Starting phenix.real_space_refine on Mon Jul 22 01:59:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud2_42144/07_2024/8ud2_42144.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud2_42144/07_2024/8ud2_42144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud2_42144/07_2024/8ud2_42144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud2_42144/07_2024/8ud2_42144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud2_42144/07_2024/8ud2_42144.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud2_42144/07_2024/8ud2_42144.cif" } resolution = 2.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.062 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 60 5.16 5 C 10620 2.51 5 N 2688 2.21 5 O 3162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 68": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 264": "OE1" <-> "OE2" Residue "C GLU 266": "OE1" <-> "OE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 68": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 264": "OE1" <-> "OE2" Residue "D GLU 266": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 41": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 264": "OE1" <-> "OE2" Residue "E GLU 266": "OE1" <-> "OE2" Residue "F GLU 21": "OE1" <-> "OE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F GLU 68": "OE1" <-> "OE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F GLU 264": "OE1" <-> "OE2" Residue "F GLU 266": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 16530 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "B" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "C" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "D" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "E" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "F" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AILE A 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE A 27 " occ=0.48 residue: pdb=" N AASN A 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN A 28 " occ=0.48 residue: pdb=" N AASN A 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN A 29 " occ=0.48 residue: pdb=" N AILE B 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE B 27 " occ=0.48 residue: pdb=" N AASN B 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 28 " occ=0.48 residue: pdb=" N AASN B 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 29 " occ=0.48 residue: pdb=" N AILE C 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE C 27 " occ=0.48 residue: pdb=" N AASN C 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN C 28 " occ=0.48 residue: pdb=" N AASN C 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN C 29 " occ=0.48 residue: pdb=" N AILE D 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE D 27 " occ=0.48 residue: pdb=" N AASN D 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 28 " occ=0.48 residue: pdb=" N AASN D 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 29 " occ=0.48 ... (remaining 6 not shown) Time building chain proxies: 16.99, per 1000 atoms: 1.03 Number of scatterers: 16530 At special positions: 0 Unit cell: (115, 107.64, 122.36, 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 60 16.00 O 3162 8.00 N 2688 7.00 C 10620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 5.5 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 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: 60 helices and 48 sheets defined 26.6% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.594A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.594A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.594A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.593A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.593A pdb=" N GLU E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 250 through 261 removed outlier: 3.594A pdb=" N GLU F 260 " --> pdb=" O LYS F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 308 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.647A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AA5, first strand: chain 'A' and resid 98 through 99 removed outlier: 7.949A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AA7, first strand: chain 'A' and resid 264 through 266 removed outlier: 4.908A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 322 removed outlier: 