Starting phenix.real_space_refine on Thu Mar 21 21:15:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/03_2024/8ert_28560_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/03_2024/8ert_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_28560/03_2024/8ert_28560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/03_2024/8ert_28560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/03_2024/8ert_28560_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ert_28560/03_2024/8ert_28560_neut.pdb" } resolution = 3.3 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= 0.012 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.56, per 1000 atoms: 0.52 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: 5.86 Conformation dependent library (CDL) restraints added in 2.9 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: 1.19 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: 3.86 Time building geometry restraints manager: 6.32 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 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.010 Extract box with map and model: 2.570 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 40.330 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 68 HIS 0.011 0.001 HIS I 51 PHE 0.009 0.001 PHE C 61 TYR 0.039 0.002 TYR I 84 ARG 0.015 0.001 ARG Q 89 *********************** 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 : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7218 (tpt) cc_final: 0.6898 (tmm) REVERT: A 16 ASP cc_start: 0.8159 (t0) cc_final: 0.7901 (t70) REVERT: A 31 ASP cc_start: 0.8139 (m-30) cc_final: 0.7910 (m-30) REVERT: C 1 MET cc_start: 0.6679 (ttp) cc_final: 0.6355 (ttp) REVERT: E 1 MET cc_start: 0.6697 (tmm) cc_final: 0.6243 (ppp) REVERT: G 15 GLU cc_start: 0.7463 (tt0) cc_final: 0.7178 (tt0) REVERT: K 70 MET cc_start: 0.8468 (mtp) cc_final: 0.8258 (mtm) REVERT: M 1 MET cc_start: 0.6300 (tmm) cc_final: 0.5964 (ppp) REVERT: N 46 THR cc_start: 0.8276 (p) cc_final: 0.8035 (p) REVERT: S 9 LYS cc_start: 0.8424 (mtmm) cc_final: 0.8205 (mttp) REVERT: S 45 GLN cc_start: 0.8394 (mp10) cc_final: 0.8191 (mp10) REVERT: S 66 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7983 (mmtp) REVERT: U 1 MET cc_start: 0.7259 (tpp) cc_final: 0.6985 (tmm) REVERT: U 58 MET cc_start: 0.8720 (mtp) cc_final: 0.8457 (ttm) REVERT: V 70 MET cc_start: 0.8195 (mtp) cc_final: 0.7555 (mtp) REVERT: X 27 MET cc_start: 0.9014 (ttp) cc_final: 0.8414 (ttm) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.3684 time to fit residues: 280.5331 Evaluate side-chains 537 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 1.875 ------------------------------------------------------------------------------- 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: 4.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.0030 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 0.0470 chunk 148 optimal weight: 0.0970 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: 0.3488 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16737 Z= 0.143 Angle : 0.533 7.943 22491 Z= 0.282 Chirality : 0.038 0.157 2310 Planarity : 0.004 0.036 2877 Dihedral : 3.824 18.479 2163 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.09 % Favored : 91.76 % Rotamer: Outliers : 0.53 % Allowed : 7.58 % Favored : 91.89 % 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: 0.44 (0.18), residues: 1953 helix: 1.08 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 94 HIS 0.013 0.001 HIS N 51 PHE 0.009 0.001 PHE N 25 TYR 0.022 0.001 TYR I 84 ARG 0.008 0.001 ARG Q 89 *********************** 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 557 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 548 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7263 (tpt) cc_final: 0.6950 (tmm) REVERT: A 31 ASP cc_start: 0.8023 (m-30) cc_final: 0.7658 (m-30) REVERT: C 1 MET cc_start: 0.6669 (ttp) cc_final: 0.6331 (ttp) REVERT: C 30 GLU cc_start: 0.7128 (mp0) cc_final: 0.6758 (mp0) REVERT: D 1 MET cc_start: 0.7911 (tmm) cc_final: 0.7457 (tpp) REVERT: E 1 MET cc_start: 0.6721 (tmm) cc_final: 0.6293 (ppp) REVERT: I 62 ASN cc_start: 0.8609 (m110) cc_final: 0.8273 (m110) REVERT: K 1 MET cc_start: 0.6496 (tmm) cc_final: 0.5248 (pmm) REVERT: K 9 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8354 (mttm) REVERT: M 1 MET cc_start: 0.6362 (tmm) cc_final: 0.6125 (ppp) REVERT: N 1 MET cc_start: 0.6651 (tmm) cc_final: 0.6194 (tpp) REVERT: O 47 GLU cc_start: 0.7828 (pm20) cc_final: 0.7616 (pm20) REVERT: O 79 ASN cc_start: 0.7581 (m-40) cc_final: 0.7184 (m110) REVERT: R 1 MET cc_start: 0.6420 (tmm) cc_final: 0.5988 (tpp) REVERT: R 66 LYS cc_start: 0.8304 (mmmm) cc_final: 0.8086 (mmtp) REVERT: S 9 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8147 (mttp) REVERT: S 66 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7988 (mmtp) REVERT: U 1 MET cc_start: 0.7332 (tpp) cc_final: 0.7039 (tmm) REVERT: W 30 GLU cc_start: 0.7247 (mp0) cc_final: 0.6768 (mp0) REVERT: X 27 MET cc_start: 0.8823 (ttp) cc_final: 0.8432 (ttm) outliers start: 9 outliers final: 3 residues processed: 550 average time/residue: 0.3671 time to fit residues: 273.7027 Evaluate side-chains 533 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 530 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain W residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 153 optimal weight: 0.2980 chunk 170 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** 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: 0.7804 moved from start: 0.1418 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= 0.180 Angle : 0.526 7.841 22491 Z= 0.281 Chirality : 0.039 0.178 2310 Planarity : 0.004 0.031 2877 Dihedral : 3.751 17.438 2163 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.53 % Favored : 92.37 % Rotamer: Outliers : 0.94 % Allowed : 10.52 % Favored : 88.54 % 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: 0.61 (0.18), residues: 1953 helix: 1.18 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 68 HIS 0.015 0.001 HIS F 51 PHE 0.008 0.001 PHE N 25 TYR 0.014 0.001 TYR I 84 ARG 0.009 0.001 ARG F 43 *********************** 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: 16 poor density : 536 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7180 (tpt) cc_final: 0.6923 (tmm) REVERT: A 31 ASP cc_start: 0.8153 (m-30) cc_final: 0.7656 (m-30) REVERT: C 1 MET cc_start: 0.6628 (ttp) cc_final: 0.6279 (ttp) REVERT: C 30 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6777 (mp0) REVERT: D 1 MET cc_start: 0.7937 (tmm) cc_final: 0.7461 (tpp) REVERT: E 1 MET cc_start: 0.6765 (tmm) cc_final: 0.6280 (ppp) REVERT: G 62 ASN cc_start: 0.9051 (m110) cc_final: 0.8750 (m110) REVERT: I 62 ASN cc_start: 0.8649 (m110) cc_final: 0.8391 (m110) REVERT: K 1 MET cc_start: 0.6404 (tmm) cc_final: 0.5264 (pmm) REVERT: K 9 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8439 (mttm) REVERT: M 1 MET cc_start: 0.6438 (tmm) cc_final: 0.6140 (ppp) REVERT: O 65 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7553 (mm-30) REVERT: O 79 ASN cc_start: 0.7610 (m-40) cc_final: 0.7287 (m110) REVERT: R 45 GLN cc_start: 0.8217 (mp10) cc_final: 0.7920 (mp10) REVERT: R 66 LYS cc_start: 0.8410 (mmmm) cc_final: 0.8067 (mttm) REVERT: U 1 MET cc_start: 0.7452 (tpp) cc_final: 0.7044 (tmm) REVERT: W 30 GLU cc_start: 0.7160 (mp0) cc_final: 0.6606 (mp0) REVERT: X 15 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8106 (mm-30) REVERT: X 27 MET cc_start: 0.8851 (ttp) cc_final: 0.8519 (ttm) outliers start: 16 outliers final: 8 residues processed: 539 average time/residue: 0.3586 time to fit residues: 261.8666 Evaluate side-chains 533 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 525 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain S residue 88 LYS