Starting phenix.real_space_refine on Sat Feb 17 01:46:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_2024/6xgc_22180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_2024/6xgc_22180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_2024/6xgc_22180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_2024/6xgc_22180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_2024/6xgc_22180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_2024/6xgc_22180.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 10668 2.51 5 N 2916 2.21 5 O 3387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17040 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2528 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "B" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "M" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "N" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2528 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "D" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "E" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2528 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 18, 'TRANS': 304} Chain: "F" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 1, 'TRANS': 162} Chain: "I" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 925 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "J" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 790 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.72, per 1000 atoms: 0.51 Number of scatterers: 17040 At special positions: 0 Unit cell: (124.962, 131.316, 150.378, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 3387 8.00 N 2916 7.00 C 10668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.08 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 285 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 146 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 29 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=1.96 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 285 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 313 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 29 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.06 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 285 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 100 " - pdb=" SG CYS E 146 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 313 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 29 " - pdb=" SG CYS J 96 " distance=2.03 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 403 " - " ASN A 286 " " NAG A 404 " - " ASN A 297 " " NAG A 405 " - " ASN A 33 " " NAG A 406 " - " ASN A 21 " " NAG B 301 " - " ASN B 154 " " NAG C 403 " - " ASN C 286 " " NAG C 404 " - " ASN C 297 " " NAG C 405 " - " ASN C 33 " " NAG C 406 " - " ASN C 21 " " NAG D 301 " - " ASN D 154 " " NAG E 403 " - " ASN E 286 " " NAG E 404 " - " ASN E 297 " " NAG E 405 " - " ASN E 33 " " NAG E 406 " - " ASN E 21 " " NAG F 301 " - " ASN F 154 " " NAG G 1 " - " ASN A 97 " " NAG K 1 " - " ASN C 97 " " NAG O 1 " - " ASN E 97 " Time building additional restraints: 6.26 Conformation dependent library (CDL) restraints added in 2.9 seconds 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 54 sheets defined 19.9% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 158 through 171 removed outlier: 4.003A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 32 through 37 removed outlier: 3.742A pdb=" N GLY N 37 " --> pdb=" O SER N 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 72 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'D' and resid 37 through 58 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 158 through 171 removed outlier: 4.002A pdb=" N TYR D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU D 165 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 32 through 37 removed outlier: 3.744A pdb=" N GLY L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 72 Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 158 through 171 removed outlier: 4.002A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 32 through 37 removed outlier: 3.743A pdb=" N GLY J 37 " --> pdb=" O SER J 33 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 removed outlier: 4.104A pdb=" N GLY B 23 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 53 removed outlier: 5.930A pdb=" N LEU A 51 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS A 285 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 61 removed outlier: 6.553A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 89 " --> pdb=" O ILE A 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 122 through 124 removed outlier: 8.041A pdb=" N LEU A 186 " --> pdb=" O PRO A 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'A' and resid 143 through 148 removed outlier: 4.649A pdb=" N CYS A 146 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 171 through 176 Processing sheet with id=AB2, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.686A pdb=" N CYS A 289 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.882A pdb=" N THR B 64 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'M' and resid 10 through 11 removed outlier: 6.438A pdb=" N GLY M 10 " --> pdb=" O THR M 124 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 100 through 104 removed outlier: 3.670A pdb=" N GLY M 100 " --> pdb=" O ASN M 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 16 through 18 removed outlier: 6.417A pdb=" N TRP N 43 " --> pdb=" O LEU N 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 16 through 18 Processing sheet with id=AB9, first strand: chain 'N' and resid 25 through 30 Processing sheet with id=AC1, first strand: chain 'D' and resid 31 through 36 removed outlier: 4.170A pdb=" N GLY D 23 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 53 removed outlier: 5.930A pdb=" N LEU C 51 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N CYS C 285 