7.446A pdb=" N SER A 328 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N MET A 330 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 341 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.647A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AB4, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.949A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AB6, first strand: chain 'B' and resid 264 through 266 removed outlier: 4.909A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 315 through 322 removed outlier: 7.447A pdb=" N SER B 328 " --> pdb=" O PRO B 343 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET B 330 " --> pdb=" O PHE B 341 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 341 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 24 through 27 removed outlier: 6.647A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AC3, first strand: chain 'C' and resid 98 through 99 removed outlier: 7.950A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AC5, first strand: chain 'C' and resid 264 through 266 removed outlier: 4.909A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 315 through 322 removed outlier: 7.447A pdb=" N SER C 328 " --> pdb=" O PRO C 343 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET C 330 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 341 " --> pdb=" O MET C 330 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP C 332 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.647A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AD2, first strand: chain 'D' and resid 98 through 99 removed outlier: 7.949A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AD4, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.908A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 315 through 322 removed outlier: 7.446A pdb=" N SER D 328 " --> pdb=" O PRO D 343 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET D 330 " --> pdb=" O PHE D 341 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE D 341 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP D 332 " --> pdb=" O GLU D 339 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.647A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AE1, first strand: chain 'E' and resid 98 through 99 removed outlier: 7.950A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AE3, first strand: chain 'E' and resid 264 through 266 removed outlier: 4.909A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.446A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.647A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.158A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS F 180 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AE9, first strand: chain 'F' and resid 98 through 99 removed outlier: 7.950A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AF2, first strand: chain 'F' and resid 264 through 266 removed outlier: 4.909A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.446A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) 663 hydrogen bonds defined for protein. 1683 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: 6.10 Time building geometry restraints manager: 6.76 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: 5346 1.34 - 1.46: 2447 1.46 - 1.57: 8989 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 16872 Sorted by residual: bond pdb=" N LEU F 345 " pdb=" CA LEU F 345 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.21e+00 bond pdb=" N LEU C 345 " pdb=" CA LEU C 345 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.20e+00 bond pdb=" N LEU B 345 " pdb=" CA LEU B 345 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.16e+00 bond pdb=" N LEU D 345 " pdb=" CA LEU D 345 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.15e+00 bond pdb=" N LEU A 345 " pdb=" CA LEU A 345 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 ... (remaining 16867 not shown) Histogram of bond angle deviations from ideal: 100.81 - 107.46: 544 107.46 - 114.11: 9702 114.11 - 120.75: 6609 120.75 - 127.40: 5926 127.40 - 134.05: 121 Bond angle restraints: 22902 Sorted by residual: angle pdb=" C GLN E 188 " pdb=" N LEU E 189 " pdb=" CA LEU E 189 " ideal model delta sigma weight residual 120.67 116.80 3.87 1.34e+00 5.57e-01 8.33e+00 angle pdb=" C GLN D 188 " pdb=" N