Starting phenix.real_space_refine (version: dev) on Wed Feb 22 09:41:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_2023/6xgc_22180.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_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_22180/02_2023/6xgc_22180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_2023/6xgc_22180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_2023/6xgc_22180.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xgc_22180/02_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 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-dev-4877/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: 9.34, per 1000 atoms: 0.55 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: 6.53 Conformation dependent library (CDL) restraints added in 2.7 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: 1.14 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: 5.47 Time building geometry restraints manager: 7.15 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=" C LEU C 186 " pdb=" O LEU C 186 " ideal model delta sigma weight residual 1.236 1.222 0.013 1.20e-02 6.94e+03 1.25e+00 bond pdb=" C LEU E 186 " pdb=" O LEU E 186 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.20e-02 6.94e+03 1.15e+00 bond pdb=" C LEU A 186 " pdb=" O LEU A 186 " ideal model delta sigma weight residual 1.236 1.223 0.012 1.20e-02 6.94e+03 1.06e+00 bond pdb=" N LEU D 126 " pdb=" CA LEU D 126 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.22e-02 6.72e+03 7.92e-01 bond pdb=" N LEU B 126 " pdb=" CA LEU B 126 " ideal model delta sigma weight residual 1.460 1.470 -0.011 1.22e-02 6.72e+03 7.68e-01 ... (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: 9999 17.31 - 34.63: 246 34.63 - 51.94: 36 51.94 - 69.25: 3 69.25 - 86.57: 9 Dihedral angle restraints: 10293 sinusoidal: 4122 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 10290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1603 0.025 - 0.050: 650 0.050 - 0.076: 167 0.076 - 0.101: 89 0.101 - 0.126: 113 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 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. 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: 2.830 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: 7.290 Check model and map are aligned: 0.250 Process input model: 43.900 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 : 0.001 0.015 17418 Z= 0.098 Angle : 0.395 4.712 23616 Z= 0.228 Chirality : 0.038 0.126 2622 Planarity : 0.003 0.034 3027 Dihedral : 7.783 86.567 6297 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 : 2.172 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: 0.3081 time to fit residues: 334.9851 Evaluate side-chains 395 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 392 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1418 time to fit residues: 3.2999 ------------------------------------------------------------------------------- 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 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN E 238 ASN E 290 GLN F 114 ASN ** 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 Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 17418 Z= 0.290 Angle : 0.608 7.498 23616 Z= 0.320 Chirality : 0.044 0.195 2622 Planarity : 0.004 0.056 3027 Dihedral : 3.864 16.572 2445 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 0.33 % 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: 1.07 (0.18), residues: 2133 helix: 3.03 (0.25), residues: 360 sheet: 1.18 (0.22), residues: 540 loop : -0.21 (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 496 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 490 time to evaluate : 2.358 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 outliers start: 6 outliers final: 1 residues processed: 494 average time/residue: 0.2720 time to fit residues: 204.8083 Evaluate side-chains 362 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 2.300 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1539 time to fit residues: 3.1239 ------------------------------------------------------------------------------- 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: 0.0970 chunk 59 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 129 optimal weight: 0.3980 chunk 52 optimal weight: 0.0870 chunk 191 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 chunk 170 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 65 optimal weight: 0.0570 chunk 153 optimal weight: 5.9990 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 GLN N 105 ASN C 290 GLN D 114 ASN D 125 GLN D 129 ASN ** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 J 46 GLN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.062 17418 Z= 0.156 Angle : 0.540 9.633 23616 Z= 0.288 Chirality : 0.043 0.294 2622 Planarity : 0.004 0.044 3027 Dihedral : 3.847 22.252 2445 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 0.91 (0.18), residues: 2133 helix: 2.93 (0.26), residues: 357 sheet: 1.28 (0.24), residues: 483 loop : -0.34 (0.17), residues: 1293 *********************** 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 490 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 488 time to evaluate : 2.042 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 outliers start: 2 outliers final: 0 residues processed: 488 average time/residue: 0.2697 time to fit residues: 200.0071 Evaluate side-chains 355 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 2.231 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7472 ------------------------------------------------------------------------------- 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: 8.9990 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 21 optimal weight: 0.0050 chunk 91 optimal weight: 4.9990 chunk 128 optimal weight: 0.0870 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 0.0870 chunk 100 optimal weight: 0.0770 chunk 181 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.1908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** 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 ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN N 40 HIS C 136 HIS C 257 ASN C 290 GLN ** D 125 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 283 HIS E 290 GLN F 62 GLN F 125 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8155 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 17418 Z= 0.148 Angle : 0.541 9.558 23616 Z= 0.289 Chirality : 0.043 0.315 2622 Planarity : 0.003 0.033 3027 Dihedral : 3.950 30.319 2445 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.27 % 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: 0.76 (0.18), residues: 2133 helix: 2.63 (0.26), residues: 357 sheet: 1.21 (0.24), residues: 489 loop : -0.40 (0.17), residues: 1287 *********************** 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 469 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 464 time to evaluate : 2.245 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 outliers start: 5 outliers final: 0 residues processed: 465 average time/residue: 0.2617 time to fit residues: 190.9128 Evaluate side-chains 346 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7871 ------------------------------------------------------------------------------- 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: 0.3980 chunk 115 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 0 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 overall best weight: 1.0962 ------------------------------------------------------------------------------- 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 