Starting phenix.real_space_refine on Sat May 11 10:33:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/05_2024/8umr_42382.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/05_2024/8umr_42382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/05_2024/8umr_42382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/05_2024/8umr_42382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/05_2024/8umr_42382.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umr_42382/05_2024/8umr_42382.pdb" } resolution = 4.42 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= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 11952 2.51 5 N 3120 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 73": "OE1" <-> "OE2" Residue "I TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "I PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J GLU 33": "OE1" <-> "OE2" Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 80": "OE1" <-> "OE2" Residue "K PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 19": "OE1" <-> "OE2" Residue "L GLU 33": "OE1" <-> "OE2" Residue "L TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 19": "OE1" <-> "OE2" Residue "N GLU 33": "OE1" <-> "OE2" Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 19": "OE1" <-> "OE2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 80": "OE1" <-> "OE2" Residue "Q PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 19": "OE1" <-> "OE2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 19": "OE1" <-> "OE2" Residue "T GLU 33": "OE1" <-> "OE2" Residue "T TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 73": "OE1" <-> "OE2" Residue "U TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 80": "OE1" <-> "OE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 19": "OE1" <-> "OE2" Residue "V GLU 33": "OE1" <-> "OE2" Residue "V TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 73": "OE1" <-> "OE2" Residue "W TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 80": "OE1" <-> "OE2" Residue "W PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 19": "OE1" <-> "OE2" Residue "X GLU 33": "OE1" <-> "OE2" Residue "X TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 18615 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "B" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "C" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "F" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "H" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "J" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "M" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "P" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Q" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "R" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "T" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "U" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "V" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "W" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 939 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "X" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 847 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Time building chain proxies: 9.74, per 1000 atoms: 0.52 Number of scatterers: 18615 At special positions: 0 Unit cell: (141.9, 134.2, 105.6, 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 21 16.00 O 3522 8.00 N 3120 7.00 C 11952 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: 8.56 Conformation dependent library (CDL) restraints added in 3.4 seconds 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4554 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 4 sheets defined 63.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.607A pdb=" N LYS A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 34 Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA A 57 " --> pdb=" O ASN A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 88 through 102 Processing helix chain 'A' and resid 105 through 121 Processing helix chain 'B' and resid 32 through 46 Processing helix chain 'B' and resid 81 through 95 removed outlier: 4.220A pdb=" N ASP B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'C' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS C 17 " --> pdb=" O ILE C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 34 Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 53 through 68 removed outlier: 3.865A pdb=" N ALA C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 88 through 102 Processing helix chain 'C' and resid 105 through 121 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 81 through 95 removed outlier: 4.222A pdb=" N ASP D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'F' and resid 32 through 46 Processing helix chain 'F' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 122 Processing helix chain 