LEU D 189 " pdb=" CA LEU D 189 " ideal model delta sigma weight residual 120.67 116.81 3.86 1.34e+00 5.57e-01 8.30e+00 angle pdb=" C GLN B 188 " pdb=" N LEU B 189 " pdb=" CA LEU B 189 " ideal model delta sigma weight residual 120.67 116.81 3.86 1.34e+00 5.57e-01 8.28e+00 angle pdb=" C GLN C 188 " pdb=" N LEU C 189 " pdb=" CA LEU C 189 " ideal model delta sigma weight residual 120.67 116.85 3.82 1.34e+00 5.57e-01 8.13e+00 angle pdb=" C GLN A 188 " pdb=" N LEU A 189 " pdb=" CA LEU A 189 " ideal model delta sigma weight residual 120.67 116.87 3.80 1.34e+00 5.57e-01 8.05e+00 ... (remaining 22897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8918 17.82 - 35.64: 868 35.64 - 53.46: 198 53.46 - 71.28: 84 71.28 - 89.11: 36 Dihedral angle restraints: 10104 sinusoidal: 4020 harmonic: 6084 Sorted by residual: dihedral pdb=" CA THR B 192 " pdb=" C THR B 192 " pdb=" N TYR B 193 " pdb=" CA TYR B 193 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR D 192 " pdb=" C THR D 192 " pdb=" N TYR D 193 " pdb=" CA TYR D 193 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA THR C 192 " pdb=" C THR C 192 " pdb=" N TYR C 193 " pdb=" CA TYR C 193 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 10101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1359 0.027 - 0.053: 729 0.053 - 0.079: 268 0.079 - 0.106: 195 0.106 - 0.132: 83 Chirality restraints: 2634 Sorted by residual: chirality pdb=" CA ILE B 168 " pdb=" N ILE B 168 " pdb=" C ILE B 168 " pdb=" CB ILE B 168 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE E 168 " pdb=" N ILE E 168 " pdb=" C ILE E 168 " pdb=" CB ILE E 168 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL B 313 " pdb=" N VAL B 313 " pdb=" C VAL B 313 " pdb=" CB VAL B 313 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2631 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 110 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO E 111 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 111 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 111 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 110 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO C 111 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 111 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 111 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 110 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.89e+00 pdb=" N PRO F 111 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO F 111 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 111 " 0.019 5.00e-02 4.00e+02 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4744 2.81 - 3.34: 14847 3.34 - 3.86: 30023 3.86 - 4.38: 35609 4.38 - 4.90: 58582 Nonbonded interactions: 143805 Sorted by model distance: nonbonded pdb=" O ALA C 117 " pdb=" ND2 ASN C 139 " model vdw 2.293 2.520 nonbonded pdb=" O ALA F 117 " pdb=" ND2 ASN F 139 " model vdw 2.293 2.520 nonbonded pdb=" O ALA A 117 " pdb=" ND2 ASN A 139 " model vdw 2.293 2.520 nonbonded pdb=" O ALA E 117 " pdb=" ND2 ASN E 139 " model vdw 2.293 2.520 nonbonded pdb=" O ALA D 117 " pdb=" ND2 ASN D 139 " model vdw 2.293 2.520 ... (remaining 143800 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' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'B' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'C' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'D' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'E' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'F' and (resid 1 through 26 or resid 30 through 346)) } 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=0.48 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 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: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 57.630 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.003 0.019 16872 Z= 0.172 Angle : 0.532 5.308 22902 Z= 0.324 Chirality : 0.045 0.132 2634 Planarity : 0.003 0.034 2952 Dihedral : 16.449 89.106 6180 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.08 % Allowed : 17.74 % Favored : 81.18 % 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: 0.47 (0.19), residues: 2094 helix: 0.69 (0.23), residues: 528 sheet: 0.50 (0.29), residues: 312 loop : 0.21 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 58 HIS 0.004 0.001 HIS C 95 PHE 0.009 