Starting phenix.real_space_refine (version: dev) on Mon Feb 27 22:40:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/02_2023/8ert_28560_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/02_2023/8ert_28560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/02_2023/8ert_28560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/02_2023/8ert_28560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/02_2023/8ert_28560_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/02_2023/8ert_28560_neut.pdb" } resolution = 3.3 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= 0.012 sd= 0.114 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14994 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "B TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "C ASP 16": "OD1" <-> "OD2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "D TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "F TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "I TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 21": "OD1" <-> "OD2" Residue "J TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 85": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "K ASP 16": "OD1" <-> "OD2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "M TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 16": "OD1" <-> "OD2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "M PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 65": "OE1" <-> "OE2" Residue "M ASP 82": "OD1" <-> "OD2" Residue "M GLU 85": "OE1" <-> "OE2" Residue "N PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 82": "OD1" <-> "OD2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "O ASP 16": "OD1" <-> "OD2" Residue "O GLU 30": "OE1" <-> "OE2" Residue "O ASP 53": "OD1" <-> "OD2" Residue "O GLU 65": "OE1" <-> "OE2" Residue "Q PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "R GLU 47": "OE1" <-> "OE2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 16": "OD1" <-> "OD2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S ASP 53": "OD1" <-> "OD2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S GLU 65": "OE1" <-> "OE2" Residue "S ASP 82": "OD1" <-> "OD2" Residue "U ASP 21": "OD1" <-> "OD2" Residue "U PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 64": "OE1" <-> "OE2" Residue "U GLU 65": "OE1" <-> "OE2" Residue "V TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 85": "OE1" <-> "OE2" Residue "X TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 47": "OE1" <-> "OE2" Residue "X PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 65": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16359 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "B" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "D" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "G" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "J" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "K" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "L" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "M" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "N" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "O" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "Q" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "R" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "S" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "V" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "W" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "X" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Time building chain proxies: 9.80, per 1000 atoms: 0.60 Number of scatterers: 16359 At special positions: 0 Unit cell: (94.34, 96.46, 128.26, 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 147 16.00 O 2940 8.00 N 2835 7.00 C 10437 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: 7.19 Conformation dependent library (CDL) restraints added in 2.4 seconds 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3822 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 0 sheets defined 69.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 5 through 17 removed outlier: 3.659A pdb=" N LEU A 17 " --> pdb=" O TYR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 31 Processing helix chain 'A' and resid 51 through 78 removed outlier: 7.736A pdb=" N GLU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N GLU A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 90 Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.575A pdb=" N LYS B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 31 Processing helix chain 'B' and resid 51 through 78 removed outlier: 7.576A pdb=" N GLU B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N GLU B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 90 Processing helix chain 'C' and resid 5 through 17 removed outlier: 3.555A pdb=" N LYS C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 17 " --> pdb=" O TYR C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 31 removed outlier: 3.569A pdb=" N ASP C 31 " --> pdb=" O MET C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 78 removed outlier: 3.577A pdb=" N ALA C 55 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLU C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 9.525A pdb=" N GLU C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'D' and resid 5 through 17 removed outlier: 3.534A pdb=" N LYS D 9 " --> pdb=" O SER D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 31 Processing helix chain 'D' and resid 51 through 78 removed outlier: 3.545A pdb=" N ALA D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU D 64 " --> pdb=" O ASP D 60 " (cutoff:3.500A) removed outlier: 9.543A pdb=" N GLU D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'E' and resid 5 through 17 removed outlier: 3.596A pdb=" N LEU E 17 " --> pdb=" O TYR E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 31 Processing