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.552A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 89 " --> pdb=" O ILE C 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 122 through 124 removed outlier: 8.039A pdb=" N LEU C 186 " --> pdb=" O PRO C 261 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 122 through 124 Processing sheet with id=AC9, first strand: chain 'C' and resid 143 through 148 removed outlier: 4.649A pdb=" N CYS C 146 " --> pdb=" O SER C 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 171 through 176 Processing sheet with id=AD2, first strand: chain 'C' and resid 289 through 290 removed outlier: 3.686A pdb=" N CYS C 289 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 310 through 311 removed outlier: 3.972A pdb=" N THR D 64 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.439A pdb=" N GLY H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 100 through 104 removed outlier: 3.668A pdb=" N GLY H 100 " --> pdb=" O ASN H 111 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 16 through 18 removed outlier: 6.416A pdb=" N TRP L 43 " --> pdb=" O LEU L 55 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 16 through 18 Processing sheet with id=AD9, first strand: chain 'L' and resid 25 through 30 Processing sheet with id=AE1, first strand: chain 'F' and resid 31 through 36 removed outlier: 4.086A pdb=" N GLY F 23 " --> pdb=" O GLY E 16 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 25 through 26 Processing sheet with id=AE3, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AE4, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AE5, first strand: chain 'E' and resid 51 through 53 removed outlier: 5.931A pdb=" N LEU E 51 " --> pdb=" O HIS E 283 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS E 285 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.552A pdb=" N LEU E 60 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE E 89 " --> pdb=" O ILE E 276 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 122 through 124 removed outlier: 8.041A pdb=" N LEU E 186 " --> pdb=" O PRO E 261 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AE9, first strand: chain 'E' and resid 143 through 148 removed outlier: 4.649A pdb=" N CYS E 146 " --> pdb=" O SER E 153 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 171 through 176 Processing sheet with id=AF2, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.687A pdb=" N CYS E 289 " --> pdb=" O ILE E 296 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 310 through 311 removed outlier: 3.868A pdb=" N THR F 64 " --> pdb=" O GLY E 311 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.438A pdb=" N GLY I 10 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 100 through 104 removed outlier: 3.671A pdb=" N GLY I 100 " --> pdb=" O ASN I 111 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 16 through 18 removed outlier: 6.415A pdb=" N TRP J 43 " --> pdb=" O LEU J 55 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 16 through 18 Processing sheet with id=AF9, first strand: chain 'J' and resid 25 through 30 738 hydrogen bonds defined for protein. 1926 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: 5.81 Time building geometry restraints manager: 6.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5547 1.34 - 1.46: 3563 1.46 - 1.58: 8218 1.58 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 17418 Sorted by residual: bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG A 403 " pdb=" O5 NAG A 403 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 ... (remaining 17413 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.10: 476 107.10 - 113.82: 9782 113.82 - 120.54: 6392 120.54 - 127.27: 6750 127.27 - 133.99: 216 Bond angle restraints: 23616 Sorted by residual: angle pdb=" C LEU F 126 " pdb=" N LYS F 127 " pdb=" CA LYS F 127 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.72e+00 angle pdb=" C LEU D 126 " pdb=" N LYS D 127 " pdb=" CA LYS D 127 " ideal model delta sigma weight residual 121.54 126.07 -4.53 1.91e+00 2.74e-01 5.62e+00 angle pdb=" C LEU B 126 " pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 121.54 126.00 -4.46 1.91e+00 2.74e-01 5.45e+00 angle pdb=" C GLY E 165 " pdb=" N ASN E 166 " pdb=" CA ASN E 166 " ideal model delta sigma weight residual 121.54 125.25 -3.71 1.91e+00 2.74e-01 3.78e+00 angle pdb=" C GLY C 165 " pdb=" N ASN C 166 " pdb=" CA ASN C 166 " ideal model delta sigma weight residual 121.54 125.24 -3.70 1.91e+00 2.74e-01 3.75e+00 ... (remaining 23611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 10266 17.31 - 34.63: 270 34.63 - 51.94: 60 51.94 - 69.25: 3 69.25 - 86.57: 9 Dihedral angle restraints: 10608 sinusoidal: 4437 harmonic: 6171 Sorted by residual: dihedral pdb=" CB GLU C 109 " pdb=" CG GLU C 109 " pdb=" CD GLU C 109 " pdb=" OE1 GLU C 109 " ideal model delta sinusoidal sigma weight residual 0.00 -86.57 86.57 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU A 109 " pdb=" CG GLU A 109 " pdb=" CD GLU A 109 " pdb=" OE1 GLU A 109 " ideal model delta sinusoidal sigma weight residual 0.00 -86.56 86.56 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU E 109 " pdb=" CG GLU E 109 " pdb=" CD GLU E 109 " pdb=" OE1 GLU E 109 " ideal model delta sinusoidal sigma weight residual 0.00 -86.54 86.54 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 10605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1561 0.025 - 0.050: 664 0.050 - 0.076: 174 0.076 - 0.101: 108 0.101 - 0.126: 115 Chirality restraints: 2622 Sorted by residual: chirality pdb=" CA ILE A 176 " pdb=" N ILE A 176 " pdb=" C ILE A 176 " pdb=" CB ILE A 176 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" C1 NAG C 406 " pdb=" ND2 ASN C 21 " pdb=" C2 NAG C 406 " pdb=" O5 NAG C 406 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE E 176 " pdb=" N ILE E 176 " pdb=" C ILE E 176 " pdb=" CB ILE E 176 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 2619 not shown) Planarity restraints: 