0.001 PHE C 221 TYR 0.006 0.001 TYR C 324 ARG 0.001 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 250 time to evaluate : 1.951 Fit side-chains REVERT: B 149 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7706 (mppt) REVERT: B 239 ASP cc_start: 0.7288 (t0) cc_final: 0.7026 (t0) REVERT: B 284 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6658 (tm130) REVERT: C 19 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7991 (mp10) REVERT: C 149 LYS cc_start: 0.8040 (mmmm) cc_final: 0.7546 (ptmm) REVERT: C 330 MET cc_start: 0.7205 (mmt) cc_final: 0.7000 (mmt) REVERT: D 19 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7994 (mp10) REVERT: D 149 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7517 (ptmm) REVERT: D 330 MET cc_start: 0.7184 (mmt) cc_final: 0.6981 (mmt) REVERT: E 149 LYS cc_start: 0.8139 (mmmm) cc_final: 0.7713 (mppt) outliers start: 20 outliers final: 9 residues processed: 268 average time/residue: 1.0471 time to fit residues: 318.0371 Evaluate side-chains 228 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 219 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain F residue 300 ASP Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.0870 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 61 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN C 152 GLN D 152 GLN E 19 GLN F 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16872 Z= 0.175 Angle : 0.514 9.505 22902 Z= 0.272 Chirality : 0.046 0.133 2634 Planarity : 0.003 0.026 2952 Dihedral : 5.186 52.936 2226 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.56 % Allowed : 18.39 % Favored : 80.05 % 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: 0.52 (0.19), residues: 2094 helix: 0.74 (0.23), residues: 540 sheet: 0.34 (0.26), residues: 342 loop : 0.29 (0.19), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 58 HIS 0.003 0.001 HIS A 95 PHE 0.022 0.002 PHE D 221 TYR 0.008 0.001 TYR A 225 ARG 0.006 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 2.047 Fit side-chains REVERT: A 259 LYS cc_start: 0.6441 (tttt) cc_final: 0.6097 (mttp) REVERT: B 149 LYS cc_start: 0.8124 (mmmm) cc_final: 0.7700 (mppt) REVERT: B 259 LYS cc_start: 0.6369 (tttt) cc_final: 0.6075 (mttp) REVERT: C 152 GLN cc_start: 0.8122 (tp40) cc_final: 0.7664 (mp10) REVERT: C 202 GLU cc_start: 0.6649 (OUTLIER) cc_final: 0.6154 (tt0) REVERT: C 215 GLU cc_start: 0.6600 (pt0) cc_final: 0.5390 (mp0) REVERT: C 259 LYS cc_start: 0.6532 (tttt) cc_final: 0.6236 (mttp) REVERT: C 330 MET cc_start: 0.7347 (mmt) cc_final: 0.7000 (mmm) REVERT: D 202 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6156 (tt0) REVERT: D 215 GLU cc_start: 0.6597 (pt0) cc_final: 0.5390 (mp0) REVERT: D 259 LYS cc_start: 0.6535 (tttt) cc_final: 0.6238 (mttp) REVERT: D 330 MET cc_start: 0.7348 (mmt) cc_final: 0.6538 (mmm) REVERT: E 149 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7705 (mppt) REVERT: E 259 LYS cc_start: 0.6371 (tttt) cc_final: 0.6087 (mttp) REVERT: F 259 LYS cc_start: 0.6442 (tttt) cc_final: 0.6106 (tppt) outliers start: 29 outliers final: 16 residues processed: 266 average time/residue: 1.1529 time to fit residues: 345.2203 Evaluate side-chains 247 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 229 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 340 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 0.3980 chunk 63 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 277 ASN B 19 GLN C 19 GLN D 19 GLN D 152 GLN E 19 GLN F 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16872 Z= 0.316 Angle : 0.591 10.498 22902 Z= 0.314 Chirality : 0.049 0.138 2634 Planarity : 0.004 0.044 2952 Dihedral : 5.338 39.933 2220 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.26 % Allowed : 17.96 % Favored : 79.78 % 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: 0.26 (0.18), residues: 2094 helix: 0.30 (0.23), residues: 552 sheet: 0.31 (0.26), residues: 342 loop : 0.20 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 58 HIS 0.005 0.001 HIS A 95 PHE 0.021 0.002 PHE D 221 TYR 0.011 0.001 TYR D 225 ARG 0.006 0.001 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 245 time to evaluate : 2.199 Fit side-chains REVERT: A 193 TYR cc_start: 0.8639 (m-80) cc_final: 0.8430 (m-80) REVERT: A 259 LYS cc_start: 0.6535 (tttt) cc_final: 