'G' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS G 17 " --> pdb=" O ILE G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 34 Processing helix chain 'G' and resid 37 through 52 Processing helix chain 'G' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA G 57 " --> pdb=" O ASN G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 86 Processing helix chain 'G' and resid 88 through 102 Processing helix chain 'G' and resid 105 through 121 Processing helix chain 'H' and resid 32 through 46 Processing helix chain 'H' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP H 85 " --> pdb=" O ARG H 81 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N ALA H 86 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 122 Processing helix chain 'I' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS I 17 " --> pdb=" O ILE I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 34 Processing helix chain 'I' and resid 37 through 52 Processing helix chain 'I' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 86 Processing helix chain 'I' and resid 88 through 102 Processing helix chain 'I' and resid 105 through 121 Processing helix chain 'J' and resid 32 through 46 Processing helix chain 'J' and resid 81 through 95 removed outlier: 4.222A pdb=" N ASP J 85 " --> pdb=" O ARG J 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA J 86 " --> pdb=" O GLU J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 122 Processing helix chain 'K' and resid 3 through 17 removed outlier: 3.607A pdb=" N LYS K 17 " --> pdb=" O ILE K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 34 Processing helix chain 'K' and resid 37 through 52 Processing helix chain 'K' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 86 Processing helix chain 'K' and resid 88 through 102 Processing helix chain 'K' and resid 105 through 121 Processing helix chain 'L' and resid 32 through 46 Processing helix chain 'L' and resid 81 through 95 removed outlier: 4.222A pdb=" N ASP L 85 " --> pdb=" O ARG L 81 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA L 86 " --> pdb=" O GLU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 122 Processing helix chain 'M' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS M 17 " --> pdb=" O ILE M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 34 Processing helix chain 'M' and resid 37 through 52 Processing helix chain 'M' and resid 53 through 68 removed outlier: 3.867A pdb=" N ALA M 57 " --> pdb=" O ASN M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 86 Processing helix chain 'M' and resid 88 through 102 Processing helix chain 'M' and resid 105 through 121 Processing helix chain 'N' and resid 32 through 46 Processing helix chain 'N' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 122 Processing helix chain 'P' and resid 32 through 46 Processing helix chain 'P' and resid 81 through 95 removed outlier: 4.222A pdb=" N ASP P 85 " --> pdb=" O ARG P 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA P 86 " --> pdb=" O GLU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 122 Processing helix chain 'Q' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS Q 17 " --> pdb=" O ILE Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 34 Processing helix chain 'Q' and resid 37 through 52 Processing helix chain 'Q' and resid 53 through 68 removed outlier: 3.865A pdb=" N ALA Q 57 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 86 Processing helix chain 'Q' and resid 88 through 102 Processing helix chain 'Q' and resid 105 through 121 Processing helix chain 'R' and resid 32 through 46 Processing helix chain 'R' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP R 85 " --> pdb=" O ARG R 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA R 86 " --> pdb=" O GLU R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 122 Processing helix chain 'T' and resid 32 through 46 Processing helix chain 'T' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP T 85 " --> pdb=" O ARG T 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA T 86 " --> pdb=" O GLU T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 112 through 122 Processing helix chain 'U' and resid 3 through 17 removed outlier: 3.608A pdb=" N LYS U 17 " --> pdb=" O ILE U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 34 Processing helix chain 'U' and resid 37 through 52 Processing helix chain 'U' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA U 57 " --> pdb=" O ASN U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 86 Processing helix chain 'U' and resid 88 through 102 Processing helix chain 'U' and resid 105 through 121 Processing helix chain 'V' and resid 32 through 46 Processing helix chain 'V' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP V 85 " --> pdb=" O ARG V 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA V 86 " --> pdb=" O GLU