : 0.005 0.051 7672 Dihedral : 7.162 48.092 6234 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.59 % Allowed : 9.00 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.50 (0.11), residues: 5280 helix: -0.68 (0.13), residues: 1320 sheet: -0.87 (0.21), residues: 680 loop : 0.07 (0.11), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 566 HIS 0.010 0.002 HIS B 561 PHE 0.026 0.003 PHE D 325 TYR 0.026 0.002 TYR E 50 ARG 0.004 0.001 ARG C 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 699 time to evaluate : 4.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.7768 (ttpt) cc_final: 0.7226 (ttmt) REVERT: A 188 GLU cc_start: 0.7354 (tt0) cc_final: 0.7151 (tt0) REVERT: A 414 MET cc_start: 0.8459 (ptt) cc_final: 0.8148 (ptt) REVERT: A 447 MET cc_start: 0.8313 (mmt) cc_final: 0.8077 (mmt) REVERT: A 515 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7340 (t70) REVERT: A 563 GLU cc_start: 0.7840 (pm20) cc_final: 0.7004 (pm20) REVERT: A 660 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7796 (pp) REVERT: B 255 HIS cc_start: 0.7609 (p-80) cc_final: 0.7402 (p-80) REVERT: B 262 LYS cc_start: 0.7533 (ptpt) cc_final: 0.7308 (mttt) REVERT: B 383 TYR cc_start: 0.8545 (t80) cc_final: 0.8323 (t80) REVERT: B 563 GLU cc_start: 0.7909 (pm20) cc_final: 0.7098 (pm20) REVERT: B 626 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6594 (mm-30) REVERT: B 660 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7780 (pp) REVERT: C 128 LYS cc_start: 0.7621 (ttpt) cc_final: 0.7138 (ttmt) REVERT: C 563 GLU cc_start: 0.7830 (pm20) cc_final: 0.7050 (pm20) REVERT: C 660 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7681 (pp) REVERT: D 523 LYS cc_start: 0.7812 (mmtm) cc_final: 0.7596 (mmtm) REVERT: D 563 GLU cc_start: 0.7790 (pm20) cc_final: 0.6997 (pm20) REVERT: D 660 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7760 (pp) REVERT: E 128 LYS cc_start: 0.7682 (ttpt) cc_final: 0.7169 (ttmt) REVERT: E 515 HIS cc_start: 0.7540 (OUTLIER) cc_final: 0.7327 (t70) REVERT: E 563 GLU cc_start: 0.7825 (pm20) cc_final: 0.7043 (pm20) REVERT: E 660 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7815 (pp) REVERT: F 413 TYR cc_start: 0.8698 (m-80) cc_final: 0.8451 (m-80) REVERT: F 563 GLU cc_start: 0.7756 (pm20) cc_final: 0.7030 (pm20) REVERT: F 660 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7816 (pp) REVERT: G 383 TYR cc_start: 0.8585 (t80) cc_final: 0.8312 (t80) REVERT: G 563 GLU cc_start: 0.7803 (pm20) cc_final: 0.7076 (pm20) REVERT: G 660 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7840 (pp) REVERT: H 128 LYS cc_start: 0.7731 (ttpt) cc_final: 0.7233 (ttmt) REVERT: H 515 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.7329 (t70) REVERT: H 563 GLU cc_start: 0.7703 (pm20) cc_final: 0.6943 (pm20) REVERT: H 660 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7836 (pp) outliers start: 116 outliers final: 48 residues processed: 788 average time/residue: 0.5883 time to fit residues: 746.6700 Evaluate side-chains 674 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 615 time to evaluate : 4.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 644 ASP Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 534 THR Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 515 HIS Chi-restraints excluded: chain H residue 646 THR Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 399 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 132 optimal weight: 0.0060 chunk 480 optimal weight: 20.0000 chunk 518 optimal weight: 10.0000 chunk 427 optimal weight: 0.8980 chunk 476 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 385 optimal weight: 0.9980 overall best weight: 2.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN B 27 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 HIS ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN F 27 ASN ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 430 HIS F 508 ASN ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 508 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 43184 Z= 0.207 Angle : 0.619 9.701 58672 Z= 0.318 Chirality : 0.046 0.155 6120 Planarity : 0.004 0.038 7672 Dihedral : 6.162 42.995 6174 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.62 % Allowed : 10.09 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.15 (0.12), residues: 5280 helix: 0.15 (0.14), residues: 1240 sheet: -0.80 (0.20), residues: 696 loop : 0.07 (0.11), residues: 3344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 566 HIS 0.008 0.001 HIS D 30 PHE 0.017 0.002 PHE F 325 TYR 0.020 0.002 TYR E 132 ARG 0.004 0.000 ARG G 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 680 time to evaluate : 5.