0.6079 (mttp) REVERT: B 149 LYS cc_start: 0.8153 (mmmm) cc_final: 0.7725 (mppt) REVERT: B 259 LYS cc_start: 0.6563 (tttt) cc_final: 0.6144 (mttp) REVERT: B 304 GLU cc_start: 0.6691 (tt0) cc_final: 0.6431 (tt0) REVERT: C 149 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7581 (tptt) REVERT: C 202 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6199 (tt0) REVERT: C 233 GLU cc_start: 0.6788 (mp0) cc_final: 0.6582 (pm20) REVERT: C 259 LYS cc_start: 0.6704 (tttt) cc_final: 0.6236 (mttp) REVERT: C 330 MET cc_start: 0.7419 (mmt) cc_final: 0.6573 (mmm) REVERT: D 149 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7579 (tptt) REVERT: D 202 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6198 (tt0) REVERT: D 259 LYS cc_start: 0.6669 (tttt) cc_final: 0.6194 (mttp) REVERT: D 330 MET cc_start: 0.7421 (mmt) cc_final: 0.6581 (mmm) REVERT: E 149 LYS cc_start: 0.8158 (mmmm) cc_final: 0.7730 (mppt) REVERT: E 259 LYS cc_start: 0.6561 (tttt) cc_final: 0.6144 (mttp) REVERT: E 304 GLU cc_start: 0.6692 (tt0) cc_final: 0.6434 (tt0) REVERT: F 259 LYS cc_start: 0.6538 (tttt) cc_final: 0.6083 (mttp) outliers start: 42 outliers final: 32 residues processed: 275 average time/residue: 1.1786 time to fit residues: 363.1437 Evaluate side-chains 276 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 242 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 287 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 186 optimal weight: 0.3980 chunk 197 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 277 ASN B 19 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 136 ASN C 152 GLN C 277 ASN D 19 GLN D 136 ASN D 152 GLN D 277 ASN E 19 GLN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16872 Z= 0.191 Angle : 0.515 10.503 22902 Z= 0.272 Chirality : 0.046 0.135 2634 Planarity : 0.003 0.044 2952 Dihedral : 4.776 23.220 2218 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.67 % Allowed : 18.39 % Favored : 79.95 % 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: 0.41 (0.18), residues: 2094 helix: 0.52 (0.23), residues: 552 sheet: 0.46 (0.26), residues: 342 loop : 0.22 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 58 HIS 0.004 0.001 HIS A 95 PHE 0.026 0.002 PHE D 221 TYR 0.009 0.001 TYR A 225 ARG 0.006 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 256 time to evaluate : 1.910 Fit side-chains REVERT: A 193 TYR cc_start: 0.8632 (m-80) cc_final: 0.8385 (m-80) REVERT: A 259 LYS cc_start: 0.6585 (tttt) cc_final: 0.6138 (mttp) REVERT: B 149 LYS cc_start: 0.8128 (mmmm) cc_final: 0.7701 (mppt) REVERT: B 259 LYS cc_start: 0.6619 (tttt) cc_final: 0.6168 (mttp) REVERT: C 149 LYS cc_start: 0.8109 (mmmm) cc_final: 0.7559 (tptt) REVERT: C 202 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6180 (tt0) REVERT: C 233 GLU cc_start: 0.6727 (mp0) cc_final: 0.6519 (pm20) REVERT: C 330 MET cc_start: 0.7446 (mmt) cc_final: 0.6802 (mmm) REVERT: D 149 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7559 (tptt) REVERT: D 202 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6187 (tt0) REVERT: D 330 MET cc_start: 0.7447 (mmt) cc_final: 0.6807 (mmm) REVERT: E 149 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7707 (mppt) REVERT: E 259 LYS cc_start: 0.6616 (tttt) cc_final: 0.6167 (mttp) REVERT: F 259 LYS cc_start: 0.6540 (tttt) cc_final: 0.6113 (mttp) outliers start: 31 outliers final: 20 residues processed: 278 average time/residue: 1.0705 time to fit residues: 337.0356 Evaluate side-chains 268 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 246 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 287 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 136 ASN C 152 GLN C 277 ASN D 19 GLN D 136 ASN D 152 GLN D 277 ASN E 19 GLN ** E 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16872 Z= 0.213 Angle : 0.529 11.686 22902 Z= 0.279 Chirality : 0.046 0.136 2634 Planarity : 0.003 0.047 2952 Dihedral : 4.760 19.192 2214 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.04 % Allowed : 18.17 % Favored : 79.78 % 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: 0.40 (0.18), residues: 2094 helix: 0.52 (0.23), residues: 552 sheet: 0.47 (0.26), residues: 342 loop : 0.20 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 58 HIS 0.004 0.001 HIS F 95 PHE 0.031 0.002 PHE D 221 TYR 