V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 112 through 122 Processing helix chain 'W' and resid 3 through 17 removed outlier: 3.607A pdb=" N LYS W 17 " --> pdb=" O ILE W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 34 Processing helix chain 'W' and resid 37 through 52 Processing helix chain 'W' and resid 53 through 68 removed outlier: 3.866A pdb=" N ALA W 57 " --> pdb=" O ASN W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 86 Processing helix chain 'W' and resid 88 through 102 Processing helix chain 'W' and resid 105 through 121 Processing helix chain 'X' and resid 32 through 46 Processing helix chain 'X' and resid 81 through 95 removed outlier: 4.221A pdb=" N ASP X 85 " --> pdb=" O ARG X 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA X 86 " --> pdb=" O GLU X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 122 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 17 through 19 current: chain 'B' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 66 through 80 current: chain 'N' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 66 through 80 current: chain 'T' and resid 66 through 80 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 17 through 19 current: chain 'D' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 66 through 80 current: chain 'J' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 66 through 80 current: chain 'V' and resid 66 through 80 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 17 through 19 current: chain 'F' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 66 through 80 current: chain 'L' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 66 through 80 current: chain 'R' and resid 66 through 80 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 17 through 19 current: chain 'H' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 66 through 80 current: chain 'P' and resid 66 through 80 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 66 through 80 current: chain 'X' and resid 66 through 80 No H-bonds generated for sheet with id=AA4 1054 hydrogen bonds defined for protein. 3162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.30 Time building geometry restraints manager: 9.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5769 1.34 - 1.45: 2229 1.45 - 1.57: 10905 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 18933 Sorted by residual: bond pdb=" N ASN P 64 " pdb=" CA ASN P 64 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.83e+00 bond pdb=" N ASN H 64 " pdb=" CA ASN H 64 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 bond pdb=" N ASN D 64 " pdb=" CA ASN D 64 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.76e+00 bond pdb=" N ASN T 64 " pdb=" CA ASN T 64 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.73e+00 bond pdb=" N ASN B 64 " pdb=" CA ASN B 64 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.68e+00 ... (remaining 18928 not shown) Histogram of bond angle deviations from ideal: 101.29 - 107.82: 602 107.82 - 114.36: 10910 114.36 - 120.90: 8872 120.90 - 127.44: 5227 127.44 - 133.98: 150 Bond angle restraints: 25761 Sorted by residual: angle pdb=" N GLN M 62 " pdb=" CA GLN M 62 " pdb=" CB GLN M 62 " ideal model delta sigma weight residual 110.28 115.63 -5.35 1.55e+00 4.16e-01 1.19e+01 angle pdb=" N GLN C 62 " pdb=" CA GLN C 62 " pdb=" CB GLN C 62 " ideal model delta sigma weight residual 110.28 115.61 -5.33 1.55e+00 4.16e-01 1.18e+01 angle pdb=" N GLN A 62 " pdb=" CA GLN A 62 " pdb=" CB GLN A 62 " ideal model delta sigma weight residual 110.28 115.60 -5.32 1.55e+00 4.16e-01 1.18e+01 angle pdb=" N GLN W 62 " pdb=" CA GLN W 62 " pdb=" CB GLN W 62 " ideal model delta sigma weight residual 110.28 115.60 -5.32 1.55e+00 4.16e-01 1.18e+01 angle pdb=" N GLN G 62 " pdb=" CA GLN G 62 " pdb=" CB GLN G 62 " ideal model delta sigma weight residual 110.28 115.59 -5.31 1.55e+00 4.16e-01 1.17e+01 ... (remaining 25756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.42: 9504 10.42 - 20.83: 1098 20.83 - 31.25: 754 31.25 - 41.66: 137 41.66 - 52.08: 36 Dihedral angle restraints: 11529 sinusoidal: 4506 harmonic: 7023 Sorted by residual: dihedral pdb=" CA ASN G 53 " pdb=" C ASN G 53 " pdb=" N TYR G 54 " pdb=" CA TYR G 54 " ideal model delta harmonic sigma weight residual -180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASN U 53 " pdb=" C ASN U 53 " pdb=" N TYR U 54 " pdb=" CA TYR U 54 " ideal model delta harmonic sigma weight residual -180.00 -159.89 -20.11 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASN A 53 " pdb=" C ASN A 53 " pdb=" N TYR A 54 " pdb=" CA TYR A 54 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 11526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2056 0.037 - 0.075: 693 0.075 - 0.112: 222 0.112 - 0.149: 68 0.149 - 0.186: 12 Chirality restraints: 3051 Sorted by residual: chirality pdb=" CG LEU T 53 " pdb=" CB