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.7478 (t0) cc_final: 0.7262 (t0) REVERT: A 563 GLU cc_start: 0.7763 (pm20) cc_final: 0.7035 (pm20) REVERT: A 660 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7730 (pp) REVERT: B 262 LYS cc_start: 0.7592 (ptpt) cc_final: 0.7128 (mttt) REVERT: B 563 GLU cc_start: 0.7699 (pm20) cc_final: 0.6938 (pm20) REVERT: B 598 VAL cc_start: 0.8406 (t) cc_final: 0.8191 (p) REVERT: B 660 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7710 (pp) REVERT: C 180 ASP cc_start: 0.7440 (t0) cc_final: 0.7236 (t0) REVERT: C 565 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8211 (m) REVERT: C 660 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7666 (pp) REVERT: D 180 ASP cc_start: 0.7435 (t0) cc_final: 0.7223 (t0) REVERT: D 565 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8140 (m) REVERT: D 660 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7700 (pp) REVERT: E 8 ASP cc_start: 0.6785 (t0) cc_final: 0.6566 (t0) REVERT: E 180 ASP cc_start: 0.7387 (t0) cc_final: 0.7178 (t0) REVERT: E 262 LYS cc_start: 0.7606 (ptpt) cc_final: 0.7089 (mttt) REVERT: E 563 GLU cc_start: 0.7740 (pm20) cc_final: 0.6979 (pm20) REVERT: E 660 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7762 (pp) REVERT: F 180 ASP cc_start: 0.7464 (t0) cc_final: 0.7256 (t0) REVERT: F 563 GLU cc_start: 0.7587 (pm20) cc_final: 0.6955 (pm20) REVERT: F 660 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7744 (pp) REVERT: G 128 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7495 (ttpp) REVERT: G 565 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8307 (m) REVERT: G 660 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7762 (pp) REVERT: H 563 GLU cc_start: 0.7725 (pm20) cc_final: 0.7089 (pm20) REVERT: H 660 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7791 (pp) outliers start: 162 outliers final: 84 residues processed: 794 average time/residue: 0.6022 time to fit residues: 751.7502 Evaluate side-chains 691 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 596 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 565 THR Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 644 ASP Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 326 ASP Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 565 THR Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 326 ASP Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 495 MET Chi-restraints excluded: chain H residue 646 THR Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 9.9990 chunk 361 optimal weight: 0.9990 chunk 249 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 482 optimal weight: 2.9990 chunk 510 optimal weight: 0.7980 chunk 251 optimal weight: 0.3980 chunk 456 optimal weight: 9.9990 chunk 137 optimal weight: 0.0370 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 HIS B 508 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 ASN ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 HIS E 508 ASN ** E 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 ASN ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 43184 Z= 0.136 Angle : 0.552 8.398 58672 Z= 0.280 Chirality : 0.043 0.147 6120 Planarity : 0.004 0.038 7672 Dihedral : 5.729 38.923 6168 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.06 % Allowed : 11.90 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.06 (0.12), residues: 5280 helix: 0.59 (0.15), residues: 1232 sheet: -0.83 (0.20), residues: 728 loop : 0.14 (0.11), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 566 HIS 0.007 0.001 HIS A 515 PHE 0.014 0.001 PHE A 312 TYR 0.017 0.001 TYR E 132 ARG 0.005 0.000 ARG B 451 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 672 time to evaluate : 4.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.7432 (t0) cc_final: 0.7203 (t0) REVERT: A 443 ASP cc_start: 0.7505 (p0) cc_final: 0.7138 (p0) REVERT: A 563 GLU cc_start: 0.7608 (pm20) cc_final: 0.6878 (pm20) REVERT: A 598 VAL cc_start: 0.8444 (t) cc_final: 0.8170 (p) REVERT: B 180 ASP cc_start: 0.7394 (t0) cc_final: 0.7173 (t0) REVERT: B 262 LYS cc_start: 0.7649 (ptpt) cc_final: 0.6970 (mttt) REVERT: B 503 TYR cc_start: 0.8201 (m-80) cc_final: 0.7619 (m-80) REVERT: B 563 GLU cc_start: 0.7504 (pm20) cc_final: 0.6838 (pm20) REVERT: B 598 VAL cc_start: 0.8453 (t) cc_final: 0.8168 (p) REVERT: C 180 ASP cc_start: 0.7408 (t0) cc_final: 0.7156 (t0) REVERT: C 456 MET cc_start: 0.8150 (mtp) cc_final: 0.7523 (mtp) REVERT: C 563 GLU cc_start: 0.7401 (pm20) cc_final: 0.6740 (pm20) REVERT: C 598 VAL cc_start: 0.8293 (t) cc_final: 0.8036 (m) REVERT: D 180 ASP cc_start: 0.7378 (t0) cc_final: 0.7118 (t0) REVERT: D 443 ASP cc_start: 0.7462 (p0) cc_final: 0.7110 (p0) REVERT: D 456 MET cc_start: 0.8245 (mtp) cc_final: 0.7848 (mtp) REVERT: D 503 TYR cc_start: 0.8180 (m-80) cc_final: 0.7750 (m-80) REVERT: D 563 GLU cc_start: 0.7399 (pm20) cc_final: 0.6732 (pm20) REVERT: D 598 VAL cc_start: 0.8363 (t) cc_final: 0.8091 (p) REVERT: E 99 MET cc_start: 0.9327 (mtm) cc_final: 0.8889 (mtm) REVERT: E 180 ASP cc_start: 0.7395 (t0) cc_final: 0.7151 (t0) REVERT: E 262 LYS cc_start: 0.7617 (ptpt) cc_final: 0.6946 (mttt) REVERT: E 503 TYR cc_start: 0.8185 (m-80) cc_final: 0.7613 (m-80) REVERT: E 563 GLU cc_start: 0.7665 (pm20) cc_final: 0.6863 (pm20) REVERT: E 598 VAL cc_start: 0.8281 (t) cc_final: 0.8079 (m) REVERT: F 128 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7526 (ttpp) REVERT: F 180 ASP cc_start: 0.7368 (t0) cc_final: 0.7110 (t0) REVERT: F 443 ASP cc_start: 0.7356 (p0) cc_final: 0.6978 (p0) REVERT: F 456 MET cc_start: 0.8220 (mtp) cc_final: 0.7830 (mtp) REVERT: F 503 TYR cc_start: 0.8165 (m-80) cc_final: 0.7593 (m-80) REVERT: F 563 GLU cc_start: 0.7550 (pm20) cc_final: 0.6898 (pm20) REVERT: F 598 VAL cc_start: 0.8224 (t) cc_final: 0.7977 (m) REVERT: G 128 LYS cc_start: 0.7852 (ttmt) cc_final: 0.7520 (ttpp) REVERT: G 180 ASP cc_start: 0.7330 (t0) cc_final: 0.7105 (t0) REVERT: G 503 TYR cc_start: 0.8160 (m-80) cc_final: 0.7629 (m-80) REVERT: H 443 ASP cc_start: 0.7448 (p0) cc_final: 0.7059 (p0) REVERT: H 503 TYR cc_start: 0.8183 (m-80) cc_final: 0.7615 (m-80) REVERT: H 563 GLU cc_start: 0.7651 (pm20) cc_final: 0.6949 (pm20) outliers start: 137 outliers final: 84 residues processed: 778 average time/residue: 0.6194 time to fit residues: 777.9218 Evaluate side-chains 675 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 591 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 644 ASP Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 326 ASP Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 477 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 6.9990 chunk 289 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 380 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 435 optimal weight: 2.9990 chunk 352 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 458 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 561 HIS ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 561 HIS F 27 ASN ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 561 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 561 HIS ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 561 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43184 Z= 0.306 Angle : 0.637 7.913 58672 Z= 0.327 Chirality : 0.047 0.152 6120 Planarity : 0.005 0.046 7672 Dihedral : 6.062 46.427 6168 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.82 % Allowed : 11.18 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.22 (0.12), residues: 5280 helix: 0.42 (0.15), residues: 1288 sheet: -1.05 (0.18), residues: 832 loop : -0.01 (0.12), residues: 3160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 566 HIS 0.007 0.002 HIS H 394 PHE 0.025 0.002 PHE D 442 TYR 0.022 0.002 TYR G 50 ARG 0.004 0.001 ARG G 491 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 612 time to evaluate : 4.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ASP cc_start: 0.7505 (t0) cc_final: 0.7255 (t0) REVERT: A 456 MET cc_start: 0.8449 (mtp) cc_final: 0.8219 (mtp) REVERT: A 563 GLU cc_start: 0.7672 (pm20) cc_final: 0.6828 (pm20) REVERT: A 598 VAL cc_start: 0.8516 (t) cc_final: 0.8257 (p) REVERT: A 660 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7766 (pp) REVERT: B 128 LYS cc_start: 0.8073 (ttmt) cc_final: 0.7598 (ttpp) REVERT: B 180 ASP cc_start: 0.7451 (t0) cc_final: 0.7187 (t0) REVERT: B 456 MET cc_start: 0.8316 (mtp) cc_final: 0.7828 (mtp) REVERT: B 563 GLU cc_start: 0.7600 (pm20) cc_final: 0.6801 (pm20) REVERT: B 598 VAL cc_start: 0.8534 (t) cc_final: 0.8290 (p) REVERT: B 660 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7728 (pp) REVERT: C 32 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7765 (mp) REVERT: C 456 MET cc_start: 0.8293 (mtp) cc_final: 0.7909 (mtp) REVERT: C 470 MET cc_start: 0.9300 (mtp) cc_final: 0.9040 (mtm) REVERT: C 563 GLU cc_start: 0.7436 (pm20) cc_final: 0.6747 (pm20) REVERT: C 598 VAL cc_start: 0.8434 (t) cc_final: 0.8143 (p) REVERT: C 660 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7650 (pp) REVERT: D 32 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7755 (mp) REVERT: D 180 ASP cc_start: 0.7446 (t0) cc_final: 0.7239 (t0) REVERT: D 413 TYR cc_start: 0.8625 (m-80) cc_final: 0.8300 (m-80) REVERT: D 456 MET cc_start: 0.8434 (mtp) cc_final: 0.8121 (mtp) REVERT: D 563 GLU cc_start: 0.7450 (pm20) cc_final: 0.6792 (pm20) REVERT: D 598 VAL cc_start: 0.8508 (t) cc_final: 0.8238 (p) REVERT: D 660 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7726 (pp) REVERT: E 32 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7759 (mp) REVERT: E 413 TYR cc_start: 0.8664 (m-80) cc_final: 0.8421 (m-80) REVERT: E 456 MET cc_start: 0.8305 (mtp) cc_final: 0.8082 (mtp) REVERT: E 563 GLU cc_start: 0.7676 (pm20) cc_final: 0.6867 (pm20) REVERT: E 660 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7823 (pp) REVERT: F 128 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7565 (ttpp) REVERT: F 180 ASP cc_start: 0.7602 (t0) cc_final: 0.7336 (t0) REVERT: F 456 MET cc_start: 0.8385 (mtp) cc_final: 0.8160 (mtp) REVERT: F 563 GLU cc_start: 0.7642 (pm20) cc_final: 0.6827 (pm20) REVERT: F 660 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7746 (pp) REVERT: G 128 LYS cc_start: 0.7993 (ttmt) cc_final: 0.7718 (ttpp) REVERT: G 180 ASP cc_start: 0.7447 (t0) cc_final: 0.7106 (t0) REVERT: G 413 TYR cc_start: 0.8669 (m-80) cc_final: 0.8434 (m-80) REVERT: G 456 MET cc_start: 0.8228 (mtp) cc_final: 0.7975 (mtp) REVERT: G 563 GLU cc_start: 0.7515 (pm20) cc_final: 0.6819 (pm20) REVERT: G 660 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7761 (pp) REVERT: H 563 GLU cc_start: 0.7676 (pm20) cc_final: 0.6876 (pm20) REVERT: H 598 VAL cc_start: 0.8361 (t) cc_final: 0.8108 (m) REVERT: H 660 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7785 (pp) outliers start: 216 outliers final: 142 residues processed: 765 average time/residue: 0.5856 time to fit residues: 708.9018 Evaluate side-chains 731 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 578 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 644 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 323 GLU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 605 ASP Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 644 ASP Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 326 ASP Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 644 ASP Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 389 ASP Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 628 THR Chi-restraints excluded: chain H residue 644 ASP Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 5.9990 chunk 459 optimal weight: 20.0000 chunk 100 optimal weight: 0.0070 chunk 299 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 510 optimal weight: 1.9990 chunk 424 optimal weight: 7.9990 chunk 236 optimal weight: 0.0970 chunk 42 optimal weight: 0.3980 chunk 168 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN A 612 ASN B 142 HIS ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS B 529 ASN B 612 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN C 612 ASN D 27 ASN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 HIS D 529 ASN D 612 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN E 612 ASN ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 HIS F 529 ASN F 612 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 515 HIS G 529 ASN G 612 ASN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN H 612 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 43184 Z= 0.143 Angle : 0.537 6.964 58672 Z= 0.273 Chirality : 0.043 0.149 6120 Planarity : 0.004 0.042 7672 Dihedral : 5.786 47.026 6168 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.50 % Allowed : 13.44 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: 0.10 (0.12), residues: 5280 helix: 0.91 (0.15), residues: 1224 sheet: -0.84 (0.20), residues: 736 loop : 0.05 (0.11), residues: 3320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 566 HIS 0.007 0.001 HIS E 394 PHE 0.012 0.001 PHE A 312 TYR 0.018 0.001 TYR F 50 ARG 0.003 0.000 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 604 time to evaluate : 4.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8274 (mtp) cc_final: 0.7994 (mtp) REVERT: A 563 GLU cc_start: 0.7549 (pm20) cc_final: 0.6804 (pm20) REVERT: A 598 VAL cc_start: 0.8525 (t) cc_final: 0.8283 (p) REVERT: A 660 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7657 (pp) REVERT: B 128 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7568 (ttpp) REVERT: B 180 ASP cc_start: 0.7422 (t0) cc_final: 0.7157 (t0) REVERT: B 563 GLU cc_start: 0.7512 (pm20) cc_final: 0.6780 (pm20) REVERT: B 660 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7659 (pp) REVERT: C 456 MET cc_start: 0.8228 (mtp) cc_final: 0.8015 (mtp) REVERT: C 470 MET cc_start: 0.9313 (mtp) cc_final: 0.9072 (mtm) REVERT: C 563 GLU cc_start: 0.7348 (pm20) cc_final: 0.6703 (pm20) REVERT: C 598 VAL cc_start: 0.8411 (t) cc_final: 0.8194 (m) REVERT: C 660 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7676 (pp) REVERT: D 413 TYR cc_start: 0.8679 (m-80) cc_final: 0.8470 (m-80) REVERT: D 563 GLU cc_start: 0.7336 (pm20) cc_final: 0.6889 (pm20) REVERT: D 598 VAL cc_start: 0.8468 (t) cc_final: 0.8212 (p) REVERT: D 599 LYS cc_start: 0.8148 (mppt) cc_final: 0.7900 (mppt) REVERT: D 660 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7684 (pp) REVERT: E 413 TYR cc_start: 0.8680 (m-80) cc_final: 0.8458 (m-80) REVERT: E 456 MET cc_start: 0.8187 (mtp) cc_final: 0.7732 (mtp) REVERT: E 563 GLU cc_start: 0.7479 (pm20) cc_final: 0.6711 (pm20) REVERT: E 660 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7710 (pp) REVERT: F 128 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7649 (ttpp) REVERT: F 418 HIS cc_start: 0.8379 (OUTLIER) cc_final: 0.8179 (m90) REVERT: F 456 MET cc_start: 0.8255 (mtp) cc_final: 0.8046 (mtp) REVERT: F 540 LEU cc_start: 0.8650 (pt) cc_final: 0.8441 (pt) REVERT: F 563 GLU cc_start: 0.7579 (pm20) cc_final: 0.6839 (pm20) REVERT: F 598 VAL cc_start: 0.8282 (t) cc_final: 0.8058 (m) REVERT: F 660 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7751 (pp) REVERT: G 128 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7664 (ttpp) REVERT: G 180 ASP cc_start: 0.7453 (t0) cc_final: 0.7150 (t0) REVERT: G 503 TYR cc_start: 0.8271 (m-80) cc_final: 0.7668 (m-80) REVERT: G 563 GLU cc_start: 0.7463 (pm20) cc_final: 0.6866 (pm20) REVERT: G 660 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7729 (pp) REVERT: H 456 