helix chain 'E' and resid 51 through 78 removed outlier: 3.574A pdb=" N ALA E 55 " --> pdb=" O HIS E 51 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU E 64 " --> pdb=" O ASP E 60 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N GLU E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS E 66 " --> pdb=" O ASN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 90 Processing helix chain 'F' and resid 5 through 17 removed outlier: 3.577A pdb=" N LEU F 17 " --> pdb=" O TYR F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 31 Processing helix chain 'F' and resid 51 through 63 removed outlier: 3.708A pdb=" N ALA F 55 " --> pdb=" O HIS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 78 Processing helix chain 'F' and resid 80 through 90 Processing helix chain 'G' and resid 5 through 16 removed outlier: 3.528A pdb=" N LYS G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 31 Processing helix chain 'G' and resid 51 through 63 removed outlier: 3.603A pdb=" N ALA G 55 " --> pdb=" O HIS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 78 Processing helix chain 'G' and resid 80 through 90 Processing helix chain 'I' and resid 5 through 17 removed outlier: 3.592A pdb=" N LEU I 17 " --> pdb=" O TYR I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 31 Processing helix chain 'I' and resid 51 through 63 Processing helix chain 'I' and resid 63 through 78 Processing helix chain 'I' and resid 80 through 90 Processing helix chain 'J' and resid 5 through 17 removed outlier: 3.600A pdb=" N LYS J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU J 17 " --> pdb=" O TYR J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 31 Processing helix chain 'J' and resid 51 through 78 removed outlier: 7.588A pdb=" N GLU J 64 " --> pdb=" O ASP J 60 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS J 66 " --> pdb=" O ASN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 Processing helix chain 'K' and resid 5 through 17 removed outlier: 3.687A pdb=" N LEU K 17 " --> pdb=" O TYR K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 31 removed outlier: 3.574A pdb=" N ASP K 31 " --> pdb=" O MET K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 78 removed outlier: 3.534A pdb=" N ALA K 55 " --> pdb=" O HIS K 51 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLU K 64 " --> pdb=" O ASP K 60 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N GLU K 65 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS K 66 " --> pdb=" O ASN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 90 Processing helix chain 'L' and resid 5 through 16 Processing helix chain 'L' and resid 18 through 31 Processing helix chain 'L' and resid 51 through 78 removed outlier: 3.840A pdb=" N ALA L 55 " --> pdb=" O HIS L 51 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLU L 64 " --> pdb=" O ASP L 60 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N GLU L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS L 66 " --> pdb=" O ASN L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 90 Processing helix chain 'M' and resid 5 through 17 removed outlier: 3.699A pdb=" N LEU M 17 " --> pdb=" O TYR M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 31 Processing helix chain 'M' and resid 51 through 78 removed outlier: 3.638A pdb=" N ALA M 55 " --> pdb=" O HIS M 51 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N GLU M 64 " --> pdb=" O ASP M 60 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N GLU M 65 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS M 66 " --> pdb=" O ASN M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 90 Processing helix chain 'N' and resid 5 through 17 removed outlier: 3.589A pdb=" N LEU N 17 " --> pdb=" O TYR N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 31 Processing helix chain 'N' and resid 51 through 78 removed outlier: 3.739A pdb=" N ALA N 55 " --> pdb=" O HIS N 51 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLU N 64 " --> pdb=" O ASP N 60 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N GLU N 65 " --> pdb=" O PHE N 61 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS N 66 " --> pdb=" O ASN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 Processing helix chain 'O' and resid 5 through 17 removed outlier: 3.545A pdb=" N LYS O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU O 17 " --> pdb=" O TYR O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 31 Processing helix chain 'O' and resid 51 through 78 removed outlier: 3.656A pdb=" N ALA O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N GLU O 65 " --> pdb=" O PHE O 61 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYS O 66 " --> pdb=" O ASN O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 90 Processing helix chain 'Q' and resid 5 through 17 removed outlier: 3.629A pdb=" N LEU Q 17 " --> pdb=" O TYR Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 31 Processing helix chain 'Q' and resid 51 through 78 removed outlier: 3.683A pdb=" N ALA Q 55 " --> pdb=" O HIS Q 51 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU Q 64 " --> pdb=" O ASP Q 60 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N GLU Q 65 " --> pdb=" O PHE Q 61 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS Q 66 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 90 Processing helix chain 'R' and resid 5 through 17 removed outlier: 3.586A pdb=" N LEU R 17 " --> pdb=" O TYR R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 31 Processing helix chain 'R' and resid 51 through 63 removed outlier: 3.724A pdb=" N ALA R 55 " --> pdb=" O HIS R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 78 Processing helix chain 'R' and resid 80 through 90 Processing helix chain 'S' and resid 5 through 17 removed outlier: 3.584A pdb=" N LYS S 9 " --> pdb=" O SER S 5 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU S 17 " --> pdb=" O