3045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 291 " -0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 292 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 291 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO E 292 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 292 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 292 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 291 " 0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO C 292 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 292 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 292 " 0.019 5.00e-02 4.00e+02 ... (remaining 3042 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1694 2.75 - 3.29: 15900 3.29 - 3.83: 28382 3.83 - 4.36: 31425 4.36 - 4.90: 56507 Nonbonded interactions: 133908 Sorted by model distance: nonbonded pdb=" OG SER J 73 " pdb=" OG SER J 80 " model vdw 2.215 2.440 nonbonded pdb=" OG SER N 73 " pdb=" OG SER N 80 " model vdw 2.216 2.440 nonbonded pdb=" OG SER L 73 " pdb=" OG SER L 80 " model vdw 2.217 2.440 nonbonded pdb=" O TYR B 159 " pdb=" OG SER B 163 " model vdw 2.286 2.440 nonbonded pdb=" O TYR D 159 " pdb=" OG SER D 163 " model vdw 2.287 2.440 ... (remaining 133903 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 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: 0.000 Extract box with map and model: 6.300 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 44.400 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.002 0.030 17418 Z= 0.151 Angle : 0.433 4.712 23616 Z= 0.235 Chirality : 0.040 0.126 2622 Planarity : 0.003 0.034 3027 Dihedral : 8.174 86.567 6612 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.16 % Allowed : 3.64 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 2133 helix: 4.15 (0.25), residues: 351 sheet: 1.15 (0.24), residues: 519 loop : -0.06 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 133 HIS 0.004 0.000 HIS H 35 PHE 0.005 0.001 PHE A 121 TYR 0.007 0.001 TYR F 94 ARG 0.002 0.000 ARG I 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 742 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9253 (mt) cc_final: 0.8983 (mp) REVERT: A 300 LEU cc_start: 0.8719 (mt) cc_final: 0.8295 (mt) REVERT: B 17 MET cc_start: 0.8247 (ttp) cc_final: 0.8013 (ttp) REVERT: B 19 ASP cc_start: 0.8801 (p0) cc_final: 0.8547 (p0) REVERT: B 26 HIS cc_start: 0.7671 (p90) cc_final: 0.7433 (p90) REVERT: B 38 LEU cc_start: 0.8215 (mt) cc_final: 0.7929 (mt) REVERT: B 90 ASP cc_start: 0.6534 (m-30) cc_final: 0.6107 (m-30) REVERT: B 99 LEU cc_start: 0.8449 (tp) cc_final: 0.8242 (tp) REVERT: B 147 THR cc_start: 0.8874 (m) cc_final: 0.8636 (p) REVERT: M 36 TRP cc_start: 0.8377 (m100) cc_final: 0.7694 (m100) REVERT: M 47 TRP cc_start: 0.8490 (t60) cc_final: 0.8280 (t60) REVERT: M 48 ILE cc_start: 0.8494 (mm) cc_final: 0.6760 (mm) REVERT: N 105 ASN cc_start: 0.7580 (m-40) cc_final: 0.7189 (m110) REVERT: C 204 ASN cc_start: 0.8741 (m-40) cc_final: 0.8500 (m-40) REVERT: C 230 VAL cc_start: 0.8622 (t) cc_final: 0.8416 (p) REVERT: C 262 ARG cc_start: 0.8385 (ttt180) cc_final: 0.8144 (ttt-90) REVERT: C 263 TYR cc_start: 0.7903 (m-80) cc_final: 0.7635 (m-80) REVERT: D 26 HIS cc_start: 0.7970 (p90) cc_final: 0.7302 (p90) REVERT: D 138 PHE cc_start: 0.8338 (m-80) cc_final: 0.8077 (m-80) REVERT: D 147 THR cc_start: 0.8975 (m) cc_final: 0.8541 (p) REVERT: H 36 TRP cc_start: 0.8464 (m100) cc_final: 0.8224 (m100) REVERT: H 48 ILE cc_start: 0.8495 (mm) cc_final: 0.8277 (mm) REVERT: H 94 TYR cc_start: 0.7169 (m-80) cc_final: 0.6966 (m-10) REVERT: L 93 ASP cc_start: 0.8351 (m-30) cc_final: 0.8081 (m-30) REVERT: L 113 ARG cc_start: 0.6793 (tpp80) cc_final: 0.6521 (tpp-160) REVERT: E 204 ASN cc_start: 0.8576 (m-40) cc_final: 0.8361 (m110) REVERT: F 26 HIS cc_start: 0.8135 (p90) cc_final: 0.7558 (p90) REVERT: F 27 GLN cc_start: 0.8415 (tt0) cc_final: 0.8215 (tm-30) REVERT: F 99 LEU cc_start: 0.8120 (tp) cc_final: 0.7503 (tt) REVERT: F 114 ASN cc_start: 0.8663 (m-40) cc_final: 0.8396 (m110) REVERT: I 34 MET cc_start: 0.7986 (mmm) cc_final: 0.7439 (mmt) REVERT: I 47 TRP cc_start: 0.8378 (t60) cc_final: 0.8111 (t60) outliers start: 3 outliers final: 3 residues processed: 745 average time/residue: 0.2979 time to fit residues: 324.2247 Evaluate side-chains 406 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 403 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 0.0270 chunk 190 optimal weight: 0.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 238 ASN A 290 GLN B 125 GLN B 129 ASN M 39 GLN ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN ** N 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 GLN C 148 HIS C 238 ASN C 257 ASN C 290 GLN D 114 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN J 46 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17418 Z= 0.231 Angle : 0.562 5.951 23616 Z= 0.293 Chirality : 0.043 0.224 2622 Planarity : 0.004 0.073 3027 Dihedral : 5.460 49.751 2760 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.22 % Allowed : 1.85 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 2133 helix: 3.42 (0.25), residues: 360 sheet: 1.21 (0.23), residues: 495 loop : -0.13 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 43 HIS 0.011 0.001 HIS I 35 PHE 0.020 0.002 PHE A 210 TYR 0.016 0.001 TYR M 94 ARG 0.004 0.001 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 506 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 TYR cc_start: 0.8275 (m-80) cc_final: 0.8068 (m-80) REVERT: A 236 ARG cc_start: 0.8132 (mmt-90) cc_final: 0.7922 (mmt-90) REVERT: B 17 MET cc_start: 0.8385 (ttp) cc_final: 0.8113 (ttp) REVERT: B 19 ASP cc_start: 0.8771 (p0) cc_final: 0.8509 (p0) REVERT: B 90 ASP cc_start: 0.6989 (m-30) cc_final: 0.6243 (m-30) REVERT: M 36 TRP cc_start: 0.8436 (m100) cc_final: 0.7369 (m100) REVERT: M 46 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7249 (tm-30) REVERT: M 47 TRP cc_start: 0.8601 (t60) cc_final: 0.8341 (t60) REVERT: M 87 ARG cc_start: 0.7249 (ptp-110) cc_final: 0.6917 (mtm-85) REVERT: M 90 ASP cc_start: 0.8297 (m-30) cc_final: 0.7989 (m-30) REVERT: M 99 ASP cc_start: 0.7808 (m-30) cc_final: 0.7449 (m-30) REVERT: N 105 ASN cc_start: 0.7707 (m-40) cc_final: 0.7407 (m-40) REVERT: C 204 ASN cc_start: 0.8975 (m-40) cc_final: 0.8605 (m-40) REVERT: D 114 ASN cc_start: 0.8766 (m-40) cc_final: 0.8252 (m-40) REVERT: D 147 THR cc_start: 0.9171 (m) cc_final: 0.8721 (p) REVERT: H 36 TRP cc_start: 0.8419 (m100) cc_final: 0.7793 (m100) REVERT: H 48 ILE cc_start: 0.8622 (mm) cc_final: 0.7522 (mm) REVERT: H 82 GLN cc_start: 0.6912 (tp40) cc_final: 0.6670 (tm-30) REVERT: H 83 MET cc_start: 0.7820 (mtt) cc_final: 0.7186 (mtt) REVERT: H 87 ARG cc_start: 0.7964 (mtp85) cc_final: 0.7525 (mtm-85) REVERT: H 94 TYR cc_start: 0.7397 (m-80) cc_final: 0.6948 (m-10) REVERT: L 43 TRP cc_start: 0.7798 (m100) cc_final: 0.7533 (m100) REVERT: E 262 ARG cc_start: 0.8419 (ttt180) cc_final: 0.8149 (ttt-90) REVERT: F 17 MET cc_start: 0.8387 (tmm) cc_final: 0.8005 (tmm) REVERT: F 26 HIS cc_start: 0.8350 (p90) cc_final: 0.7446 (p90) REVERT: F 114 ASN cc_start: 0.8822 (m-40) cc_final: 0.8352 (m110) REVERT: I 6 GLU cc_start: 0.8549 (mp0) cc_final: 0.8283 (mp0) REVERT: I 34 MET cc_start: 0.8174 (mmm) cc_final: 0.7481 (mmt) REVERT: I 47 TRP cc_start: 0.8481 (t60) cc_final: 0.8120 (t60) REVERT: I 48 ILE cc_start: 0.8803 (mm) cc_final: 0.7354 (mm) REVERT: I 82 GLN cc_start: 0.7305 (tp40) cc_final: 0.6915 (tm-30) REVERT: J 93 ASP cc_start: 0.8527 (m-30) cc_final: 0.7433 (p0) REVERT: J 94 TYR cc_start: 0.7902 (m-10) cc_final: 0.7669 (m-10) outliers start: 4 outliers final: 0 residues processed: 508 average time/residue: 0.2770 time to fit residues: 214.2152 Evaluate side-chains 366 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 366 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 0.0020 chunk 189 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 chunk 153 optimal weight: 4.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 283 HIS A 290 GLN B 125 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN N 46 GLN N 87 GLN C 136 HIS C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN E 257 ASN E 283 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17418 Z= 0.214 Angle : 0.555 12.922 23616 Z= 0.292 Chirality : 0.043 0.246 2622 Planarity : 0.004 0.055 3027 Dihedral : 5.378 58.309 2760 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.18), residues: 2133 helix: 2.89 (0.25), residues: 357 sheet: 1.21 (0.24), residues: 489 loop : -0.32 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 241 HIS 0.012 0.001 HIS I 35 PHE 0.036 0.002 PHE C 105 TYR 0.014 0.001 TYR D 141 ARG 0.005 0.001 ARG E 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 479 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.8313 (ttp) cc_final: 0.7969 (ttp) REVERT: B 19 ASP cc_start: 0.8721 (p0) cc_final: 0.8381 (p0) REVERT: B 27 GLN cc_start: 0.8314 (tp40) cc_final: 0.7917 (tp-100) REVERT: B 28 ASN cc_start: 0.8618 (p0) cc_final: 0.8264 (p0) REVERT: B 32 SER cc_start: 0.8883 (p) cc_final: 0.8678 (p) REVERT: M 36 TRP cc_start: 0.8263 (m100) cc_final: 0.7584 (m100) REVERT: M 47 TRP cc_start: 0.8642 (t60) cc_final: 0.8350 (t60) REVERT: M 48 ILE cc_start: 0.8595 (mm) cc_final: 0.8248 (mm) REVERT: M 82 GLN cc_start: 0.7297 (tm-30) cc_final: 0.6833 (tm-30) REVERT: M 90 ASP cc_start: 0.8129 (m-30) cc_final: 0.7643 (m-30) REVERT: M 99 ASP cc_start: 0.7778 (m-30) cc_final: 0.7478 (m-30) REVERT: N 46 GLN cc_start: 0.8415 (tt0) cc_final: 0.8058 (tt0) REVERT: N 56 ILE cc_start: 0.8559 (mm) cc_final: 0.8214 (tt) REVERT: C 204 ASN cc_start: 0.9074 (m-40) cc_final: 0.8570 (m-40) REVERT: C 262 ARG cc_start: 0.8623 (ttt180) cc_final: 0.8318 (ttt-90) REVERT: C 330 ASN cc_start: 0.8719 (t0) cc_final: 0.8512 (t0) REVERT: D 78 GLU cc_start: 0.7865 (tp30) cc_final: 0.7592 (tp30) REVERT: D 147 THR cc_start: 0.9187 (m) cc_final: 0.8822 (p) REVERT: H 36 TRP cc_start: 0.8344 (m100) cc_final: 0.7809 (m100) REVERT: H 82 GLN cc_start: 0.7053 (tp40) cc_final: 0.6692 (tm-30) REVERT: H 83 MET cc_start: 0.7919 (mtt) cc_final: 0.7505 (mtt) REVERT: H 90 ASP cc_start: 0.8212 (m-30) cc_final: 0.7743 (m-30) REVERT: L 27 ILE cc_start: 0.9053 (mt) cc_final: 0.8750 (mt) REVERT: L 43 TRP cc_start: 0.7789 (m100) cc_final: 0.7373 (m-10) REVERT: L 46 GLN cc_start: 0.8500 (tp40) cc_final: 0.8264 (tp-100) REVERT: L 81 LEU cc_start: 0.8907 (tp) cc_final: 0.7871 (tp) REVERT: L 93 ASP cc_start: 0.8127 (m-30) cc_final: 0.7691 (m-30) REVERT: F 17 MET cc_start: 0.8486 (tmm) cc_final: 0.8114 (tmm) REVERT: F 32 SER cc_start: 0.8410 (p) cc_final: 0.8184 (p) REVERT: F 114 ASN cc_start: 0.8909 (m-40) cc_final: 0.8443 (m110) REVERT: I 6 GLU cc_start: 0.8555 (mp0) cc_final: 0.8327 (mp0) REVERT: I 34 MET cc_start: 0.8023 (mmm) cc_final: 0.7572 (mmt) REVERT: I 46 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7356 (tm-30) REVERT: I 47 TRP cc_start: 0.8458 (t60) cc_final: 0.8186 (t60) REVERT: I 48 ILE cc_start: 0.8916 (mm) cc_final: 0.8268 (mm) REVERT: I 82 GLN cc_start: 0.7479 (tp40) cc_final: 0.6806 (tm-30) REVERT: I 90 ASP cc_start: 0.8071 (m-30) cc_final: 0.7821 (m-30) REVERT: J 43 TRP cc_start: 0.8022 (m100) cc_final: 0.7669 (m100) outliers start: 2 outliers final: 0 residues processed: 480 average time/residue: 0.2628 time to fit residues: 192.7408 Evaluate side-chains 353 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN C 290 GLN D 125 GLN H 39 GLN L 40 HIS ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 283 HIS E 290 GLN F 125 GLN F 142 HIS ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 46 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 17418 Z= 0.221 Angle : 0.566 10.199 23616 Z= 0.298 Chirality : 0.043 0.213 2622 Planarity : 0.004 0.054 3027 Dihedral : 5.127 57.237 2760 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.16 % Allowed : 1.63 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 2133 helix: 2.37 (0.26), residues: 357 sheet: 