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 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 129 ASN H 82 GLN L 45 GLN E 290 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN J 40 HIS ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 17418 Z= 0.215 Angle : 0.560 10.313 23616 Z= 0.299 Chirality : 0.043 0.256 2622 Planarity : 0.004 0.059 3027 Dihedral : 4.125 33.421 2445 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % 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: 0.64 (0.18), residues: 2133 helix: 2.37 (0.26), residues: 357 sheet: 1.13 (0.23), residues: 504 loop : -0.45 (0.17), residues: 1272 *********************** 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 443 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 442 time to evaluate : 2.102 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: 442 average time/residue: 0.2694 time to fit residues: 184.1130 Evaluate side-chains 329 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.085 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7223 ------------------------------------------------------------------------------- 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: 7.9990 chunk 182 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 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** ** M 35 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN D 142 HIS ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 257 ASN E 290 GLN F 125 GLN ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 17418 Z= 0.438 Angle : 0.720 8.437 23616 Z= 0.385 Chirality : 0.048 0.263 2622 Planarity : 0.005 0.075 3027 Dihedral : 4.865 36.608 2445 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.09 (0.17), residues: 2133 helix: 1.30 (0.25), residues: 357 sheet: 0.82 (0.22), residues: 510 loop : -0.86 (0.16), residues: 1266 *********************** 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 411 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.2588 time to fit residues: 167.4597 Evaluate side-chains 326 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6458 ------------------------------------------------------------------------------- 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: 0.7980 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 171 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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** 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 46 GLN E 136 HIS ** E 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 17418 Z= 0.196 Angle : 0.612 12.147 23616 Z= 0.322 Chirality : 0.044 0.183 2622 Planarity : 0.004 0.052 3027 Dihedral : 4.530 31.830 2445 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: 0.06 (0.17), residues: 2133 helix: 1.58 (0.26), residues: 357 sheet: 0.89 (0.22), residues: 510 loop : -0.80 (0.16), residues: 1266 *********************** 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 409 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 2.145 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 409 average time/residue: 0.2563 time to fit residues: 164.9722 Evaluate side-chains 322 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5134 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 0.0000 chunk 39 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 overall best weight: 1.2990 ------------------------------------------------------------------------------- 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 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 ** 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 17418 Z= 0.240 Angle : 0.605 9.777 23616 Z= 0.324 Chirality : 0.044 0.175 2622 Planarity : 0.004 0.067 3027 Dihedral : 4.566 31.041 2445 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -0.01 (0.17), residues: 2133 helix: 1.45 (0.26), residues: 357 sheet: 0.82 (0.22), residues: 510 loop : -0.81 (0.16), residues: 1266 *********************** 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 393 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.2542 time to fit residues: 158.2657 Evaluate side-chains 310 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 2.212 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7098 ------------------------------------------------------------------------------- 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: 2.9990 chunk 176 optimal weight: 1.9990 chunk 188 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 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 ** 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 87 GLN E 257 ASN E 290 GLN ** F 125 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 17418 Z= 0.245 Angle : 0.615 8.086 23616 Z= 0.328 Chirality : 0.045 0.175 2622 Planarity : 0.004 0.060 3027 Dihedral : 4.596 33.751 2445 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: -0.03 (0.17), residues: 2133 helix: 1.43 (0.26), residues: 357 sheet: 0.76 (0.22), residues: 510 loop : -0.80 (0.16), residues: 1266 *********************** 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 384 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.2613 time to fit residues: 156.6922 Evaluate side-chains 307 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7148 ------------------------------------------------------------------------------- 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: 0.9980 chunk 121 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 209 optimal weight: 0.3980 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 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 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** D 142 HIS L 87 GLN E 257 ASN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 17418 Z= 0.258 Angle : 0.627 7.624 23616 Z= 0.337 Chirality : 0.045 0.182 2622 Planarity : 0.004 0.056 3027 Dihedral : 4.653 33.209 2445 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % 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: -0.13 (0.17), residues: 2133 helix: 1.23 (0.26), residues: 357 sheet: 0.72 (0.22), residues: 510 loop : -0.83 (0.16), residues: 1266 ********************** 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 384 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.2568 time to fit residues: 156.7338 Evaluate side-chains 304 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8559 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 146 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 13 GLN ** 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** E 257 ASN E 290 GLN F 114 ASN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 87 GLN ** 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 = 0.3475 r_free = 0.3475 target = 0.108235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.090402 restraints weight = 36125.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.091774 restraints weight = 25355.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.093059 restraints weight = 19328.703| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4564 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= 0.176 Angle : 0.634 11.612 23616 Z= 0.334 Chirality : 0.045 0.180 2622 Planarity : 0.004 0.054 3027 Dihedral : 4.591 31.461 2445 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -0.05 (0.17), residues: 2133 helix: 1.26 (0.27), residues: 357 sheet: 0.75 (0.22), residues: 510 loop : -0.76 (0.16), residues: 1266 =============================================================================== Job complete usr+sys time: 3850.90 seconds wall clock time: 70 minutes 30.47 seconds (4230.47 seconds total)