TYR S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 31 Processing helix chain 'S' and resid 34 through 38 removed outlier: 3.955A pdb=" N GLY S 37 " --> pdb=" O PRO S 34 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS S 38 " --> pdb=" O GLN S 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 34 through 38' Processing helix chain 'S' and resid 51 through 78 removed outlier: 3.624A pdb=" N ALA S 55 " --> pdb=" O HIS S 51 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLU S 64 " --> pdb=" O ASP S 60 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU S 65 " --> pdb=" O PHE S 61 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS S 66 " --> pdb=" O ASN S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 90 Processing helix chain 'U' and resid 5 through 17 removed outlier: 3.673A pdb=" N LEU U 17 " --> pdb=" O TYR U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 31 Processing helix chain 'U' and resid 51 through 78 removed outlier: 7.716A pdb=" N GLU U 64 " --> pdb=" O ASP U 60 " (cutoff:3.500A) removed outlier: 9.520A pdb=" N GLU U 65 " --> pdb=" O PHE U 61 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS U 66 " --> pdb=" O ASN U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 90 Processing helix chain 'V' and resid 5 through 17 removed outlier: 3.592A pdb=" N LYS V 9 " --> pdb=" O SER V 5 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU V 17 " --> pdb=" O TYR V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 31 Processing helix chain 'V' and resid 51 through 78 removed outlier: 3.515A pdb=" N ALA V 55 " --> pdb=" O HIS V 51 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLU V 64 " --> pdb=" O ASP V 60 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N GLU V 65 " --> pdb=" O PHE V 61 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS V 66 " --> pdb=" O ASN V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 80 through 90 Processing helix chain 'W' and resid 5 through 17 removed outlier: 3.502A pdb=" N LYS W 9 " --> pdb=" O SER W 5 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU W 17 " --> pdb=" O TYR W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 31 removed outlier: 3.636A pdb=" N ASP W 31 " --> pdb=" O MET W 27 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 78 removed outlier: 7.737A pdb=" N GLU W 64 " --> pdb=" O ASP W 60 " (cutoff:3.500A) removed outlier: 9.510A pdb=" N GLU W 65 " --> pdb=" O PHE W 61 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 90 Processing helix chain 'X' and resid 5 through 17 removed outlier: 3.609A pdb=" N LYS X 9 " --> pdb=" O SER X 5 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU X 17 " --> pdb=" O TYR X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 18 through 31 Processing helix chain 'X' and resid 51 through 78 removed outlier: 3.649A pdb=" N ALA X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLU X 64 " --> pdb=" O ASP X 60 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N GLU X 65 " --> pdb=" O PHE X 61 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS X 66 " --> pdb=" O ASN X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 80 through 90 939 hydrogen bonds defined for protein. 2817 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: 4.33 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5313 1.34 - 1.46: 3488 1.46 - 1.58: 7684 1.58 - 1.70: 0 1.70 - 1.81: 252 Bond restraints: 16737 Sorted by residual: bond pdb=" CG LYS I 88 " pdb=" CD LYS I 88 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 bond pdb=" CE LYS I 88 " pdb=" NZ LYS I 88 " ideal model delta sigma weight residual 1.489 1.446 0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CG ARG E 89 " pdb=" CD ARG E 89 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CA ILE L 39 " pdb=" C ILE L 39 " ideal model delta sigma weight residual 1.528 1.519 0.009 8.50e-03 1.38e+04 1.05e+00 bond pdb=" CG ARG L 89 " pdb=" CD ARG L 89 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 16732 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 621 106.97 - 113.73: 9015 113.73 - 120.49: 6845 120.49 - 127.25: 5763 127.25 - 134.01: 247 Bond angle restraints: 22491 Sorted by residual: angle pdb=" CG LYS I 88 " pdb=" CD LYS I 88 " pdb=" CE LYS I 88 " ideal model delta sigma weight residual 111.30 103.00 8.30 2.30e+00 1.89e-01 1.30e+01 angle pdb=" N LYS I 88 " pdb=" CA LYS I 88 " pdb=" CB LYS I 88 " ideal model delta sigma weight residual 110.01 114.39 -4.38 1.45e+00 4.76e-01 9.13e+00 angle pdb=" C ALA I 87 " pdb=" N LYS I 88 " pdb=" CA LYS I 88 " ideal model delta sigma weight residual 120.44 116.76 3.68 1.30e+00 5.92e-01 8.00e+00 angle pdb=" CA TYR X 84 " pdb=" CB TYR X 84 " pdb=" CG TYR X 84 " ideal model delta sigma weight residual 113.90 118.88 -4.98 1.80e+00 3.09e-01 7.65e+00 angle pdb=" CB MET I 3 " pdb=" CG MET I 3 " pdb=" SD MET I 3 " ideal model delta sigma weight residual 112.70 120.79 -8.09 3.00e+00 1.11e-01 7.27e+00 ... (remaining 22486 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9182 17.75 - 35.51: 935 35.51 - 53.26: 196 53.26 - 71.02: 16 71.02 - 88.77: 3 Dihedral angle restraints: 10332 sinusoidal: 4473 harmonic: 5859 Sorted by residual: dihedral pdb=" CA GLU X 47 " pdb=" C GLU X 47 " pdb=" N LYS X 48 " pdb=" CA LYS X 48 " ideal model delta harmonic sigma weight residual 180.00 159.02 20.98 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA PHE O 61 " pdb=" C PHE O 61 " pdb=" N ASN O 62 " pdb=" CA ASN O 62 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE I 61 " pdb=" C PHE I 61 " pdb=" N ASN I 62 " pdb=" CA ASN I 62 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 10329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1330 0.028 - 0.056: 723 0.056 - 0.084: 131 0.084 - 0.111: 97 0.111 - 0.139: 29 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA GLU X 85 " pdb=" N GLU X 85 " pdb=" C GLU X 85 " pdb=" CB GLU X 85 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA LYS I 36 " pdb=" N LYS I 36 " pdb=" C LYS I 36 " pdb=" CB LYS I 36 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA GLU L 85 " pdb=" N GLU L 85 " pdb=" C GLU L 85 " pdb=" CB GLU L 85 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 2307 not shown) Planarity restraints: 2877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 84 " -0.013 2.00e-02 2.50e+03 1.60e-02 5.14e+00 pdb=" CG TYR I 84 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR I 84 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR I 84 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR I 84 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR I 84 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR I 84 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 84 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 89 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.97e+00 pdb=" NE ARG L 89 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG L 89 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG L 89 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG L 89 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 89 " 0.133 9.50e-02 1.11e+02 6.00e-02 2.87e+00 pdb=" NE ARG A 89 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 89 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 89 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 89 " 0.000 2.00e-02 2.50e+03 ... (remaining 2874 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1810 2.74 - 3.28: 16426 3.28 - 3.82: 26610 3.82 - 4.36: 31261 4.36 - 4.90: 54350 Nonbonded interactions: 130457 Sorted by model distance: nonbonded pdb=" OG1 THR I 6 " pdb=" OE2 GLU I 64 " model vdw 2.203 2.440 nonbonded pdb=" NH2 ARG M 43 " pdb=" OE2 GLU U 18 " model vdw 2.243 2.520 nonbonded pdb=" NZ LYS I 24 " pdb=" OE1 GLU M 15 " model vdw 2.265 2.520 nonbonded pdb=" OE2 GLU C 15 " pdb=" NE2 GLN S 45 " model vdw 2.268 2.520 nonbonded pdb=" OE2 GLU G 30 " pdb=" OG1 THR G 46 " model vdw 2.273 2.440 ... (remaining 130452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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 147 5.16 5 C 10437 2.51 5 N 2835 2.21 5 O 2940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 3.450 Check model and map are aligned: 0.230 Process input model: 43.990 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.150 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.470 ------------------------------------------------------------------------------- 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 : 0.003 0.050 16737 Z= 0.183 Angle : 0.588 8.296 22491 Z= 0.324 Chirality : 0.038 0.139 2310 Planarity : 0.005 0.062 2877 Dihedral : 14.141 88.773 6510 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.22 (0.18), residues: 1953 helix: 0.79 (0.13), residues: 1386 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.3791 time to fit residues: 288.5751 Evaluate side-chains 536 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.0030 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 0.0470 chunk 148 optimal weight: 0.1980 chunk 57 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 ASN U 45 GLN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 16737 Z= 0.148 Angle : 0.543 7.743 22491 Z= 0.286 Chirality : 0.038 0.156 2310 Planarity : 0.004 0.032 2877 Dihedral : 3.827 18.476 2163 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.19 % Favored : 91.65 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 1953 helix: 1.07 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.53 (0.25), residues: 588 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 549 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 551 average time/residue: 0.3802 time to fit residues: 284.5319 Evaluate side-chains 537 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 532 time to evaluate : 2.188 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1941 time to fit residues: 4.6391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN ** D 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN U 45 GLN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 16737 Z= 0.163 Angle : 0.528 7.989 22491 Z= 0.281 Chirality : 0.038 0.177 2310 Planarity : 0.004 0.032 2877 Dihedral : 3.758 17.458 2163 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.37 % Favored : 92.47 % Rotamer Outliers : 0.59 % 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: 0.57 (0.18), residues: 1953 helix: 1.15 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 542 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 544 average time/residue: 0.3844 time to fit residues: 283.8377 Evaluate side-chains 534 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 530 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2670 time to fit residues: 4.6533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 0.6980 chunk 129 optimal weight: 0.5980 chunk 89 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN G 62 ASN G 79 ASN I 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN Q 62 ASN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16737 Z= 0.185 Angle : 0.552 9.288 22491 Z= 0.290 Chirality : 0.039 0.184 2310 Planarity : 0.004 0.041 2877 Dihedral : 3.735 16.831 2163 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.04 % Favored : 91.86 % Rotamer Outliers : 0.71 % 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: 0.63 (0.18), residues: 1953 helix: 1.18 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 537 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 538 average time/residue: 0.3930 time to fit residues: 285.5084 Evaluate side-chains 528 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 523 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2331 time to fit residues: 4.8424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 