1.09 (0.23), residues: 492 loop : -0.48 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 47 HIS 0.014 0.001 HIS H 35 PHE 0.027 0.002 PHE C 105 TYR 0.025 0.002 TYR I 112 ARG 0.006 0.001 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 449 time to evaluate : 2.038 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: A 237 MET cc_start: 0.8795 (tpp) cc_final: 0.8579 (mmt) REVERT: B 17 MET cc_start: 0.8314 (ttp) cc_final: 0.8021 (ttp) REVERT: B 19 ASP cc_start: 0.8851 (p0) cc_final: 0.8539 (p0) REVERT: B 27 GLN cc_start: 0.8287 (tp40) cc_final: 0.7875 (tp-100) REVERT: B 28 ASN cc_start: 0.8792 (p0) cc_final: 0.8315 (p0) REVERT: B 32 SER cc_start: 0.8925 (p) cc_final: 0.8476 (p) REVERT: B 133 ILE cc_start: 0.8927 (mt) cc_final: 0.8636 (mm) REVERT: M 36 TRP cc_start: 0.8188 (m100) cc_final: 0.7639 (m100) REVERT: M 46 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7466 (tm-30) REVERT: M 47 TRP cc_start: 0.8618 (t60) cc_final: 0.8349 (t60) REVERT: M 82 GLN cc_start: 0.7359 (tm-30) cc_final: 0.7024 (tm-30) REVERT: M 87 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7532 (mtm-85) REVERT: M 90 ASP cc_start: 0.8156 (m-30) cc_final: 0.7759 (m-30) REVERT: M 99 ASP cc_start: 0.8112 (m-30) cc_final: 0.7682 (m-30) REVERT: N 46 GLN cc_start: 0.8182 (tt0) cc_final: 0.7979 (tp40) REVERT: N 93 ASP cc_start: 0.8104 (m-30) cc_final: 0.7159 (p0) REVERT: N 94 TYR cc_start: 0.7624 (m-10) cc_final: 0.7352 (m-10) REVERT: C 108 TYR cc_start: 0.7568 (t80) cc_final: 0.7360 (t80) REVERT: C 204 ASN cc_start: 0.8896 (m-40) cc_final: 0.8536 (m-40) REVERT: C 330 ASN cc_start: 0.8733 (t0) cc_final: 0.8500 (t0) REVERT: D 37 ASP cc_start: 0.8299 (m-30) cc_final: 0.7923 (m-30) REVERT: D 114 ASN cc_start: 0.8816 (m-40) cc_final: 0.8498 (m-40) REVERT: D 147 THR cc_start: 0.9181 (m) cc_final: 0.8925 (p) REVERT: H 36 TRP cc_start: 0.8243 (m100) cc_final: 0.7672 (m100) REVERT: H 82 GLN cc_start: 0.7204 (tp40) cc_final: 0.6874 (tm-30) REVERT: H 83 MET cc_start: 0.7954 (mtt) cc_final: 0.7563 (mtt) REVERT: H 90 ASP cc_start: 0.8356 (m-30) cc_final: 0.7793 (m-30) REVERT: L 43 TRP cc_start: 0.7506 (m100) cc_final: 0.6346 (m100) REVERT: L 46 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7948 (tp40) REVERT: E 330 ASN cc_start: 0.8573 (t0) cc_final: 0.8345 (t0) REVERT: F 17 MET cc_start: 0.8531 (tmm) cc_final: 0.8218 (tmm) REVERT: F 27 GLN cc_start: 0.8184 (tp40) cc_final: 0.7785 (tp-100) REVERT: F 28 ASN cc_start: 0.9004 (p0) cc_final: 0.8618 (p0) REVERT: F 114 ASN cc_start: 0.8952 (m-40) cc_final: 0.8712 (m-40) REVERT: F 133 ILE cc_start: 0.8912 (mt) cc_final: 0.8529 (mm) REVERT: I 34 MET cc_start: 0.8131 (mmm) cc_final: 0.7898 (mmt) REVERT: I 46 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7273 (tm-30) REVERT: I 48 ILE cc_start: 0.8970 (mm) cc_final: 0.8472 (mm) REVERT: I 82 GLN cc_start: 0.7616 (tp40) cc_final: 0.6841 (tm-30) REVERT: I 87 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7510 (mtm-85) REVERT: I 90 ASP cc_start: 0.8199 (m-30) cc_final: 0.7927 (m-30) REVERT: J 43 TRP cc_start: 0.8088 (m100) cc_final: 0.7657 (m100) outliers start: 3 outliers final: 0 residues processed: 449 average time/residue: 0.2467 time to fit residues: 173.6474 Evaluate side-chains 338 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 337 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 GLN N 105 ASN C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN E 257 ASN E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 17418 Z= 0.324 Angle : 0.627 10.203 23616 Z= 0.330 Chirality : 0.044 0.215 2622 Planarity : 0.004 0.058 3027 Dihedral : 5.070 40.668 2760 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.27 (0.17), residues: 2133 helix: 1.86 (0.25), residues: 357 sheet: 0.90 (0.22), residues: 522 loop : -0.64 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 47 HIS 0.013 0.001 HIS H 35 PHE 0.018 0.002 PHE C 105 TYR 0.026 0.002 TYR H 112 ARG 0.005 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 410 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ASP cc_start: 0.8796 (p0) cc_final: 0.8511 (p0) REVERT: B 27 GLN cc_start: 0.8386 (tp40) cc_final: 0.8159 (tp-100) REVERT: B 28 ASN cc_start: 0.8944 (p0) cc_final: 0.8353 (p0) REVERT: B 32 SER cc_start: 0.8768 (p) cc_final: 0.8431 (p) REVERT: M 46 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7698 (tm-30) REVERT: M 47 TRP cc_start: 0.8568 (t60) cc_final: 0.8233 (t60) REVERT: M 48 ILE cc_start: 0.8801 (mm) cc_final: 0.8363 (mt) REVERT: M 82 GLN cc_start: 0.7453 (tm-30) cc_final: 0.6988 (tm-30) REVERT: M 87 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7700 (mtm-85) REVERT: M 90 ASP cc_start: 0.8330 (m-30) cc_final: 0.7844 (m-30) REVERT: M 99 ASP cc_start: 0.8399 (m-30) cc_final: 0.8022 (m-30) REVERT: N 36 PHE cc_start: 0.7517 (t80) cc_final: 0.7298 (t80) REVERT: N 99 TRP cc_start: 0.7986 (t-100) cc_final: 0.7170 (t-100) REVERT: N 105 ASN cc_start: 0.7389 (m110) cc_final: 0.6286 (m110) REVERT: C 204 ASN cc_start: 0.8863 (m-40) cc_final: 0.8436 (m-40) REVERT: H 68 PHE cc_start: 0.8426 (m-10) cc_final: 0.7341 (m-10) REVERT: H 82 GLN cc_start: 0.7482 (tp40) cc_final: 0.6956 (tm-30) REVERT: H 83 MET cc_start: 0.8021 (mtt) cc_final: 0.7473 (mtt) REVERT: H 87 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7286 (mtm-85) REVERT: H 90 ASP cc_start: 0.8330 (m-30) cc_final: 0.7785 (m-30) REVERT: L 43 TRP cc_start: 0.7513 (m100) cc_final: 0.6315 (m100) REVERT: E 77 CYS cc_start: 0.6051 (m) cc_final: 0.5812 (m) REVERT: F 17 MET cc_start: 0.8659 (tmm) cc_final: 0.8262 (tmm) REVERT: F 19 ASP cc_start: 0.8417 (p0) cc_final: 0.8199 (p0) REVERT: F 27 GLN cc_start: 0.8258 (tp40) cc_final: 0.7905 (tp-100) REVERT: F 28 ASN cc_start: 0.9043 (p0) cc_final: 0.8511 (p0) REVERT: I 34 MET cc_start: 0.8039 (mmm) cc_final: 0.7678 (mmt) REVERT: I 36 TRP cc_start: 0.8779 (m100) cc_final: 0.8481 (m100) REVERT: I 82 GLN cc_start: 0.7760 (tp40) cc_final: 0.7020 (tm-30) REVERT: I 87 