MET cc_start: 0.8214 (mtp) cc_final: 0.7979 (mtp) REVERT: H 503 TYR cc_start: 0.8217 (m-80) cc_final: 0.7602 (m-80) REVERT: H 563 GLU cc_start: 0.7581 (pm20) cc_final: 0.6836 (pm20) REVERT: H 598 VAL cc_start: 0.8426 (t) cc_final: 0.8216 (m) REVERT: H 599 LYS cc_start: 0.8285 (mppt) cc_final: 0.8084 (mppt) REVERT: H 660 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7761 (pp) outliers start: 157 outliers final: 102 residues processed: 708 average time/residue: 0.6064 time to fit residues: 675.0718 Evaluate side-chains 702 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 591 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 644 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 605 ASP Chi-restraints excluded: chain E residue 644 ASP Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 644 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 291 optimal weight: 7.9990 chunk 373 optimal weight: 0.0870 chunk 289 optimal weight: 0.9990 chunk 430 optimal weight: 0.0040 chunk 285 optimal weight: 10.0000 chunk 508 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 chunk 310 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 overall best weight: 2.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN D 30 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 133 GLN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43184 Z= 0.205 Angle : 0.565 7.245 58672 Z= 0.288 Chirality : 0.044 0.155 6120 Planarity : 0.004 0.044 7672 Dihedral : 5.832 49.771 6168 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.84 % Allowed : 14.24 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.02 (0.12), residues: 5280 helix: 0.81 (0.15), residues: 1272 sheet: -0.97 (0.18), residues: 824 loop : 0.02 (0.11), residues: 3184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 566 HIS 0.009 0.001 HIS H 394 PHE 0.017 0.002 PHE D 325 TYR 0.018 0.001 TYR G 50 ARG 0.005 0.000 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 607 time to evaluate : 4.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 413 TYR cc_start: 0.8638 (m-80) cc_final: 0.8359 (m-80) REVERT: A 456 MET cc_start: 0.8247 (mtp) cc_final: 0.7923 (mtp) REVERT: A 563 GLU cc_start: 0.7455 (pm20) cc_final: 0.6693 (pm20) REVERT: A 598 VAL cc_start: 0.8536 (t) cc_final: 0.8284 (p) REVERT: A 660 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7702 (pp) REVERT: B 128 LYS cc_start: 0.8036 (ttmt) cc_final: 0.7725 (ttpp) REVERT: B 180 ASP cc_start: 0.7424 (t0) cc_final: 0.7173 (t0) REVERT: B 413 TYR cc_start: 0.8564 (m-80) cc_final: 0.8348 (m-80) REVERT: B 563 GLU cc_start: 0.7422 (pm20) cc_final: 0.6727 (pm20) REVERT: B 660 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7714 (pp) REVERT: C 456 MET cc_start: 0.8254 (mtp) cc_final: 0.8026 (mtp) REVERT: C 470 MET cc_start: 0.9321 (mtp) cc_final: 0.9066 (mtm) REVERT: C 563 GLU cc_start: 0.7458 (pm20) cc_final: 0.6909 (pm20) REVERT: C 598 VAL cc_start: 0.8396 (t) cc_final: 0.8156 (m) REVERT: C 660 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7691 (pp) REVERT: D 456 MET cc_start: 0.8411 (mtp) cc_final: 0.8151 (mtp) REVERT: D 563 GLU cc_start: 0.7508 (pm20) cc_final: 0.6820 (pm20) REVERT: D 598 VAL cc_start: 0.8485 (t) cc_final: 0.8233 (p) REVERT: D 599 LYS cc_start: 0.8208 (mppt) cc_final: 0.7971 (mppt) REVERT: D 660 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7716 (pp) REVERT: E 456 MET cc_start: 0.8232 (mtp) cc_final: 0.7815 (mtp) REVERT: E 563 GLU cc_start: 0.7500 (pm20) cc_final: 0.6714 (pm20) REVERT: E 660 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7645 (pp) REVERT: F 128 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7736 (ttpp) REVERT: F 563 GLU cc_start: 0.7491 (pm20) cc_final: 0.6718 (pm20) REVERT: F 598 VAL cc_start: 0.8332 (t) cc_final: 0.8087 (m) REVERT: F 660 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7791 (pp) REVERT: G 180 ASP cc_start: 0.7463 (t0) cc_final: 0.7191 (t0) REVERT: G 456 MET cc_start: 0.7946 (mtp) cc_final: 0.7736 (mtp) REVERT: G 563 GLU cc_start: 0.7637 (pm20) cc_final: 0.6905 (pm20) REVERT: G 660 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7745 (pp) REVERT: H 413 TYR cc_start: 0.8632 (m-80) cc_final: 0.8392 (m-80) REVERT: H 456 MET cc_start: 0.8206 (mtp) cc_final: 0.7828 (mtp) REVERT: H 563 GLU cc_start: 0.7487 (pm20) cc_final: 0.6762 (pm20) REVERT: H 598 VAL cc_start: 0.8409 (t) cc_final: 0.8176 (m) REVERT: H 660 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7759 (pp) outliers start: 172 outliers final: 129 residues processed: 715 average time/residue: 0.6005 time to fit residues: 681.2879 Evaluate side-chains 729 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 592 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 644 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 605 ASP Chi-restraints excluded: chain E residue 644 ASP Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 644 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 471 ASP Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 644 