0.009 0.001 TYR F 225 ARG 0.006 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 246 time to evaluate : 1.879 Fit side-chains REVERT: A 193 TYR cc_start: 0.8646 (m-80) cc_final: 0.8411 (m-80) REVERT: A 259 LYS cc_start: 0.6660 (tttt) cc_final: 0.6179 (mttp) REVERT: B 68 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: B 149 LYS cc_start: 0.8130 (mmmm) cc_final: 0.7705 (mppt) REVERT: B 259 LYS cc_start: 0.6633 (tttt) cc_final: 0.6270 (ttpp) REVERT: C 149 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7516 (tptt) REVERT: C 202 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6271 (tt0) REVERT: C 233 GLU cc_start: 0.6728 (mp0) cc_final: 0.6513 (pm20) REVERT: C 330 MET cc_start: 0.7339 (mmt) cc_final: 0.6675 (mmm) REVERT: D 149 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7515 (tptt) REVERT: D 202 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6271 (tt0) REVERT: D 330 MET cc_start: 0.7347 (mmt) cc_final: 0.6676 (mmm) REVERT: E 68 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: E 149 LYS cc_start: 0.8134 (mmmm) cc_final: 0.7709 (mppt) REVERT: E 259 LYS cc_start: 0.6628 (tttt) cc_final: 0.6268 (ttpp) REVERT: F 193 TYR cc_start: 0.8646 (m-80) cc_final: 0.8411 (m-80) REVERT: F 259 LYS cc_start: 0.6654 (tttt) cc_final: 0.6175 (mttp) outliers start: 38 outliers final: 28 residues processed: 268 average time/residue: 1.1819 time to fit residues: 356.3261 Evaluate side-chains 269 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 220 GLU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 287 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN B 277 ASN C 19 GLN C 152 GLN C 277 ASN D 19 GLN D 152 GLN D 277 ASN E 19 GLN E 277 ASN F 19 GLN F 277 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16872 Z= 0.214 Angle : 0.527 10.942 22902 Z= 0.278 Chirality : 0.046 0.135 2634 Planarity : 0.003 0.047 2952 Dihedral : 4.763 19.184 2214 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.15 % Allowed : 18.28 % Favored : 79.57 % 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: 0.42 (0.18), residues: 2094 helix: 0.55 (0.23), residues: 552 sheet: 0.48 (0.26), residues: 342 loop : 0.22 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 58 HIS 0.004 0.001 HIS F 95 PHE 0.032 0.002 PHE D 221 TYR 0.009 0.001 TYR A 225 ARG 0.006 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 1.830 Fit side-chains REVERT: A 259 LYS cc_start: 0.6655 (tttt) cc_final: 0.6173 (mttp) REVERT: B 68 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: B 149 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7706 (mppt) REVERT: C 149 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7506 (tptt) REVERT: C 202 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6270 (tt0) REVERT: C 233 GLU cc_start: 0.6733 (mp0) cc_final: 0.6515 (pm20) REVERT: C 330 MET cc_start: 0.7301 (mmt) cc_final: 0.6651 (mmm) REVERT: D 149 LYS cc_start: 0.8047 (mmmm) cc_final: 0.7505 (tptt) REVERT: D 202 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6269 (tt0) REVERT: D 330 MET cc_start: 0.7298 (mmt) cc_final: 0.6650 (mmm) REVERT: E 68 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: E 149 LYS cc_start: 0.8135 (mmmm) cc_final: 0.7709 (mppt) REVERT: F 259 LYS cc_start: 0.6666 (tttt) cc_final: 0.6185 (mttp) outliers start: 40 outliers final: 30 residues processed: 258 average time/residue: 1.1569 time to fit residues: 335.6519 Evaluate side-chains 264 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 230 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 287 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 144 optimal weight: 0.0870 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN C 19 GLN C 152 GLN C 277 ASN D 19 GLN D 152 GLN D 277 ASN E 19 GLN F 277 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16872 Z= 0.165 Angle : 0.498 11.057 22902 Z= 0.262 Chirality : 0.045 0.135 2634 Planarity : 0.003 0.045 2952 Dihedral : 4.549 18.125 2214 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.88 % Allowed : 18.71 % Favored : 79.41 % 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: 0.55 (0.18), residues: 2094 helix: 0.69 (0.23), residues: 552 sheet: 0.52 (0.26), residues: 342 loop : 0.29 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 58 HIS 0.003 0.001 HIS A 95 PHE 0.030 