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7720 (mtm-85) REVERT: I 89 GLU cc_start: 0.8825 (pm20) cc_final: 0.8579 (pm20) REVERT: I 90 ASP cc_start: 0.8343 (m-30) cc_final: 0.8099 (m-30) REVERT: J 43 TRP cc_start: 0.8032 (m100) cc_final: 0.7548 (m100) outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.2420 time to fit residues: 156.4806 Evaluate side-chains 323 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 203 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 HIS N 87 GLN C 257 ASN C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 283 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17418 Z= 0.214 Angle : 0.595 10.973 23616 Z= 0.311 Chirality : 0.044 0.166 2622 Planarity : 0.004 0.055 3027 Dihedral : 4.832 38.935 2760 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.17 (0.17), residues: 2133 helix: 1.85 (0.26), residues: 357 sheet: 0.81 (0.23), residues: 507 loop : -0.71 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 43 HIS 0.004 0.001 HIS D 26 PHE 0.027 0.002 PHE C 105 TYR 0.022 0.002 TYR I 112 ARG 0.005 0.001 ARG J 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 2.094 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: B 17 MET cc_start: 0.8502 (ttp) cc_final: 0.8004 (ttp) REVERT: B 19 ASP cc_start: 0.8810 (p0) cc_final: 0.8523 (p0) REVERT: B 27 GLN cc_start: 0.8267 (tp40) cc_final: 0.8042 (tp-100) REVERT: B 28 ASN cc_start: 0.8844 (p0) cc_final: 0.8286 (p0) REVERT: B 32 SER cc_start: 0.8715 (p) cc_final: 0.8269 (p) REVERT: M 36 TRP cc_start: 0.8594 (m100) cc_final: 0.8188 (m100) REVERT: M 46 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7614 (tm-30) REVERT: M 47 TRP cc_start: 0.8533 (t60) cc_final: 0.8076 (t60) REVERT: M 82 GLN cc_start: 0.7486 (tm-30) cc_final: 0.6990 (tm-30) REVERT: M 87 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7760 (mtm-85) REVERT: M 90 ASP cc_start: 0.8287 (m-30) cc_final: 0.7816 (m-30) REVERT: M 99 ASP cc_start: 0.8199 (m-30) cc_final: 0.7641 (m-30) REVERT: N 36 PHE cc_start: 0.7479 (t80) cc_final: 0.7260 (t80) REVERT: N 99 TRP cc_start: 0.8065 (t-100) cc_final: 0.7117 (t-100) REVERT: N 105 ASN cc_start: 0.7165 (m-40) cc_final: 0.6590 (m110) REVERT: C 23 THR cc_start: 0.9001 (p) cc_final: 0.8798 (t) REVERT: C 65 CYS cc_start: 0.6659 (m) cc_final: 0.6246 (m) REVERT: C 204 ASN cc_start: 0.8880 (m-40) cc_final: 0.8487 (m-40) REVERT: H 36 TRP cc_start: 0.8556 (m100) cc_final: 0.8243 (m100) REVERT: H 68 PHE cc_start: 0.8312 (m-10) cc_final: 0.7230 (m-10) REVERT: H 82 GLN cc_start: 0.7499 (tp40) cc_final: 0.6939 (tm-30) REVERT: H 83 MET cc_start: 0.7948 (mtt) cc_final: 0.7484 (mtt) REVERT: H 87 ARG cc_start: 0.7783 (mtm-85) cc_final: 0.7259 (mtm-85) REVERT: H 90 ASP cc_start: 0.8330 (m-30) cc_final: 0.7827 (m-30) REVERT: L 43 TRP cc_start: 0.7605 (m100) cc_final: 0.6812 (m100) REVERT: E 77 CYS cc_start: 0.5986 (m) cc_final: 0.5757 (m) REVERT: F 27 GLN cc_start: 0.8238 (tp40) cc_final: 0.7945 (tp40) REVERT: F 28 ASN cc_start: 0.9067 (p0) cc_final: 0.8346 (p0) REVERT: F 30 GLN cc_start: 0.8793 (mp10) cc_final: 0.8266 (mp10) REVERT: I 34 MET cc_start: 0.8058 (mmm) cc_final: 0.7751 (mmt) REVERT: I 36 TRP cc_start: 0.8786 (m100) cc_final: 0.8544 (m100) REVERT: I 46 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7596 (tm-30) REVERT: I 48 ILE cc_start: 0.8899 (mm) cc_final: 0.8406 (mm) REVERT: I 82 GLN cc_start: 0.7786 (tp40) cc_final: 0.6914 (tm-30) REVERT: I 87 ARG cc_start: 0.7966 (mtm-85) cc_final: 0.7642 (mtm-85) REVERT: I 90 ASP cc_start: 0.8299 (m-30) cc_final: 0.8000 (m-30) REVERT: J 43 TRP cc_start: 0.7691 (m100) cc_final: 0.7364 (m100) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.2583 time to fit residues: 165.8671 Evaluate side-chains 320 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 GLN C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17418 Z= 0.424 Angle : 0.690 9.453 23616 Z= 0.365 Chirality : 0.046 0.200 2622 Planarity : 0.005 0.065 3027 Dihedral : 5.388 40.010 2760 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.17 (0.17), residues: 2133 helix: 1.30 (0.25), residues: 357 sheet: 0.62 (0.22), residues: 516 loop : -0.87 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 241 HIS 0.006 0.001 HIS D 26 PHE 0.041 0.003 PHE A 210 TYR 0.028 0.002 TYR H 112 ARG 0.004 0.001 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.8517 (t80) cc_final: 0.8200 (t80) REVERT: B 27 GLN cc_start: 0.8368 (tp40) cc_final: 0.8084 (tp-100) REVERT: B 28 ASN cc_start: 0.8985 (p0) cc_final: 0.8469 (p0) REVERT: B 32 SER cc_start: 0.8777 (p) cc_final: 0.8368 (p) REVERT: B 90 ASP cc_start: 0.7233 (m-30) cc_final: 0.5864 (m-30) REVERT: B 105 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7801 (mm-30) REVERT: B 133 ILE cc_start: 0.8783 (mt) cc_final: 0.8532 (mt) REVERT: M 36 TRP cc_start: 0.8779 (m100) cc_final: 0.8337 (m100) REVERT: M 46 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7571 (tm-30) REVERT: M 47 TRP cc_start: 0.8552 (t60) cc_final: 0.8177 (t60) REVERT: M 82 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7424 (tm-30) REVERT: M 87 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7755 (mtm-85) REVERT: M 90 ASP cc_start: 0.8414 (m-30) cc_final: 0.7878 (m-30) REVERT: M 99 ASP cc_start: 0.8481 (m-30) cc_final: 0.8001 (m-30) REVERT: N 36 PHE cc_start: 0.7678 (t80) cc_final: 0.7463 (t80) REVERT: N 99 TRP cc_start: 0.8276 (t-100) cc_final: 0.7420 (t-100) REVERT: N 105 ASN cc_start: 0.7520 (m-40) cc_final: 0.7070 (m-40) REVERT: C 204 ASN cc_start: 0.9062 (m-40) cc_final: 0.8653 (m-40) REVERT: H 36 TRP cc_start: 0.8794 (m100) cc_final: 0.8453 (m100) REVERT: H 87 ARG cc_start: 0.7822 (mtm-85) cc_final: 0.7341 (mtm-85) REVERT: H 90 ASP cc_start: 0.8484 (m-30) cc_final: 0.7952 (m-30) REVERT: L 43 TRP cc_start: 0.7574 (m100) cc_final: 0.6975 (m100) REVERT: E 77 CYS cc_start: 0.5972 (m) cc_final: 0.5714 (m) REVERT: F 17 MET cc_start: 0.8821 (tmm) cc_final: 0.8568 (tmm) REVERT: F 27 GLN cc_start: 0.8320 (tp40) cc_final: 