Chi-restraints excluded: chain W residue 6 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 5.9990 chunk 129 optimal weight: 0.0570 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 62 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1733 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= 0.153 Angle : 0.531 8.901 22491 Z= 0.281 Chirality : 0.038 0.188 2310 Planarity : 0.004 0.035 2877 Dihedral : 3.693 17.009 2163 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.96 % Rotamer: Outliers : 0.76 % Allowed : 12.87 % Favored : 86.36 % 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: 0.64 (0.18), residues: 1953 helix: 1.20 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 94 HIS 0.013 0.001 HIS R 51 PHE 0.007 0.001 PHE N 25 TYR 0.017 0.001 TYR C 32 ARG 0.010 0.001 ARG Q 89 *********************** 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: 13 poor density : 536 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6847 (mp0) REVERT: D 1 MET cc_start: 0.7890 (tmm) cc_final: 0.7454 (tpp) REVERT: E 1 MET cc_start: 0.6864 (tmm) cc_final: 0.6388 (ppp) REVERT: F 62 ASN cc_start: 0.8840 (m110) cc_final: 0.8485 (m110) REVERT: G 62 ASN cc_start: 0.9041 (m110) cc_final: 0.8748 (m110) REVERT: G 79 ASN cc_start: 0.7431 (m-40) cc_final: 0.7187 (m110) REVERT: I 62 ASN cc_start: 0.8618 (m110) cc_final: 0.8377 (m110) REVERT: K 1 MET cc_start: 0.6639 (tmm) cc_final: 0.5426 (pmm) REVERT: K 3 MET cc_start: 0.6902 (ppp) cc_final: 0.6525 (ppp) REVERT: K 9 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8436 (mttm) REVERT: L 30 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6835 (mp0) REVERT: M 1 MET cc_start: 0.6460 (tmm) cc_final: 0.6195 (ppp) REVERT: M 13 TYR cc_start: 0.8366 (m-10) cc_final: 0.7879 (m-80) REVERT: O 79 ASN cc_start: 0.7474 (m-40) cc_final: 0.7198 (m110) REVERT: R 1 MET cc_start: 0.6485 (tmm) cc_final: 0.5988 (tpp) REVERT: R 45 GLN cc_start: 0.8191 (mp10) cc_final: 0.7886 (mp10) REVERT: S 9 LYS cc_start: 0.8349 (mttt) cc_final: 0.8100 (mttp) REVERT: S 66 LYS cc_start: 0.8235 (mmtp) cc_final: 0.7902 (mmtt) REVERT: U 1 MET cc_start: 0.7378 (tpp) cc_final: 0.6965 (tmm) REVERT: W 30 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6854 (mp0) REVERT: X 24 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8413 (mtmt) REVERT: X 27 MET cc_start: 0.8893 (ttp) cc_final: 0.8540 (ttm) outliers start: 13 outliers final: 7 residues processed: 540 average time/residue: 0.3589 time to fit residues: 263.0864 Evaluate side-chains 528 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 521 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 75 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 163 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 J 62 ASN M 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 79 ASN ** U 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 ASN ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16737 Z= 0.245 Angle : 0.566 8.892 22491 Z= 0.299 Chirality : 0.040 0.209 2310 Planarity : 0.004 0.037 2877 Dihedral : 3.730 16.163 2163 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.14 % Favored : 91.81 % Rotamer: Outliers : 1.41 % Allowed : 13.58 % Favored : 85.01 % 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: 0.70 (0.18), residues: 1953 helix: 1.22 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.30 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 94 HIS 0.015 0.002 HIS X 51 PHE 0.008 0.001 PHE N 25 TYR 0.015 0.001 TYR C 32 ARG 0.010 0.001 ARG F 43 *********************** 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 564 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 540 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6877 (mp0) REVERT: D 1 MET cc_start: 0.7795 (tmm) cc_final: 0.7351 (tpp) REVERT: E 1 MET cc_start: 0.6963 (tmm) cc_final: 0.6343 (ppp) REVERT: E 3 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.5625 (tmm) REVERT: G 62 ASN cc_start: 0.9066 (m110) cc_final: 0.8784 (m-40) REVERT: G 79 ASN cc_start: 0.7601 (m-40) cc_final: 0.7364 (m110) REVERT: I 62 ASN cc_start: 0.8856 (m110) cc_final: 0.8630 (m110) REVERT: K 1 MET cc_start: 0.6690 (tmm) cc_final: 0.5524 (pmm) REVERT: K 3 MET cc_start: 0.6917 (ppp) cc_final: 0.6124 (ppp) REVERT: K 9 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8487 (mttm) REVERT: L 13 TYR cc_start: 0.8389 (m-80) cc_final: 0.8164 (m-80) REVERT: M 62 ASN cc_start: 0.8708 (m-40) cc_final: 0.8318 (m-40) REVERT: O 79 ASN cc_start: 0.7769 (m-40) cc_final: 0.7499 (m110) REVERT: R 1 MET cc_start: 0.6528 (tmm) cc_final: 0.6118 (tpp) REVERT: R 45 GLN cc_start: 0.8326 (mp10) cc_final: 0.7993 (mp10) REVERT: R 66 LYS cc_start: 0.8464 (mmmm) cc_final: 0.8126 (mttm) REVERT: S 65 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7594 (mm-30) REVERT: S 66 LYS cc_start: 0.8315 (mmtp) cc_final: 0.8082 (mmtt) REVERT: U 1 MET cc_start: 0.7505 (tpp) cc_final: 0.6996 (tmm) REVERT: W 30 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6966 (mp0) REVERT: X 27 MET cc_start: 0.8892 (ttp) cc_final: 0.8519 (ttm) REVERT: X 66 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7577 (mmmt) outliers start: 24 outliers final: 15 residues processed: 544 average time/residue: 0.3623 time to fit residues: 266.5556 Evaluate side-chains 548 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 532 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain S residue 88 LYS Chi-restraints excluded: chain U residue 27 MET Chi-restraints excluded: chain W residue 6 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 84 optimal weight: 0.0770 chunk 15 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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 62 ASN ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** V 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16737 Z= 0.176 Angle : 0.558 9.168 22491 Z= 0.296 Chirality : 0.039 0.213 2310 Planarity : 0.004 0.043 2877 Dihedral : 3.718 16.167 2163 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 0.94 % Allowed : 15.64 % Favored : 83.42 % 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: 0.68 (0.18), residues: 1953 helix: 1.20 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.29 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 68 HIS 0.013 0.001 HIS R 51 PHE 0.008 0.001 PHE N 25 TYR 0.014 0.001 TYR C 32 ARG 0.012 0.001 ARG F 43 *********************** 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 547 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 531 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6894 (tmm) cc_final: 0.6385 (ppp) REVERT: A 64 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6838 (mm-30) REVERT: C 30 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6863 (mp0) REVERT: D 1 MET cc_start: 0.7727 (tmm) cc_final: 0.7300 (tpp) REVERT: E 1 MET cc_start: 0.6964 (tmm) cc_final: 0.6374 (ppp) REVERT: E 3 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.5688 (tmm) REVERT: F 62 ASN cc_start: 0.8840 (m-40) cc_final: 0.8529 (m110) REVERT: G 62 ASN cc_start: 0.8992 (m-40) cc_final: 0.8701 (m110) REVERT: I 62 ASN cc_start: 0.8759 (m110) cc_final: 0.8530 (m110) REVERT: K 1 MET cc_start: 0.6835 (tmm) cc_final: 0.5600 (pmm) REVERT: K 3 MET cc_start: 0.6947 (ppp) cc_final: 0.6027 (ppp) REVERT: K 26 LYS cc_start: 0.8701 (mttt) cc_final: 0.8018 (mttt) REVERT: L 13 TYR cc_start: 0.8372 (m-80) cc_final: 0.8137 (m-80) REVERT: M 62 ASN cc_start: 0.8546 (m-40) cc_final: 0.8259 (m-40) REVERT: O 79 ASN cc_start: 0.7579 (m-40) cc_final: 0.7349 (m110) REVERT: R 45 GLN cc_start: 0.8279 (mp10) cc_final: 0.7973 (mp10) REVERT: R 66 LYS cc_start: 0.8376 (mmmm) cc_final: 0.8033 (mttm) REVERT: S 65 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7529 (mm-30) REVERT: S 66 LYS cc_start: 0.8268 (mmtp) cc_final: 0.8034 (mmtt) REVERT: U 1 MET cc_start: 0.7457 (tpp) cc_final: 0.6948 (tmm) REVERT: W 30 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6887 (mp0) REVERT: X 24 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8428 (mtmt) REVERT: X 27 MET cc_start: 0.8883 (ttp) cc_final: 0.8509 (ttm) REVERT: X 66 LYS cc_start: 0.7748 (mmtm) cc_final: 0.7525 (mmmt) outliers start: 16 outliers final: 11 residues processed: 534 average time/residue: 0.3706 time to fit residues: 267.6576 Evaluate side-chains 536 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 524 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 153 optimal weight: 9.9990 chunk 102 optimal weight: 0.0770 chunk 182 optimal weight: 4.9990 chunk 114 optimal weight: 0.0270 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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 ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 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: 0.7834 moved from start: 0.1962 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= 0.208 Angle : 0.576 9.656 22491 Z= 0.303 Chirality : 0.040 0.235 2310 Planarity : 0.005 0.048 2877 Dihedral : 3.722 17.044 2163 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 1.06 % Allowed : 16.17 % Favored : 82.77 % 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: 0.69 (0.18), residues: 1953 helix: 1.21 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 68 HIS 0.016 0.002 HIS L 51 PHE 0.008 0.001 PHE N 25 TYR 0.014 0.001 TYR K 32 ARG 0.013 0.001 ARG F 43 *********************** 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 557 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 539 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6416 (tmm) cc_final: 0.6077 (ppp) REVERT: C 30 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6878 (mp0) REVERT: D 1 MET cc_start: 0.7714 (tmm) cc_final: 0.7284 (tpp) REVERT: E 3 MET cc_start: 0.6104 (tmm) cc_final: 0.5730 (tmm) REVERT: G 62 ASN cc_start: 0.8988 (m-40) cc_final: 0.8753 (m-40) REVERT: I 62 ASN cc_start: 0.8743 (m110) cc_final: 0.8521 (m110) REVERT: K 1 MET cc_start: 0.6855 (tmm) cc_final: 0.5692 (pmm) REVERT: K 3 MET cc_start: 0.6918 (ppp) cc_final: 0.5987 (ppp) REVERT: K 26 LYS cc_start: 0.8728 (mttt) cc_final: 0.7984 (mttt) REVERT: L 13 TYR cc_start: 0.8359 (m-80) cc_final: 0.8111 (m-80) REVERT: M 62 ASN cc_start: 0.8554 (m-40) cc_final: 0.8276 (m-40) REVERT: O 79 ASN cc_start: 0.7659 (m-40) cc_final: 0.7445 (m110) REVERT: R 1 MET cc_start: 0.6544 (tmm) cc_final: 0.5936 (tpp) REVERT: R 45 GLN cc_start: 0.8326 (mp10) cc_final: 0.8016 (mp10) REVERT: U 1 MET cc_start: 0.7450 (tpp) cc_final: 0.6759 (ppp) REVERT: W 30 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6838 (mp0) REVERT: X 24 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8425 (mtmt) REVERT: X 27 MET cc_start: 0.8902 (ttp) cc_final: 0.8544 (ttm) REVERT: X 66 LYS cc_start: 0.7796 (mmtm) cc_final: 0.7574 (mmmt) outliers start: 18 outliers final: 13 residues processed: 542 average time/residue: 0.3649 time to fit residues: 267.4375 Evaluate side-chains 545 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 532 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain O residue 43 ARG Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 83 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 0.0770 chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 165 optimal weight: 0.3980 overall best weight: 2.0944 ------------------------------------------------------------------------------- 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 G 79 ASN ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7858 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16737 Z= 0.248 Angle : 0.603 9.712 22491 Z= 0.318 Chirality : 0.041 0.250 2310 Planarity : 0.005 0.052 2877 Dihedral : 3.788 15.778 2163 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.35 % Allowed : 16.40 % Favored : 82.25 % 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: 1.05 (0.13), residues: 1386 sheet: None (None), residues: 0 loop : -1.06 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 68 HIS 0.015 0.002 HIS L 51 PHE 0.008 0.001 PHE N 25 TYR 0.014 0.001 TYR K 32 ARG 0.014 0.001 ARG F 43 *********************** 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 560 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 537 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6149 (tmm) cc_final: 0.5696 (tpp) REVERT: C 30 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6859 (mp0) REVERT: D 1 MET cc_start: 0.7810 (tmm) cc_final: 0.7326 (tpp) REVERT: E 3 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5701 (tmm) REVERT: G 62 ASN cc_start: 0.8983 (m-40) cc_final: 0.8744 (m-40) REVERT: K 1 MET cc_start: 0.6854 (tmm) cc_final: 0.5728 (pmm) REVERT: K 3 MET cc_start: 0.6883 (ppp) cc_final: 0.5911 (ppp) REVERT: L 13 TYR cc_start: 0.8393 (m-80) cc_final: 0.8152 (m-80) REVERT: M 62 ASN cc_start: 0.8541 (m-40) cc_final: 0.8272 (m-40) REVERT: O 65 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7540 (mm-30) REVERT: O 79 ASN cc_start: 0.7744 (m-40) cc_final: 0.7544 (m110) REVERT: R 45 GLN cc_start: 0.8358 (mp10) cc_final: 0.8026 (mp10) REVERT: S 65 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7580 (mm-30) REVERT: U 1 MET cc_start: 0.7512 (tpp) cc_final: 0.6720 (ppp) REVERT: W 30 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6768 (mp0) REVERT: X 24 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8413 (mtmt) REVERT: X 27 MET cc_start: 0.8911 (ttp) cc_final: 0.8553 (ttm) REVERT: X 66 LYS cc_start: 0.7822 (mmtm) cc_final: 0.7581 (mmmt) outliers start: 23 outliers final: 15 residues processed: 542 average time/residue: 0.3711 time to fit residues: 271.3499 Evaluate side-chains 547 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 531 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain X residue 16 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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** R 62 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: 0.7843 moved from start: 0.2085 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= 0.214 Angle : 0.603 10.382 22491 Z= 0.318 Chirality : 0.040 0.256 2310 Planarity : 0.005 0.056 2877 Dihedral : 3.771 15.708 2163 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 1.12 % Allowed : 16.99 % Favored : 81.89 % 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: 1.12 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.28 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 68 HIS 0.013 0.001 HIS R 51 PHE 0.008 0.001 PHE N 25 TYR 0.013 0.001 TYR K 32 ARG 0.015 0.001 ARG F 43 *********************** 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 556 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 537 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6062 (tmm) cc_final: 0.5678 (tpp) REVERT: C 30 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6877 (mp0) REVERT: D 1 MET cc_start: 0.7801 (tmm) cc_final: 0.7316 (tpp) REVERT: E 3 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5672 (tmm) REVERT: G 62 ASN cc_start: 0.8997 (m-40) cc_final: 0.8751 (m-40) REVERT: K 1 MET cc_start: 0.6867 (tmm) cc_final: 0.5915 (pmm) REVERT: K 3 MET cc_start: 0.6834 (ppp) cc_final: 0.5867 (ppp) REVERT: L 13 TYR cc_start: 0.8391 (m-80) cc_final: 0.8147 (m-80) REVERT: M 62 ASN cc_start: 0.8491 (m-40) cc_final: 0.8233 (m-40) REVERT: R 1 MET cc_start: 0.6771 (tmm) cc_final: 0.6516 (tmm) REVERT: R 45 GLN cc_start: 0.8335 (mp10) cc_final: 0.7998 (mp10) REVERT: S 65 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7514 (mm-30) REVERT: U 1 MET cc_start: 0.7540 (tpp) cc_final: 0.6773 (ppp) REVERT: W 30 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6768 (mp0) REVERT: X 24 