0.002 PHE C 221 TYR 0.008 0.001 TYR F 225 ARG 0.007 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 235 time to evaluate : 2.020 Fit side-chains REVERT: B 149 LYS cc_start: 0.8100 (mmmm) cc_final: 0.7689 (mppt) REVERT: C 149 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7488 (tptt) REVERT: C 202 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6250 (tt0) REVERT: C 233 GLU cc_start: 0.6698 (mp0) cc_final: 0.6480 (pm20) REVERT: C 330 MET cc_start: 0.7296 (mmt) cc_final: 0.6728 (mmm) REVERT: D 149 LYS cc_start: 0.8039 (mmmm) cc_final: 0.7648 (mppt) REVERT: D 202 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.6241 (tt0) REVERT: D 330 MET cc_start: 0.7292 (mmt) cc_final: 0.6721 (mmm) REVERT: E 149 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7693 (mppt) REVERT: E 221 PHE cc_start: 0.7007 (t80) cc_final: 0.6759 (t80) outliers start: 35 outliers final: 20 residues processed: 256 average time/residue: 1.0336 time to fit residues: 301.9388 Evaluate side-chains 251 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.4980 chunk 78 optimal weight: 0.2980 chunk 117 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 97 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 154 optimal weight: 0.0270 chunk 178 optimal weight: 1.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN C 136 ASN C 152 GLN C 277 ASN D 152 GLN D 277 ASN E 19 GLN F 19 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16872 Z= 0.128 Angle : 0.477 11.876 22902 Z= 0.248 Chirality : 0.045 0.132 2634 Planarity : 0.003 0.043 2952 Dihedral : 4.268 16.905 2214 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.40 % Allowed : 19.19 % Favored : 79.41 % 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: 0.75 (0.19), residues: 2094 helix: 0.96 (0.23), residues: 546 sheet: 0.64 (0.26), residues: 342 loop : 0.36 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 58 HIS 0.002 0.001 HIS A 95 PHE 0.030 0.001 PHE C 221 TYR 0.007 0.001 TYR E 225 ARG 0.006 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 232 time to evaluate : 2.106 Fit side-chains REVERT: A 218 MET cc_start: 0.6085 (ttm) cc_final: 0.5877 (ttm) REVERT: B 149 LYS cc_start: 0.8095 (mmmm) cc_final: 0.7676 (mppt) REVERT: B 202 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6029 (tt0) REVERT: B 265 LEU cc_start: 0.8014 (mt) cc_final: 0.7747 (tp) REVERT: C 149 LYS cc_start: 0.8018 (mmmm) cc_final: 0.7493 (tptt) REVERT: C 202 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6135 (tt0) REVERT: C 233 GLU cc_start: 0.6693 (mp0) cc_final: 0.6483 (pm20) REVERT: C 330 MET cc_start: 0.7271 (mmt) cc_final: 0.6911 (mmm) REVERT: D 68 GLU cc_start: 0.7196 (mp0) cc_final: 0.6918 (mp0) REVERT: D 149 LYS cc_start: 0.8007 (mmmm) cc_final: 0.7491 (tptt) REVERT: D 202 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6124 (tt0) REVERT: D 330 MET cc_start: 0.7270 (mmt) cc_final: 0.6907 (mmm) REVERT: E 149 LYS cc_start: 0.8108 (mmmm) cc_final: 0.7691 (mppt) REVERT: E 221 PHE cc_start: 0.6999 (t80) cc_final: 0.6671 (t80) REVERT: E 265 LEU cc_start: 0.8020 (mt) cc_final: 0.7703 (tp) outliers start: 26 outliers final: 17 residues processed: 251 average time/residue: 1.0693 time to fit residues: 303.9677 Evaluate side-chains 240 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 220 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 287 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.8980 chunk 171 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 143 optimal weight: 0.0870 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN C 19 GLN C 152 GLN D 19 GLN D 152 GLN E 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16872 Z= 0.188 Angle : 0.509 11.155 22902 Z= 0.268 Chirality : 0.046 0.135 2634 Planarity : 0.003 0.045 2952 Dihedral : 4.558 18.527 2214 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.40 % Allowed : 19.09 % Favored : 79.52 % 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: 0.65 (0.18), residues: 2094 helix: 0.76 (0.23), residues: 552 sheet: 0.62 (0.26), residues: 342 loop : 0.34 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 58 HIS 0.003 0.001 HIS A 95 PHE 0.032 0.002 PHE C 221 TYR 0.008 0.001 TYR F 32 ARG 0.007 0.000 ARG B 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 1.763 Fit side-chains REVERT: B 149 