ASP Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 10.0000 chunk 203 optimal weight: 0.8980 chunk 303 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 323 optimal weight: 5.9990 chunk 346 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 400 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN C 210 HIS ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 133 GLN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43184 Z= 0.225 Angle : 0.572 7.400 58672 Z= 0.292 Chirality : 0.045 0.153 6120 Planarity : 0.004 0.044 7672 Dihedral : 5.884 51.558 6168 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.02 % Allowed : 14.69 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.07 (0.12), residues: 5280 helix: 0.73 (0.15), residues: 1288 sheet: -1.03 (0.18), residues: 824 loop : 0.01 (0.12), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 566 HIS 0.009 0.001 HIS A 394 PHE 0.019 0.002 PHE A 325 TYR 0.021 0.002 TYR H 132 ARG 0.004 0.000 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 590 time to evaluate : 4.790 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: A 456 MET cc_start: 0.8342 (mtp) cc_final: 0.7843 (mtp) REVERT: A 563 GLU cc_start: 0.7447 (pm20) cc_final: 0.6764 (pm20) REVERT: A 598 VAL cc_start: 0.8525 (t) cc_final: 0.8274 (p) REVERT: A 599 LYS cc_start: 0.8258 (mppt) cc_final: 0.8017 (mppt) REVERT: A 660 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7746 (pp) REVERT: B 128 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7746 (ttpp) REVERT: B 413 TYR cc_start: 0.8615 (m-80) cc_final: 0.8387 (m-80) REVERT: B 563 GLU cc_start: 0.7433 (pm20) cc_final: 0.6743 (pm20) REVERT: B 660 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7749 (pp) REVERT: C 563 GLU cc_start: 0.7563 (pm20) cc_final: 0.6851 (pm20) REVERT: C 660 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7718 (pp) REVERT: D 413 TYR cc_start: 0.8677 (m-80) cc_final: 0.8432 (m-80) REVERT: D 456 MET cc_start: 0.8426 (mtp) cc_final: 0.7962 (mtp) REVERT: D 563 GLU cc_start: 0.7447 (pm20) cc_final: 0.6774 (pm20) REVERT: D 598 VAL cc_start: 0.8494 (t) cc_final: 0.8233 (p) REVERT: D 599 LYS cc_start: 0.8217 (mppt) cc_final: 0.7982 (mppt) REVERT: D 660 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7746 (pp) REVERT: E 413 TYR cc_start: 0.8705 (m-80) cc_final: 0.8417 (m-80) REVERT: E 456 MET cc_start: 0.8229 (mtp) cc_final: 0.7980 (mtp) REVERT: E 563 GLU cc_start: 0.7479 (pm20) cc_final: 0.6736 (pm20) REVERT: E 660 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7736 (pp) REVERT: F 128 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7769 (ttpp) REVERT: F 456 MET cc_start: 0.8328 (mtp) cc_final: 0.8021 (mtp) REVERT: F 563 GLU cc_start: 0.7468 (pm20) cc_final: 0.6901 (pm20) REVERT: F 598 VAL cc_start: 0.8336 (t) cc_final: 0.8082 (m) REVERT: F 660 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7800 (pp) REVERT: G 413 TYR cc_start: 0.8690 (m-80) cc_final: 0.8400 (m-80) REVERT: G 456 MET cc_start: 0.8091 (mtp) cc_final: 0.7775 (mtp) REVERT: G 563 GLU cc_start: 0.7581 (pm20) cc_final: 0.6861 (pm20) REVERT: G 660 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7774 (pp) REVERT: H 413 TYR cc_start: 0.8669 (m-80) cc_final: 0.8454 (m-80) REVERT: H 456 MET cc_start: 0.8289 (mtp) cc_final: 0.7822 (mtp) REVERT: H 563 GLU cc_start: 0.7475 (pm20) cc_final: 0.6769 (pm20) REVERT: H 598 VAL cc_start: 0.8407 (t) cc_final: 0.8192 (m) REVERT: H 660 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7678 (pp) outliers start: 180 outliers final: 143 residues processed: 705 average time/residue: 0.5981 time to fit residues: 666.7396 Evaluate side-chains 728 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 577 time to evaluate : 4.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 133 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 644 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 605 ASP Chi-restraints excluded: chain E residue 644 ASP Chi-restraints excluded: chain E residue 658 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 562 THR Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 644 ASP Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 133 GLN Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 471 ASP Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 495 MET Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 644 ASP Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 4.9990 chunk 487 optimal weight: 10.0000 chunk 444 optimal weight: 0.0010 chunk 474 optimal weight: 5.9990 chunk 285 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 372 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 428 optimal weight: 0.9990 chunk 448 optimal weight: 0.8980 chunk 472 optimal weight: 8.9990 overall best weight: 1.