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8417 (mtmt) REVERT: X 27 MET cc_start: 0.8897 (ttp) cc_final: 0.8593 (ttm) REVERT: X 66 LYS cc_start: 0.7811 (mmtm) cc_final: 0.7579 (mmmt) outliers start: 19 outliers final: 15 residues processed: 540 average time/residue: 0.3573 time to fit residues: 260.8969 Evaluate side-chains 551 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 535 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain V residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16737 Z= 0.203 Angle : 0.610 10.168 22491 Z= 0.321 Chirality : 0.040 0.256 2310 Planarity : 0.005 0.061 2877 Dihedral : 3.761 15.700 2163 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.00 % Allowed : 17.87 % Favored : 81.13 % 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: 1.11 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 94 HIS 0.013 0.001 HIS R 51 PHE 0.008 0.001 PHE N 25 TYR 0.012 0.001 TYR M 84 ARG 0.016 0.001 ARG F 43 ********************** 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 553 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 536 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6076 (tmm) cc_final: 0.5749 (tpp) REVERT: C 30 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6869 (mp0) REVERT: D 1 MET cc_start: 0.7793 (tmm) cc_final: 0.7323 (tpp) REVERT: E 3 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.5667 (tmm) REVERT: G 62 ASN cc_start: 0.8995 (m-40) cc_final: 0.8736 (m-40) REVERT: K 1 MET cc_start: 0.6838 (tmm) cc_final: 0.5954 (pmm) REVERT: L 13 TYR cc_start: 0.8379 (m-80) cc_final: 0.8144 (m-80) REVERT: M 62 ASN cc_start: 0.8461 (m-40) cc_final: 0.8201 (m-40) REVERT: R 45 GLN cc_start: 0.8326 (mp10) cc_final: 0.7983 (mp10) REVERT: R 66 LYS cc_start: 0.8159 (mmtp) cc_final: 0.7692 (mttt) REVERT: S 65 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7568 (mm-30) REVERT: U 1 MET cc_start: 0.7502 (tpp) cc_final: 0.6799 (ppp) REVERT: W 30 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6770 (mp0) REVERT: X 24 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8411 (mtmt) REVERT: X 27 MET cc_start: 0.8848 (ttp) cc_final: 0.8550 (ttm) REVERT: X 66 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7574 (mmmt) outliers start: 17 outliers final: 16 residues processed: 539 average time/residue: 0.3792 time to fit residues: 278.2642 Evaluate side-chains 549 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 532 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain E residue 3 MET Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 15 GLU Chi-restraints excluded: chain S residue 27 MET Chi-restraints excluded: chain U residue 57 LEU Chi-restraints excluded: chain V residue 27 MET Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 9.9990 chunk 138 optimal weight: 0.0070 chunk 22 optimal weight: 0.0010 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7206 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.158872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132291 restraints weight = 19304.051| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.07 r_work: 0.3420 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2209 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= 0.171 Angle : 0.594 8.391 22491 Z= 0.315 Chirality : 0.039 0.258 2310 Planarity : 0.005 0.060 2877 Dihedral : 3.705 15.744 2163 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.88 % Allowed : 17.93 % Favored : 81.19 % 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: 0.62 (0.18), residues: 1953 helix: 1.13 (0.13), residues: 1365 sheet: None (None), residues: 0 loop : -1.26 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 94 HIS 0.014 0.001 HIS R 51 PHE 0.008 0.001 PHE N 25 TYR 0.012 0.001 TYR M 84 ARG 0.015 0.001 ARG Q 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4745.92 seconds wall clock time: 85 minutes 30.92 seconds (5130.92 seconds total)