0.7995 (tp-100) REVERT: F 28 ASN cc_start: 0.9139 (p0) cc_final: 0.8620 (p0) REVERT: F 105 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7540 (mm-30) REVERT: I 34 MET cc_start: 0.8364 (mmm) cc_final: 0.8085 (mmt) REVERT: I 46 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7510 (tm-30) REVERT: I 48 ILE cc_start: 0.8900 (mm) cc_final: 0.8435 (mm) REVERT: I 82 GLN cc_start: 0.8083 (tp40) cc_final: 0.7235 (tm-30) REVERT: I 90 ASP cc_start: 0.8335 (m-30) cc_final: 0.8112 (m-30) REVERT: J 43 TRP cc_start: 0.7675 (m100) cc_final: 0.7440 (m100) REVERT: J 61 ARG cc_start: 0.8916 (ptp90) cc_final: 0.8714 (ptp-170) REVERT: J 99 TRP cc_start: 0.8006 (t-100) cc_final: 0.7710 (t-100) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.2530 time to fit residues: 152.7142 Evaluate side-chains 315 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 184 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 ASN A 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 ASN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 283 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17418 Z= 0.187 Angle : 0.603 7.816 23616 Z= 0.318 Chirality : 0.044 0.164 2622 Planarity : 0.004 0.059 3027 Dihedral : 4.937 39.977 2760 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2133 helix: 1.37 (0.26), residues: 357 sheet: 0.72 (0.22), residues: 510 loop : -0.81 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 241 HIS 0.004 0.001 HIS D 26 PHE 0.026 0.002 PHE C 105 TYR 0.028 0.001 TYR D 110 ARG 0.004 0.001 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8296 (tp40) cc_final: 0.8063 (tp-100) REVERT: B 28 ASN cc_start: 0.8960 (p0) cc_final: 0.8398 (p0) REVERT: B 32 SER cc_start: 0.8724 (p) cc_final: 0.8343 (p) REVERT: B 105 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7756 (mm-30) REVERT: M 36 TRP cc_start: 0.8667 (m100) cc_final: 0.8243 (m100) REVERT: M 46 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7587 (tm-30) REVERT: M 47 TRP cc_start: 0.8539 (t60) cc_final: 0.8071 (t60) REVERT: M 82 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7084 (tm-30) REVERT: M 87 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7870 (mtm-85) REVERT: M 90 ASP cc_start: 0.8383 (m-30) cc_final: 0.7821 (m-30) REVERT: M 99 ASP cc_start: 0.8212 (m-30) cc_final: 0.7553 (m-30) REVERT: M 112 TYR cc_start: 0.8120 (m-80) cc_final: 0.7205 (m-10) REVERT: N 36 PHE cc_start: 0.7521 (t80) cc_final: 0.7309 (t80) REVERT: N 99 TRP cc_start: 0.8245 (t-100) cc_final: 0.7526 (t-100) REVERT: N 105 ASN cc_start: 0.7553 (m-40) cc_final: 0.6995 (m-40) REVERT: C 204 ASN cc_start: 0.9060 (m-40) cc_final: 0.8484 (m-40) REVERT: D 37 ASP cc_start: 0.8516 (m-30) cc_final: 0.7664 (m-30) REVERT: H 36 TRP cc_start: 0.8658 (m100) cc_final: 0.8020 (m100) REVERT: H 82 GLN cc_start: 0.7652 (tp40) cc_final: 0.6974 (tm-30) REVERT: H 83 MET cc_start: 0.8058 (mtt) cc_final: 0.7549 (mtt) REVERT: H 87 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7251 (mtm-85) REVERT: H 90 ASP cc_start: 0.8384 (m-30) cc_final: 0.7855 (m-30) REVERT: F 17 MET cc_start: 0.8736 (tmm) cc_final: 0.8151 (ppp) REVERT: F 19 ASP cc_start: 0.8377 (p0) cc_final: 0.8128 (p0) REVERT: F 27 GLN cc_start: 0.8264 (tp40) cc_final: 0.7890 (tp-100) REVERT: F 28 ASN cc_start: 0.9088 (p0) cc_final: 0.8769 (p0) REVERT: F 30 GLN cc_start: 0.8723 (mp10) cc_final: 0.8332 (mp10) REVERT: F 32 SER cc_start: 0.8675 (p) cc_final: 0.8243 (p) REVERT: I 6 GLU cc_start: 0.8810 (mp0) cc_final: 0.8520 (mp0) REVERT: I 34 MET cc_start: 0.8208 (mmm) cc_final: 0.7975 (mmt) REVERT: I 46 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7462 (tm-30) REVERT: I 48 ILE cc_start: 0.8953 (mm) cc_final: 0.8411 (mm) REVERT: I 64 VAL cc_start: 0.8624 (m) cc_final: 0.8370 (m) REVERT: I 68 PHE cc_start: 0.8057 (m-10) cc_final: 0.7822 (m-10) REVERT: I 87 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: I 90 ASP cc_start: 0.8227 (m-30) cc_final: 0.8010 (m-30) REVERT: J 99 TRP cc_start: 0.7911 (t-100) cc_final: 0.7588 (t-100) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.2445 time to fit residues: 160.5011 Evaluate side-chains 324 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 148 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 170 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 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 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN N 87 GLN C 290 GLN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17418 Z= 0.205 Angle : 0.603 7.274 23616 Z= 0.320 Chirality : 0.044 0.180 2622 Planarity : 0.004 0.055 3027 Dihedral : 4.869 36.533 2760 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2133 helix: 1.33 (0.27), residues: 357 sheet: 0.70 (0.22), residues: 510 loop : -0.78 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 43 HIS 0.006 0.001 HIS H 35 PHE 0.024 0.002 PHE I 68 TYR 0.019 0.001 TYR H 112 ARG 0.004 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.8678 (ttp) cc_final: 0.8219 (tmm) REVERT: B 27 GLN cc_start: 0.8326 (tp40) cc_final: 0.8077 (tp40) REVERT: B 28 ASN cc_start: 0.8934 (p0) cc_final: 0.8441 (p0) REVERT: B 32 SER cc_start: 0.8745 (p) cc_final: 0.8416 (p) REVERT: M 36 TRP cc_start: 0.8654 (m100) cc_final: 0.7900 (m100) REVERT: M 46 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7651 (tm-30) REVERT: M 47 TRP cc_start: 0.8487 (t60) cc_final: 0.8124 (t60) REVERT: M 82 GLN cc_start: 0.7611 (tm-30) cc_final: 0.7102 (tm-30) REVERT: M 87 ARG cc_start: 0.8181 (mtp85) cc_final: 0.7783 (mtm-85) REVERT: M 90 ASP cc_start: 0.8443 (m-30) cc_final: 0.7901 (m-30) REVERT: M 99 ASP cc_start: 0.8448 (m-30) cc_final: 0.7939 (m-30) REVERT: M 112 TYR cc_start: 0.8112 (m-80) cc_final: 0.7230 (m-10) REVERT: N 36 PHE cc_start: 0.7540 (t80) cc_final: 0.7326 (t80) REVERT: N 99 TRP cc_start: 0.8267 (t-100) cc_final: 0.7568 (t-100) REVERT: N 105 ASN cc_start: 0.7579 (m-40) cc_final: 0.7015 (m110) REVERT: C 204 ASN cc_start: 0.9019 (m-40) cc_final: 