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN C 27 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43184 Z= 0.188 Angle : 0.568 7.548 58672 Z= 0.288 Chirality : 0.044 0.153 6120 Planarity : 0.004 0.044 7672 Dihedral : 5.863 52.887 6168 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.79 % Allowed : 14.93 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.04 (0.12), residues: 5280 helix: 0.76 (0.15), residues: 1288 sheet: -1.10 (0.18), residues: 904 loop : 0.10 (0.12), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 566 HIS 0.008 0.001 HIS H 394 PHE 0.016 0.002 PHE D 325 TYR 0.030 0.001 TYR A 132 ARG 0.016 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 587 time to evaluate : 4.589 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: A 456 MET cc_start: 0.8347 (mtp) cc_final: 0.7860 (mtp) REVERT: A 563 GLU cc_start: 0.7451 (pm20) cc_final: 0.6785 (pm20) REVERT: A 598 VAL cc_start: 0.8508 (t) cc_final: 0.8248 (p) REVERT: A 599 LYS cc_start: 0.8290 (mppt) cc_final: 0.8070 (mppt) REVERT: A 660 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7722 (pp) REVERT: B 128 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7746 (ttpp) REVERT: B 413 TYR cc_start: 0.8600 (m-80) cc_final: 0.8379 (m-80) REVERT: B 563 GLU cc_start: 0.7435 (pm20) cc_final: 0.6942 (pm20) REVERT: B 660 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7752 (pp) REVERT: C 563 GLU cc_start: 0.7485 (pm20) cc_final: 0.6811 (pm20) REVERT: C 660 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7706 (pp) REVERT: D 413 TYR cc_start: 0.8699 (m-80) cc_final: 0.8493 (m-80) REVERT: D 456 MET cc_start: 0.8440 (mtp) cc_final: 0.7929 (mtp) REVERT: D 563 GLU cc_start: 0.7538 (pm20) cc_final: 0.6885 (pm20) REVERT: D 598 VAL cc_start: 0.8481 (t) cc_final: 0.8215 (p) REVERT: D 599 LYS cc_start: 0.8258 (mppt) cc_final: 0.8043 (mppt) REVERT: D 660 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7740 (pp) REVERT: E 456 MET cc_start: 0.8212 (mtp) cc_final: 0.7993 (mtp) REVERT: E 563 GLU cc_start: 0.7446 (pm20) cc_final: 0.6680 (pm20) REVERT: E 660 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7695 (pp) REVERT: F 128 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7886 (ttpp) REVERT: F 456 MET cc_start: 0.8355 (mtp) cc_final: 0.8036 (mtp) REVERT: F 563 GLU cc_start: 0.7586 (pm20) cc_final: 0.6901 (pm20) REVERT: F 598 VAL cc_start: 0.8329 (t) cc_final: 0.8081 (m) REVERT: F 660 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7816 (pp) REVERT: G 456 MET cc_start: 0.8095 (mtp) cc_final: 0.7861 (mtp) REVERT: G 563 GLU cc_start: 0.7510 (pm20) cc_final: 0.6753 (pm20) REVERT: G 660 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7746 (pp) REVERT: H 413 TYR cc_start: 0.8660 (m-80) cc_final: 0.8412 (m-80) REVERT: H 456 MET cc_start: 0.8318 (mtp) cc_final: 0.7938 (mtp) REVERT: H 563 GLU cc_start: 0.7485 (pm20) cc_final: 0.6941 (pm20) REVERT: H 598 VAL cc_start: 0.8395 (t) cc_final: 0.8188 (m) REVERT: H 660 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7760 (pp) outliers start: 170 outliers final: 140 residues processed: 690 average time/residue: 0.6050 time to fit residues: 658.0348 Evaluate side-chains 714 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 566 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 644 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 605 ASP Chi-restraints excluded: chain E residue 644 ASP Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 562 THR Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 644 ASP Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 471 ASP Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 495 MET Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 644 ASP Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 10.0000 chunk 501 optimal weight: 5.9990 chunk 306 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 526 optimal weight: 0.9980 chunk 484 optimal weight: 9.9990 chunk 418 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 323 optimal weight: 9.9990 chunk 256 optimal weight: 20.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN C 27 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN D 210 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN E 133 GLN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN G 210 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 210 HIS ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 43184 Z= 0.278 Angle : 0.610 7.975 58672 Z= 0.311 Chirality : 0.046 0.148 6120 Planarity : 0.005 0.045 7672 Dihedral : 6.022 53.980 6168 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.62 % Allowed : 15.22 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.09 (0.12), residues: 5280 helix: 0.72 (0.15), residues: 1280 sheet: -1.08 (0.18), residues: 872 loop : 0.03 (0.12), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 566 HIS 0.010 0.001 HIS B 515 PHE 0.022 0.002 PHE D 325 TYR 0.021 0.002 TYR E 50 ARG 0.004 0.000 ARG C 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 577 time to evaluate : 4.