Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 16:34:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/07_2023/6xgc_22180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/07_2023/6xgc_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_22180/07_2023/6xgc_22180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/07_2023/6xgc_22180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/07_2023/6xgc_22180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/07_2023/6xgc_22180.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 7.82, per 1000 atoms: 0.46 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: 6.96 Conformation dependent library (CDL) restraints added in 2.6 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: 1.27 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: 5.52 Time building geometry restraints manager: 7.50 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: 9873 17.31 - 34.63: 246 34.63 - 51.94: 36 51.94 - 69.25: 3 69.25 - 86.57: 9 Dihedral angle restraints: 10167 sinusoidal: 3996 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 10164 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: 1.150 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: 0.010 Extract box with map and model: 6.920 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 43.830 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.350 ------------------------------------------------------------------------------- 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 : 7.789 86.567 6171 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 % 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 *********************** 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 : 1.954 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 outliers start: 3 outliers final: 3 residues processed: 745 average time/residue: 0.2993 time to fit residues: 327.9255 Evaluate side-chains 395 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 392 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1488 time to fit residues: 3.5375 ------------------------------------------------------------------------------- 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: 4.9990 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 238 ASN C 257 ASN C 290 GLN D 114 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN L 45 GLN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 238 ASN E 290 GLN F 114 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN J 45 GLN J 46 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 17418 Z= 0.295 Angle : 0.622 7.336 23616 Z= 0.324 Chirality : 0.044 0.234 2622 Planarity : 0.004 0.072 3027 Dihedral : 3.585 17.557 2319 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 0.22 % 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: 1.04 (0.18), residues: 2133 helix: 2.98 (0.25), residues: 360 sheet: 1.17 (0.22), residues: 540 loop : -0.22 (0.17), residues: 1233 *********************** 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 490 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 486 time to evaluate : 1.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 488 average time/residue: 0.2732 time to fit residues: 204.0395 Evaluate side-chains 357 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 1.909 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1460 time to fit residues: 2.8343 ------------------------------------------------------------------------------- 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: 0.0870 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 0.0670 chunk 52 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 65 optimal weight: 0.0370 chunk 153 optimal weight: 2.9990 overall best weight: 0.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS A 290 GLN B 125 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN N 105 ASN C 290 GLN D 114 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN ** 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** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 17418 Z= 0.172 Angle : 0.547 10.174 23616 Z= 0.288 Chirality : 0.043 0.275 2622 Planarity : 0.004 0.047 3027 Dihedral : 3.592 23.704 2319 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 0.11 % 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: 0.80 (0.18), residues: 2133 helix: 2.86 (0.26), residues: 357 sheet: 1.25 (0.25), residues: 423 loop : -0.36 (0.16), residues: 1353 *********************** 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 486 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 484 time to evaluate : 1.901 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 outliers start: 2 outliers final: 0 residues processed: 484 average time/residue: 0.2707 time to fit residues: 202.3423 Evaluate side-chains 360 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6642 ------------------------------------------------------------------------------- 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: 9.9990 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 0.0470 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 128 optimal weight: 0.0030 chunk 191 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 100 optimal weight: 0.0970 chunk 181 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN A 290 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 HIS N 46 GLN C 257 ASN C 290 GLN D 125 GLN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN E 257 ASN E 290 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 142 HIS ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 17418 Z= 0.256 Angle : 0.594 12.351 23616 Z= 0.314 Chirality : 0.043 0.295 2622 Planarity : 0.004 0.060 3027 Dihedral : 3.942 30.874 2319 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.05 % 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: 0.50 (0.18), residues: 2133 helix: 2.23 (0.25), residues: 357 sheet: 0.97 (0.22), residues: 537 loop : -0.54 (0.17), residues: 1239 *********************** 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 446 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 445 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.2630 time to fit residues: 184.0181 Evaluate side-chains 330 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5175 ------------------------------------------------------------------------------- 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: 2.9990 chunk 115 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 0.0050 chunk 83 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 182 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 129 ASN ** 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** H 39 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 290 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 17418 Z= 0.240 Angle : 0.597 9.209 23616 Z= 0.317 Chirality : 0.044 0.202 2622 Planarity : 0.004 0.059 3027 Dihedral : 4.125 33.009 2319 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.31 (0.17), residues: 2133 helix: 1.85 (0.26), residues: 357 sheet: 1.01 (0.22), residues: 516 loop : -0.65 (0.16), residues: 1260 *********************** 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 420 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 