Starting phenix.real_space_refine (version: dev) on Wed Dec 21 07:48:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/12_2022/5i68_8072_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/12_2022/5i68_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_8072/12_2022/5i68_8072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/12_2022/5i68_8072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/12_2022/5i68_8072_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i68_8072/12_2022/5i68_8072_updated.pdb" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 22.32, per 1000 atoms: 0.53 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: 16.58 Conformation dependent library (CDL) restraints added in 6.3 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: 5.00 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: 14.53 Time building geometry restraints manager: 17.96 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: 24120 16.40 - 32.79: 1064 32.79 - 49.19: 216 49.19 - 65.58: 16 65.58 - 81.98: 32 Dihedral angle restraints: 25448 sinusoidal: 10272 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 25445 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 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. 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: 0.580 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: 0.040 Extract box with map and model: 5.790 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.410 Process input model: 100.280 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 10.364 81.980 15800 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 1.25 % 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 *********************** 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 : 4.732 Fit side-chains outliers start: 56 outliers final: 12 residues processed: 1191 average time/residue: 0.5764 time to fit residues: 1087.7745 Evaluate side-chains 671 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 659 time to evaluate : 4.955 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4234 time to fit residues: 16.7599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 222 optimal weight: 7.9990 chunk 136 optimal weight: 0.6980 chunk 269 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 413 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 479 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 ** 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 B 541 HIS ** 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 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 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: 0.8090 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 43184 Z= 0.271 Angle : 0.718 10.133 58672 Z= 0.366 Chirality : 0.048 0.151 6120 Planarity : 0.005 0.045 7672 Dihedral : 5.824 33.128 5824 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 2.43 % 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: -0.57 (0.13), residues: 1320 sheet: -0.76 (0.20), residues: 696 loop : 0.11 (0.11), residues: 3264 *********************** 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 831 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 722 time to evaluate : 5.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 46 residues processed: 796 average time/residue: 0.5639 time to fit residues: 722.1108 Evaluate side-chains 649 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 603 time to evaluate : 4.774 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.3749 time to fit residues: 39.2958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 399 optimal weight: 8.9990 chunk 326 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 480 optimal weight: 20.0000 chunk 518 optimal weight: 1.9990 chunk 427 optimal weight: 4.9990 chunk 476 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 385 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 561 HIS B 27 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 HIS C 27 ASN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 HIS D 27 ASN D 430 HIS ** D 508 ASN ** 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 E 515 HIS E 561 HIS F 27 ASN ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 HIS F 561 HIS G 27 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 561 HIS H 27 ASN ** 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 561 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 43184 Z= 0.280 Angle : 0.659 10.168 58672 Z= 0.337 Chirality : 0.047 0.156 6120 Planarity : 0.005 0.039 7672 Dihedral : 5.482 33.389 5824 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 3.01 % 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: -0.25 (0.12), residues: 5280 helix: 0.02 (0.14), residues: 1288 sheet: -0.85 (0.20), residues: 696 loop : 0.03 (0.11), residues: 3296 *********************** 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 798 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 663 time to evaluate : 4.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 61 residues processed: 763 average time/residue: 0.6111 time to fit residues: 733.8978 Evaluate side-chains 653 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 592 time to evaluate : 5.191 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.4431 time to fit residues: 55.1525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 249 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 322 optimal weight: 7.9990 chunk 482 optimal weight: 10.0000 chunk 510 optimal weight: 6.9990 chunk 251 optimal weight: 0.1980 chunk 456 optimal weight: 0.2980 chunk 137 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 HIS C 508 ASN C 515 HIS ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 HIS ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN E 515 HIS ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 HIS ** G 215 ASN ** 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 ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 430 HIS ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 43184 Z= 0.145 Angle : 0.569 9.703 58672 Z= 0.285 Chirality : 0.044 0.151 6120 Planarity : 0.004 0.039 7672 Dihedral : 5.024 34.097 5824 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.72 % 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: 0.53 (0.15), residues: 1240 sheet: -0.78 (0.19), residues: 744 loop : 0.14 (0.11), residues: 3296 *********************** 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 745 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 668 time to evaluate : 4.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 38 residues processed: 732 average time/residue: 0.5889 time to fit residues: 680.1034 Evaluate side-chains 600 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 562 time to evaluate : 4.727 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4562 time to fit residues: 36.7524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 20.0000 chunk 289 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 380 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 435 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 458 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 27 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN E 27 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 43184 Z= 0.289 Angle : 0.632 10.071 58672 Z= 0.322 Chirality : 0.047 0.153 6120 Planarity : 0.005 0.045 7672 Dihedral : 5.164 32.680 5824 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 2.54 % 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: -0.19 (0.12), residues: 5280 helix: 0.37 (0.15), residues: 1288 sheet: -1.02 (0.20), residues: 704 loop : -0.02 (0.11), residues: 3288 *********************** 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 705 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 591 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 61 residues processed: 662 average time/residue: 0.6052 time to fit residues: 631.4131 Evaluate side-chains 627 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 566 time to evaluate : 4.757 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.4051 time to fit residues: 51.9279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 8.9990 chunk 459 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 299 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 510 optimal weight: 0.9980 chunk 424 optimal weight: 0.0570 chunk 236 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 overall best weight: 3.