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 MET cc_start: 0.8371 (mtp) cc_final: 0.7977 (mtp) REVERT: A 563 GLU cc_start: 0.7489 (pm20) cc_final: 0.6748 (pm20) REVERT: A 598 VAL cc_start: 0.8538 (t) cc_final: 0.8303 (p) REVERT: A 660 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7786 (pp) REVERT: B 563 GLU cc_start: 0.7639 (pm20) cc_final: 0.6934 (pm20) REVERT: B 660 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7802 (pp) REVERT: C 563 GLU cc_start: 0.7464 (pm20) cc_final: 0.6743 (pm20) REVERT: C 660 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7741 (pp) REVERT: D 413 TYR cc_start: 0.8734 (m-80) cc_final: 0.8530 (m-80) REVERT: D 456 MET cc_start: 0.8520 (mtp) cc_final: 0.8053 (mtp) REVERT: D 563 GLU cc_start: 0.7498 (pm20) cc_final: 0.6820 (pm20) REVERT: D 598 VAL cc_start: 0.8514 (t) cc_final: 0.8256 (p) REVERT: D 599 LYS cc_start: 0.8273 (mppt) cc_final: 0.8048 (mppt) REVERT: D 660 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7743 (pp) REVERT: E 413 TYR cc_start: 0.8725 (m-80) cc_final: 0.8467 (m-80) REVERT: E 456 MET cc_start: 0.8194 (mtp) cc_final: 0.7975 (mtp) REVERT: E 563 GLU cc_start: 0.7477 (pm20) cc_final: 0.6710 (pm20) REVERT: E 660 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7778 (pp) REVERT: F 128 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7884 (ttpp) REVERT: F 456 MET cc_start: 0.8446 (mtp) cc_final: 0.8098 (mtp) REVERT: F 470 MET cc_start: 0.9151 (mtp) cc_final: 0.8894 (mtm) REVERT: F 563 GLU cc_start: 0.7546 (pm20) cc_final: 0.6813 (pm20) REVERT: F 598 VAL cc_start: 0.8260 (t) cc_final: 0.8055 (m) REVERT: F 660 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7772 (pp) REVERT: G 413 TYR cc_start: 0.8696 (m-80) cc_final: 0.8441 (m-80) REVERT: G 563 GLU cc_start: 0.7520 (pm20) cc_final: 0.6732 (pm20) REVERT: G 660 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7754 (pp) REVERT: H 456 MET cc_start: 0.8407 (mtp) cc_final: 0.8067 (mtp) REVERT: H 563 GLU cc_start: 0.7591 (pm20) cc_final: 0.6842 (pm20) REVERT: H 660 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7857 (pp) outliers start: 162 outliers final: 147 residues processed: 677 average time/residue: 0.6091 time to fit residues: 650.5442 Evaluate side-chains 723 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 568 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 605 ASP Chi-restraints excluded: chain A residue 644 ASP Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 108 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 425 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 644 ASP Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 425 SER Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 644 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 644 ASP Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 57 ARG Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 133 GLN Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 425 SER Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 605 ASP Chi-restraints excluded: chain E residue 644 ASP Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 57 ARG Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 425 SER Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 605 ASP Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 57 ARG Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 562 THR Chi-restraints excluded: chain G residue 605 ASP Chi-restraints excluded: chain G residue 644 ASP Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 57 ARG Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 121 ASP Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 425 SER Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 471 ASP Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 495 MET Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 605 ASP Chi-restraints excluded: chain H residue 644 ASP Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 6.9990 chunk 446 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 386 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 419 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 430 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** E 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN G 27 ASN G 189 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 27 ASN H 133 GLN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.137299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.110033 restraints weight = 48978.511| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.78 r_work: 0.2981 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 43184 Z= 0.254 Angle : 0.601 8.261 58672 Z= 0.306 Chirality : 0.045 0.139 6120 Planarity : 0.004 0.046 7672 Dihedral : 6.052 55.137 6168 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.71 % Allowed : 15.33 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % 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: -0.06 (0.12), residues: 5280 helix: 0.69 (0.15), residues: 1280 sheet: -1.00 (0.20), residues: 712 loop : -0.01 (0.11), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP F 566 HIS 0.010 0.001 HIS B 515 PHE 0.020 0.002 PHE D 325 TYR 0.048 0.002 TYR E 132 ARG 0.006 0.000 ARG E 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11840.00 seconds wall clock time: 213 minutes 25.63 seconds (12805.63 seconds total)