LYS cc_start: 0.8123 (mmmm) cc_final: 0.7697 (mppt) REVERT: B 202 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6070 (tt0) REVERT: C 149 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7638 (mppt) REVERT: C 202 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6200 (tt0) REVERT: C 233 GLU cc_start: 0.6708 (mp0) cc_final: 0.6490 (pm20) REVERT: C 330 MET cc_start: 0.7350 (mmt) cc_final: 0.6670 (mmm) REVERT: D 149 LYS cc_start: 0.8025 (mmmm) cc_final: 0.7644 (mppt) REVERT: D 202 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.6207 (tt0) REVERT: D 330 MET cc_start: 0.7314 (mmt) cc_final: 0.6649 (mmm) REVERT: E 149 LYS cc_start: 0.8129 (mmmm) cc_final: 0.7703 (mppt) REVERT: F 221 PHE cc_start: 0.7075 (t80) cc_final: 0.6713 (t80) outliers start: 26 outliers final: 21 residues processed: 246 average time/residue: 1.0860 time to fit residues: 302.1203 Evaluate side-chains 247 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 223 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 161 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN C 19 GLN C 152 GLN C 277 ASN D 19 GLN D 152 GLN D 199 ASN D 277 ASN E 19 GLN F 19 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16872 Z= 0.199 Angle : 0.519 11.221 22902 Z= 0.274 Chirality : 0.046 0.135 2634 Planarity : 0.003 0.045 2952 Dihedral : 4.637 18.857 2214 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.45 % Allowed : 19.19 % Favored : 79.35 % 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: 0.60 (0.18), residues: 2094 helix: 0.68 (0.23), residues: 552 sheet: 0.61 (0.26), residues: 342 loop : 0.33 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 58 HIS 0.003 0.001 HIS A 95 PHE 0.033 0.002 PHE D 221 TYR 0.008 0.001 TYR A 32 ARG 0.007 0.000 ARG B 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 226 time to evaluate : 1.806 Fit side-chains REVERT: A 193 TYR cc_start: 0.8628 (m-80) cc_final: 0.8364 (m-80) REVERT: B 149 LYS cc_start: 0.8126 (mmmm) cc_final: 0.7700 (mppt) REVERT: C 149 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7652 (mppt) REVERT: C 202 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6204 (tt0) REVERT: C 233 GLU cc_start: 0.6717 (mp0) cc_final: 0.6495 (pm20) REVERT: C 330 MET cc_start: 0.7316 (mmt) cc_final: 0.7019 (mmm) REVERT: D 149 LYS cc_start: 0.8028 (mmmm) cc_final: 0.7648 (mppt) REVERT: D 202 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6221 (tt0) REVERT: D 330 MET cc_start: 0.7316 (mmt) cc_final: 0.7015 (mmm) REVERT: E 149 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7706 (mppt) REVERT: E 265 LEU cc_start: 0.8101 (mt) cc_final: 0.7859 (tp) REVERT: F 193 TYR cc_start: 0.8629 (m-80) cc_final: 0.8366 (m-80) REVERT: F 221 PHE cc_start: 0.7133 (t80) cc_final: 0.6873 (t80) outliers start: 27 outliers final: 23 residues processed: 244 average time/residue: 1.1128 time to fit residues: 307.3323 Evaluate side-chains 248 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 223 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 147 SER Chi-restraints excluded: chain E residue 232 PHE Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain F residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 0.0970 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN B 19 GLN C 19 GLN C 152 GLN C 277 ASN D 19 GLN D 152 GLN D 277 ASN E 19 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.170246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129149 restraints weight = 93862.123| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 5.61 r_work: 0.2909 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16872 Z= 0.212 Angle : 0.525 11.070 22902 Z= 0.278 Chirality : 0.046 0.135 2634 Planarity : 0.003 0.046 2952 Dihedral : 4.694 19.086 2214 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.45 % Allowed : 19.25 % Favored : 79.30 % 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: 0.56 (0.18), residues: 2094 helix: 0.60 (0.23), residues: 552 sheet: 0.62 (0.26), residues: 342 loop : 0.33 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 58 HIS 0.003 0.001 HIS A 95 PHE 0.034 0.002 PHE C 221 TYR 0.008 0.001 TYR D 225 ARG 0.006 0.000 ARG B 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6047.51 seconds wall clock time: 106 minutes 48.08 seconds (6408.08 seconds total)