419 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.2544 time to fit residues: 167.1320 Evaluate side-chains 324 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.788 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4046 ------------------------------------------------------------------------------- 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: 5.9990 chunk 182 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 168 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** N 87 GLN C 257 ASN C 290 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN H 39 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 39 GLN ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3984 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= 0.223 Angle : 0.588 7.212 23616 Z= 0.312 Chirality : 0.043 0.170 2622 Planarity : 0.004 0.054 3027 Dihedral : 4.162 32.957 2319 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.11 % 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: 0.13 (0.17), residues: 2133 helix: 1.69 (0.26), residues: 357 sheet: 0.93 (0.23), residues: 501 loop : -0.76 (0.16), residues: 1275 *********************** 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 417 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 415 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 416 average time/residue: 0.2551 time to fit residues: 166.5510 Evaluate side-chains 322 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7956 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 126 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 290 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 GLN C 290 GLN ** D 124 ASN ** 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 290 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 17418 Z= 0.206 Angle : 0.591 10.352 23616 Z= 0.312 Chirality : 0.043 0.181 2622 Planarity : 0.004 0.059 3027 Dihedral : 4.168 34.018 2319 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.00 % 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: 0.16 (0.17), residues: 2133 helix: 1.63 (0.26), residues: 357 sheet: 0.96 (0.22), residues: 516 loop : -0.74 (0.16), residues: 1260 *********************** 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 405 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.2490 time to fit residues: 158.6992 Evaluate side-chains 318 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4657 ------------------------------------------------------------------------------- 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: 6.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 128 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 100 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 159 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS 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** C 257 ASN C 290 GLN ** D 124 ASN ** 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 87 GLN ** E 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 290 GLN F 62 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 17418 Z= 0.161 Angle : 0.577 9.211 23616 Z= 0.304 Chirality : 0.043 0.155 2622 Planarity : 0.004 0.052 3027 Dihedral : 4.087 31.593 2319 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 0.05 % 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: 0.23 (0.17), residues: 2133 helix: 1.76 (0.27), residues: 357 sheet: 1.04 (0.23), residues: 492 loop : -0.69 (0.16), residues: 1284 *********************** 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 411 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 410 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.2512 time to fit residues: 165.0844 Evaluate side-chains 317 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6174 ------------------------------------------------------------------------------- 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: 0.6980 chunk 176 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 178 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 GLN C 290 GLN D 104 ASN ** D 124 ASN ** 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN E 257 ASN E 283 HIS E 290 GLN F 62 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 17418 Z= 0.192 Angle : 0.592 8.221 23616 Z= 0.312 Chirality : 0.043 0.180 2622 Planarity : 0.004 0.049 3027 Dihedral : 4.133 31.198 2319 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.11 % 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: 0.21 (0.17), residues: 2133 helix: 1.67 (0.26), residues: 357 sheet: 0.98 (0.23), residues: 495 loop : -0.67 (0.16), residues: 1281 *********************** 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: 2 poor density : 399 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 399 average time/residue: 0.2577 time to fit residues: 161.3556 Evaluate side-chains 315 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6062 ------------------------------------------------------------------------------- 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: 2.9990 chunk 121 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 209 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 17418 Z= 0.265 Angle : 0.637 10.776 23616 Z= 0.336 Chirality : 0.044 0.204 2622 Planarity : 0.004 0.046 3027 Dihedral : 4.386 31.228 2319 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.11 % 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: 0.01 (0.17), residues: 2133 helix: 1.34 (0.26), residues: 357 sheet: 0.86 (0.23), residues: 495 loop : -0.74 (0.16), residues: 1281 ********************** 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 389 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 387 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 387 average time/residue: 0.2575 time to fit residues: 158.4779 Evaluate side-chains 306 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5887 ------------------------------------------------------------------------------- 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: 4.9990 chunk 51 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 46 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS 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 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 GLN E 283 HIS E 290 GLN F 125 GLN ** J 13 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.108848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.091152 restraints weight = 36153.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092014 restraints weight = 26313.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093387 restraints weight = 20863.321| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 17418 Z= 0.204 Angle : 0.612 9.768 23616 Z= 0.324 Chirality : 0.044 0.189 2622 Planarity : 0.004 0.044 3027 Dihedral : 4.315 29.997 2319 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 0.05 % 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: 0.02 (0.17), residues: 2133 helix: 1.44 (0.27), residues: 357 sheet: 0.84 (0.23), residues: 495 loop : -0.75 (0.16), residues: 1281 =============================================================================== Job complete usr+sys time: 3834.58 seconds wall clock time: 70 minutes 20.71 seconds (4220.71 seconds total)