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN B 142 HIS ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN B 612 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN E 142 HIS E 210 HIS ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN H 210 HIS ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 43184 Z= 0.264 Angle : 0.606 10.025 58672 Z= 0.307 Chirality : 0.045 0.141 6120 Planarity : 0.005 0.047 7672 Dihedral : 5.120 32.422 5824 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.83 % 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: -0.23 (0.12), residues: 5280 helix: 0.52 (0.15), residues: 1280 sheet: -1.06 (0.18), residues: 824 loop : -0.08 (0.11), residues: 3176 *********************** 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 677 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 595 time to evaluate : 4.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 38 residues processed: 650 average time/residue: 0.5978 time to fit residues: 615.6329 Evaluate side-chains 610 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 572 time to evaluate : 4.639 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4750 time to fit residues: 37.7644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 10.0000 chunk 57 optimal weight: 0.0870 chunk 291 optimal weight: 10.0000 chunk 373 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 430 optimal weight: 0.8980 chunk 285 optimal weight: 6.9990 chunk 508 optimal weight: 5.9990 chunk 318 optimal weight: 7.9990 chunk 310 optimal weight: 0.9990 chunk 234 optimal weight: 10.0000 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 HIS ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN C 612 ASN ** D 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN D 612 ASN ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN E 612 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN F 612 ASN ** G 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN G 612 ASN ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 612 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 43184 Z= 0.198 Angle : 0.574 9.921 58672 Z= 0.290 Chirality : 0.044 0.138 6120 Planarity : 0.004 0.045 7672 Dihedral : 4.975 32.308 5824 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.18 % 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: -0.16 (0.12), residues: 5280 helix: 0.68 (0.15), residues: 1272 sheet: -1.09 (0.18), residues: 824 loop : -0.06 (0.11), residues: 3184 *********************** 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 653 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 600 time to evaluate : 4.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 26 residues processed: 630 average time/residue: 0.6067 time to fit residues: 608.2020 Evaluate side-chains 599 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 573 time to evaluate : 5.064 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3782 time to fit residues: 25.9231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 303 optimal weight: 5.9990 chunk 153 optimal weight: 0.0070 chunk 99 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 323 optimal weight: 20.0000 chunk 346 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS F 529 ASN G 210 HIS ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 43184 Z= 0.305 Angle : 0.627 10.006 58672 Z= 0.318 Chirality : 0.046 0.152 6120 Planarity : 0.005 0.048 7672 Dihedral : 5.112 32.007 5824 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 1.16 % 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: -0.28 (0.12), residues: 5280 helix: 0.56 (0.15), residues: 1288 sheet: -1.20 (0.17), residues: 872 loop : -0.10 (0.12), residues: 3120 *********************** 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 645 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 593 time to evaluate : 4.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 19 residues processed: 635 average time/residue: 0.5956 time to fit residues: 600.9405 Evaluate side-chains 582 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 563 time to evaluate : 4.724 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3709 time to fit residues: 19.9465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 10.0000 chunk 487 optimal weight: 8.9990 chunk 444 optimal weight: 0.4980 chunk 474 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 372 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 428 optimal weight: 4.9990 chunk 448 optimal weight: 7.9990 chunk 472 optimal weight: 8.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 43184 Z= 0.309 Angle : 0.638 10.065 58672 Z= 0.324 Chirality : 0.047 0.156 6120 Planarity : 0.005 0.048 7672 Dihedral : 5.164 32.208 5824 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.65 % 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: -0.48 (0.12), residues: 5280 helix: 0.29 (0.15), residues: 1360 sheet: -1.25 (0.17), residues: 872 loop : -0.21 (0.12), residues: 3048 *********************** 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 615 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 586 time to evaluate : 4.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 605 average time/residue: 0.6162 time to fit residues: 592.0606 Evaluate side-chains 583 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 565 time to evaluate : 4.935 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3855 time to fit residues: 20.1056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 9.9990 chunk 501 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 chunk 237 optimal weight: 0.9980 chunk 348 optimal weight: 10.0000 chunk 526 optimal weight: 2.9990 chunk 484 optimal weight: 6.9990 chunk 418 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 323 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS B 529 ASN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 430 HIS ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 43184 Z= 0.176 Angle : 0.571 9.745 58672 Z= 0.287 Chirality : 0.044 0.136 6120 Planarity : 0.004 0.045 7672 Dihedral : 4.854 33.294 5824 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 0.11 % 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: -0.30 (0.12), residues: 5280 helix: 0.57 (0.15), residues: 1328 sheet: -1.16 (0.18), residues: 824 loop : -0.17 (0.11), residues: 3128 ********************** 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 607 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 602 time to evaluate : 5.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 607 average time/residue: 0.6187 time to fit residues: 596.9056 Evaluate side-chains 554 residues out of total 4480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 552 time to evaluate : 4.489 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3923 time to fit residues: 7.7918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 5.9990 chunk 446 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 386 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 419 optimal weight: 6.9990 chunk 175 optimal weight: 0.0570 chunk 430 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** 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** ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 189 HIS ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.147832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.121678 restraints weight = 47841.685| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.74 r_work: 0.3030 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 43184 Z= 0.163 Angle : 0.576 10.625 58672 Z= 0.289 Chirality : 0.044 0.177 6120 Planarity : 0.004 0.045 7672 Dihedral : 4.779 33.347 5824 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 0.31 % 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: -0.23 (0.12), residues: 5280 helix: 0.63 (0.15), residues: 1328 sheet: -1.06 (0.18), residues: 824 loop : -0.14 (0.11), residues: 3128 =============================================================================== Job complete usr+sys time: 11089.20 seconds wall clock time: 201 minutes 45.26 seconds (12105.26 seconds total)