0.8424 (m-40) REVERT: H 36 TRP cc_start: 0.8666 (m100) cc_final: 0.8251 (m100) REVERT: H 82 GLN cc_start: 0.7693 (tp40) cc_final: 0.6993 (tm-30) REVERT: H 83 MET cc_start: 0.8108 (mtt) cc_final: 0.7523 (mtt) REVERT: H 87 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7242 (mtm-85) REVERT: H 90 ASP cc_start: 0.8364 (m-30) cc_final: 0.7932 (m-30) REVERT: L 43 TRP cc_start: 0.7233 (m100) cc_final: 0.6892 (m100) REVERT: E 241 TRP cc_start: 0.9149 (p-90) cc_final: 0.8910 (p-90) REVERT: F 17 MET cc_start: 0.8723 (tmm) cc_final: 0.8432 (tmm) REVERT: F 19 ASP cc_start: 0.8364 (p0) cc_final: 0.8160 (p0) REVERT: F 27 GLN cc_start: 0.8248 (tp40) cc_final: 0.7888 (tp-100) REVERT: F 28 ASN cc_start: 0.9075 (p0) cc_final: 0.8771 (p0) REVERT: F 30 GLN cc_start: 0.8676 (mp10) cc_final: 0.8317 (mp10) REVERT: F 32 SER cc_start: 0.8623 (p) cc_final: 0.8188 (p) REVERT: I 6 GLU cc_start: 0.8832 (mp0) cc_final: 0.8579 (mp0) REVERT: I 34 MET cc_start: 0.8187 (mmm) cc_final: 0.7980 (mmt) REVERT: I 46 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7362 (tm-30) REVERT: I 48 ILE cc_start: 0.8872 (mm) cc_final: 0.8246 (mm) REVERT: I 82 GLN cc_start: 0.8054 (tp40) cc_final: 0.6949 (tm-30) REVERT: I 87 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7583 (mtm-85) REVERT: I 90 ASP cc_start: 0.8230 (m-30) cc_final: 0.7934 (m-30) REVERT: J 99 TRP cc_start: 0.7803 (t-100) cc_final: 0.7433 (t-100) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2544 time to fit residues: 160.8750 Evaluate side-chains 324 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 209 optimal weight: 0.8980 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN E 257 ASN E 283 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 17418 Z= 0.308 Angle : 0.640 7.178 23616 Z= 0.340 Chirality : 0.044 0.167 2622 Planarity : 0.004 0.052 3027 Dihedral : 5.086 35.038 2760 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.05 % Allowed : 0.27 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.27 (0.17), residues: 2133 helix: 1.09 (0.26), residues: 357 sheet: 0.66 (0.22), residues: 495 loop : -0.92 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP N 43 HIS 0.005 0.001 HIS H 35 PHE 0.029 0.002 PHE E 124 TYR 0.022 0.002 TYR I 112 ARG 0.005 0.001 ARG I 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4266 Ramachandran restraints generated. 2133 Oldfield, 0 Emsley, 2133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 391 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 MET cc_start: 0.8784 (ttp) cc_final: 0.8320 (tmm) REVERT: B 27 GLN cc_start: 0.8343 (tp40) cc_final: 0.8085 (tp40) REVERT: B 28 ASN cc_start: 0.8997 (p0) cc_final: 0.8550 (p0) REVERT: B 32 SER cc_start: 0.8770 (p) cc_final: 0.8444 (p) REVERT: B 90 ASP cc_start: 0.7399 (m-30) cc_final: 0.6581 (m-30) REVERT: M 36 TRP cc_start: 0.8722 (m100) cc_final: 0.8379 (m100) REVERT: M 46 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7605 (tm-30) REVERT: M 47 TRP cc_start: 0.8604 (t60) cc_final: 0.8185 (t60) REVERT: M 48 ILE cc_start: 0.8794 (mm) cc_final: 0.8416 (mt) REVERT: M 82 GLN cc_start: 0.7669 (tm-30) cc_final: 0.7133 (tm-30) REVERT: M 87 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7810 (mtm-85) REVERT: M 90 ASP cc_start: 0.8523 (m-30) cc_final: 0.7947 (m-30) REVERT: M 99 ASP cc_start: 0.8432 (m-30) cc_final: 0.7808 (m-30) REVERT: M 112 TYR cc_start: 0.8105 (m-80) cc_final: 0.7092 (m-10) REVERT: N 55 LEU cc_start: 0.8256 (mp) cc_final: 0.8045 (mp) REVERT: N 94 TYR cc_start: 0.7618 (m-10) cc_final: 0.7350 (m-10) REVERT: N 99 TRP cc_start: 0.8354 (t-100) cc_final: 0.7696 (t-100) REVERT: N 105 ASN cc_start: 0.7434 (m-40) cc_final: 0.6952 (m-40) REVERT: C 204 ASN cc_start: 0.9086 (m-40) cc_final: 0.8544 (m-40) REVERT: H 36 TRP cc_start: 0.8735 (m100) cc_final: 0.8142 (m100) REVERT: H 87 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7080 (mtm-85) REVERT: H 90 ASP cc_start: 0.8456 (m-30) cc_final: 0.7974 (m-30) REVERT: L 43 TRP cc_start: 0.7349 (m100) cc_final: 0.7002 (m100) REVERT: F 17 MET cc_start: 0.8799 (tmm) cc_final: 0.8434 (tmm) REVERT: F 27 GLN cc_start: 0.8274 (tp40) cc_final: 0.7865 (tp40) REVERT: F 28 ASN cc_start: 0.9125 (p0) cc_final: 0.8694 (p0) REVERT: F 32 SER cc_start: 0.8667 (p) cc_final: 0.8278 (p) REVERT: I 6 GLU cc_start: 0.8857 (mp0) cc_final: 0.8557 (mp0) REVERT: I 46 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7397 (tm-30) REVERT: I 48 ILE cc_start: 0.8794 (mm) cc_final: 0.8225 (mm) REVERT: I 87 ARG cc_start: 0.7973 (mtm-85) cc_final: 0.7508 (mtm-85) REVERT: I 90 ASP cc_start: 0.8354 (m-30) cc_final: 0.7962 (m-30) REVERT: J 43 TRP cc_start: 0.7759 (m100) cc_final: 0.7371 (m100) REVERT: J 99 TRP cc_start: 0.7943 (t-100) cc_final: 0.7553 (t-100) outliers start: 1 outliers final: 0 residues processed: 391 average time/residue: 0.2459 time to fit residues: 151.6062 Evaluate side-chains 308 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN N 87 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN E 257 ASN E 283 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.106652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.088996 restraints weight = 36643.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.090069 restraints weight = 25496.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.091294 restraints weight = 20007.770| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17418 Z= 0.212 Angle : 0.618 7.358 23616 Z= 0.327 Chirality : 0.044 0.171 2622 Planarity : 0.004 0.047 3027 Dihedral : 4.901 34.650 2760 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2133 helix: 1.20 (0.27), residues: 351 sheet: 0.62 (0.22), residues: 510 loop : -0.90 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 241 HIS 0.005 0.001 HIS H 35 PHE 0.023 0.002 PHE C 105 TYR 0.017 0.001 TYR A 17 ARG 0.003 0.000 ARG I 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3939.89 seconds wall clock time: 72 minutes 27.88 seconds (4347.88 seconds total)