ASN ** I 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN M 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 16737 Z= 0.295 Angle : 0.591 8.992 22491 Z= 0.313 Chirality : 0.041 0.202 2310 Planarity : 0.004 0.039 2877 Dihedral : 3.849 15.970 2163 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.29 % Favored : 91.60 % Rotamer Outliers : 1.12 % 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: 1953 helix: 0.99 (0.13), residues: 1386 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 537 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 540 average time/residue: 0.3977 time to fit residues: 291.1170 Evaluate side-chains 537 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 525 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2652 time to fit residues: 7.8403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 107 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.6682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN O 79 ASN U 45 GLN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16737 Z= 0.165 Angle : 0.575 9.896 22491 Z= 0.303 Chirality : 0.039 0.214 2310 Planarity : 0.005 0.045 2877 Dihedral : 3.756 16.293 2163 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.78 % Favored : 92.17 % Rotamer Outliers : 0.41 % 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: 1953 helix: 1.08 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 588 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 528 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 528 average time/residue: 0.3867 time to fit residues: 275.7291 Evaluate side-chains 511 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 508 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1320 time to fit residues: 3.5372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 114 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN Q 62 ASN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 16737 Z= 0.185 Angle : 0.582 9.416 22491 Z= 0.307 Chirality : 0.039 0.227 2310 Planarity : 0.005 0.050 2877 Dihedral : 3.720 15.625 2163 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 1953 helix: 1.11 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 588 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 521 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 521 average time/residue: 0.3837 time to fit residues: 269.8049 Evaluate side-chains 521 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 516 time to evaluate : 2.066 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1747 time to fit residues: 4.4502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN R 62 ASN U 45 GLN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16737 Z= 0.183 Angle : 0.605 10.850 22491 Z= 0.316 Chirality : 0.039 0.240 2310 Planarity : 0.005 0.053 2877 Dihedral : 3.700 15.536 2163 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 0.35 % 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: 1953 helix: 1.12 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 588 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 523 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 525 average time/residue: 0.3828 time to fit residues: 271.6164 Evaluate side-chains 519 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 516 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1705 time to fit residues: 3.7381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 0.8980 chunk 159 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 111 optimal weight: 0.0970 chunk 179 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN I 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 16737 Z= 0.219 Angle : 0.624 11.012 22491 Z= 0.326 Chirality : 0.040 0.248 2310 Planarity : 0.005 0.056 2877 Dihedral : 3.743 15.431 2163 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer Outliers : 0.29 % 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: 0.59 (0.18), residues: 1953 helix: 1.11 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.25 (0.25), residues: 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 524 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 526 average time/residue: 0.3955 time to fit residues: 280.3541 Evaluate side-chains 524 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 521 time to evaluate : 1.883 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2726 time to fit residues: 3.8225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 16737 Z= 0.198 Angle : 0.637 11.158 22491 Z= 0.333 Chirality : 0.040 0.257 2310 Planarity : 0.005 0.065 2877 Dihedral : 3.745 15.633 2163 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.18), residues: 1953 helix: 1.10 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.24 (0.25), residues: 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 522 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 523 average time/residue: 0.3896 time to fit residues: 275.6323 Evaluate side-chains 519 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 8 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 ASN U 45 GLN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.128048 restraints weight = 19580.312| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.38 r_work: 0.3406 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16737 Z= 0.224 Angle : 0.635 11.060 22491 Z= 0.333 Chirality : 0.040 0.259 2310 Planarity : 0.005 0.060 2877 Dihedral : 3.749 15.571 2163 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer Outliers : 0.29 % 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: 0.57 (0.18), residues: 1953 helix: 1.08 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.22 (0.25), residues: 588 =============================================================================== Job complete usr+sys time: 4605.68 seconds wall clock time: 84 minutes 12.44 seconds (5052.44 seconds total)