LEU T 53 " pdb=" CD1 LEU T 53 " pdb=" CD2 LEU T 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CG LEU H 53 " pdb=" CB LEU H 53 " pdb=" CD1 LEU H 53 " pdb=" CD2 LEU H 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CG LEU B 53 " pdb=" CB LEU B 53 " pdb=" CD1 LEU B 53 " pdb=" CD2 LEU B 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.56e-01 ... (remaining 3048 not shown) Planarity restraints: 3249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 38 " 0.007 2.00e-02 2.50e+03 1.46e-02 4.25e+00 pdb=" CG TYR J 38 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR J 38 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR J 38 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR J 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR J 38 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 38 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR J 38 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 38 " 0.007 2.00e-02 2.50e+03 1.45e-02 4.22e+00 pdb=" CG TYR R 38 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR R 38 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR R 38 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR R 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR R 38 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 38 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 38 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 38 " 0.007 2.00e-02 2.50e+03 1.45e-02 4.18e+00 pdb=" CG TYR F 38 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR F 38 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 38 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR F 38 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 38 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR F 38 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 38 " -0.001 2.00e-02 2.50e+03 ... (remaining 3246 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 484 2.62 - 3.19: 19027 3.19 - 3.76: 33025 3.76 - 4.33: 41605 4.33 - 4.90: 64594 Nonbonded interactions: 158735 Sorted by model distance: nonbonded pdb=" O ALA K 110 " pdb=" OH TYR L 38 " model vdw 2.052 2.440 nonbonded pdb=" O VAL N 52 " pdb=" NH2 ARG T 61 " model vdw 2.167 2.520 nonbonded pdb=" O ALA C 110 " pdb=" OH TYR D 38 " model vdw 2.172 2.440 nonbonded pdb=" NH2 ARG H 61 " pdb=" O VAL X 52 " model vdw 2.202 2.520 nonbonded pdb=" OH TYR A 54 " pdb=" NH1 ARG B 93 " model vdw 2.217 2.520 ... (remaining 158730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'Q' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.490 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 50.810 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.170 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.004 0.032 18933 Z= 0.274 Angle : 0.822 8.084 25761 Z= 0.449 Chirality : 0.045 0.186 3051 Planarity : 0.007 0.048 3249 Dihedral : 12.523 52.077 6975 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2322 helix: 0.38 (0.13), residues: 1437 sheet: -0.07 (0.27), residues: 300 loop : -0.68 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 117 HIS 0.001 0.000 HIS F 95 PHE 0.017 0.003 PHE D 77 TYR 0.034 0.004 TYR R 38 ARG 0.012 0.001 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 775 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.9703 (tttt) cc_final: 0.9422 (mttt) REVERT: B 24 ARG cc_start: 0.9099 (mpt180) cc_final: 0.8192 (mmt-90) REVERT: B 52 VAL cc_start: 0.8383 (m) cc_final: 0.7415 (m) REVERT: B 103 LEU cc_start: 0.9333 (mt) cc_final: 0.8685 (mp) REVERT: C 14 GLU cc_start: 0.9508 (tp30) cc_final: 0.9006 (tp30) REVERT: C 80 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8243 (pt0) REVERT: D 26 LEU cc_start: 0.9624 (tp) cc_final: 0.9404 (tp) REVERT: D 28 THR cc_start: 0.8695 (m) cc_final: 0.8350 (m) REVERT: D 52 VAL cc_start: 0.9408 (m) cc_final: 0.9193 (m) REVERT: D 63 GLU cc_start: 0.8911 (tp30) cc_final: 0.8144 (pm20) REVERT: D 66 LYS cc_start: 0.8895 (mptt) cc_final: 0.8552 (mmmm) REVERT: D 68 VAL cc_start: 0.9536 (p) cc_final: 0.9192 (m) REVERT: D 80 THR cc_start: 0.9677 (p) cc_final: 0.9440 (p) REVERT: D 83 ARG cc_start: 0.8787 (tpp80) cc_final: 0.8415 (ttt180) REVERT: D 95 HIS cc_start: 0.7394 (t-90) cc_final: 0.6903 (t-170) REVERT: F 85 ASP cc_start: 0.9290 (m-30) cc_final: 0.8842 (t70) REVERT: F 116 ASP cc_start: 0.8510 (m-30) cc_final: 0.8229 (p0) REVERT: G 20 TYR cc_start: 0.8927 (m-10) cc_final: 0.8665 (m-10) REVERT: G 68 ASP cc_start: 0.8380 (t0) cc_final: 0.8099 (p0) REVERT: G 78 LEU cc_start: 0.9543 (tp) cc_final: 0.9243 (tp) REVERT: G 99 LEU cc_start: 0.9411 (pp) cc_final: 0.9202 (pp) REVERT: H 101 GLU cc_start: 0.8763 (tp30) cc_final: 0.8272 (tp30) REVERT: H 103 LEU cc_start: 0.9035 (mt) cc_final: 0.8583 (mp) REVERT: K 14 GLU cc_start: 0.9100 (tp30) cc_final: 0.8440 (tp30) REVERT: K 19 ASN cc_start: 0.8803 (m110) cc_final: 0.8165 (m110) REVERT: K 22 THR cc_start: 0.9438 (p) cc_final: 0.8988 (p) REVERT: L 26 LEU cc_start: 0.9592 (tp) cc_final: 0.9314 (tp) REVERT: L 39 LEU cc_start: 0.9530 (mm) cc_final: 0.9121 (pp) REVERT: L 73 TYR cc_start: 0.8900 (m-80) cc_final: 0.8490 (m-80) REVERT: L 75 LEU cc_start: 0.9606 (mt) cc_final: 0.9299 (mt) REVERT: L 77 PHE cc_start: 0.9171 (m-10) cc_final: 0.8508 (m-80) REVERT: L 90 TRP cc_start: 0.9342 (t60) cc_final: 0.9131 (t60) REVERT: N 75 LEU cc_start: 0.9408 (mt) cc_final: 0.8853 (tp) REVERT: P 24 ARG cc_start: 0.8405 (mpt180) cc_final: 0.8076 (mmt-90) REVERT: P 55 THR cc_start: 0.9046 (p) cc_final: 0.8819 (t) REVERT: P 94 ARG cc_start: 0.8511 (tpm170) cc_final: 0.7830 (tpm170) REVERT: P 100 PRO cc_start: 0.2611 (Cg_exo) cc_final: 0.2410 (Cg_endo) REVERT: R 25 LEU cc_start: 0.9542 (mm) cc_final: 0.9293 (mm) REVERT: R 71 ASP cc_start: 0.8662 (m-30) cc_final: 0.8049 (t0) REVERT: T 26 LEU cc_start: 0.9532 (tp) cc_final: 0.9129 (tp) REVERT: T 101 GLU cc_start: 0.8516 (tp30) cc_final: 0.8167 (mp0) REVERT: U 14 GLU cc_start: 0.9189 (tp30) cc_final: 0.8670 (tp30) REVERT: U 93 GLU cc_start: 0.9323 (mp0) cc_final: 0.9018 (mp0) REVERT: V 24 ARG cc_start: 0.8508 (mpt180) cc_final: 0.7834 (mmt-90) REVERT: V 52 VAL cc_start: 0.7939 (m) cc_final: 0.7430 (m) REVERT: V 87 LEU cc_start: 0.9576 (tt) cc_final: 0.9307 (pp) REVERT: W 39 GLU cc_start: 0.9375 (mp0) cc_final: 0.9075 (mp0) REVERT: X 24 ARG cc_start: 0.8700 (mpt180) cc_final: 0.8438 (mmt-90) REVERT: X 26 LEU cc_start: 0.9527 (tp) cc_final: 0.9222 (tp) REVERT: X 75 LEU cc_start: 0.9562 (mt) cc_final: 0.9286 (pp) REVERT: X 103 LEU cc_start: 0.9262 (mt) cc_final: 0.8843 (mt) outliers start: 0 outliers final: 0 residues processed: 775 average time/residue: 0.3981 time to fit residues: 431.2300 Evaluate side-chains 445 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 8.9990 chunk 172 optimal weight: 0.4980 chunk 95 optimal weight: 0.1980 chunk 59 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 77 ASN A 90 ASN C 19 ASN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN G 19 ASN G 43 ASN G 77 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 ASN ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 ASN K 43 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN M 19 ASN M 43 ASN M 77 ASN Q 19 ASN Q 43 ASN Q 90 ASN U 19 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 77 ASN W 19 ASN ** W 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 77 ASN W 90 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18933 Z= 0.297 Angle : 0.745 10.790 25761 Z= 0.389 Chirality : 0.043 0.157 3051 Planarity : 0.005 0.059 3249 Dihedral : 4.620 22.922 2601 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 29.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.42 % Allowed : 8.82 % Favored : 90.77 % 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: 0.47 (0.17), residues: 2322 helix: 0.86 (0.13), residues: 1452 sheet: 0.04 (0.28), residues: 300 loop : -0.72 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 117 HIS 0.007 0.002 HIS T 95 PHE 0.020 0.003 PHE W 95 TYR 0.035 0.003 TYR L 73 ARG 0.015 0.001 ARG N 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 520 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9303 (pt0) cc_final: 0.8984 (pp20) REVERT: B 24 ARG cc_start: 0.9111 (mpt180) cc_final: 0.8342 (mmt-90) REVERT: B 52 VAL cc_start: 0.8928 (m) cc_final: 0.8517 (m) REVERT: B 101 GLU cc_start: 0.8790 (tp30) cc_final: 0.8532 (tp30) REVERT: B 103 LEU cc_start: 0.9481 (mt) cc_final: 0.9149 (mp) REVERT: D 26 LEU cc_start: 0.9676 (tp) cc_final: 0.9441 (tp) REVERT: D 28 THR cc_start: 0.8888 (m) cc_final: 0.8479 (m) REVERT: D 74 ARG cc_start: 0.9442 (tmm-80) cc_final: 0.9132 (tmm-80) REVERT: F 85 ASP cc_start: 0.9211 (m-30) cc_final: 0.8840 (t70) REVERT: F 102 CYS cc_start: 0.7825 (t) cc_final: 0.7441 (t) REVERT: F 116 ASP cc_start: 0.8521 (m-30) cc_final: 0.8137 (p0) REVERT: G 82 TYR cc_start: 0.8669 (m-80) cc_final: 0.8448 (m-80) REVERT: H 90 TRP cc_start: 0.9059 (t60) cc_final: 0.8709 (t60) REVERT: H 101 GLU cc_start: 0.8887 (tp30) cc_final: 0.8549 (tp30) REVERT: H 103 LEU cc_start: 0.9385 (mt) cc_final: 0.8974 (mt) REVERT: J 22 ASP cc_start: 0.8559 (t0) cc_final: 0.8215 (t0) REVERT: K 14 GLU cc_start: 0.9008 (tp30) cc_final: 0.8200 (tp30) REVERT: K 19 ASN cc_start: 0.8884 (m-40) cc_final: 0.8505 (m110) REVERT: K 22 THR cc_start: 0.9300 (p) cc_final: 0.9072 (p) REVERT: K 39 GLU cc_start: 0.9460 (mp0) cc_final: 0.9197 (mp0) REVERT: L 39 LEU cc_start: 0.9547 (mm) cc_final: 0.9116 (pp) REVERT: L 73 TYR cc_start: 0.8878 (m-80) cc_final: 0.8677 (m-10) REVERT: L 84 LEU cc_start: 0.9550 (tp) cc_final: 0.9140 (tt) REVERT: M 112 LEU cc_start: 0.9501 (mt) cc_final: 0.9121 (pp) REVERT: N 48 LEU cc_start: 0.9219 (mm) cc_final: 0.8917 (tp) REVERT: N 92 GLN cc_start: 0.9124 (mt0) cc_final: 0.8916 (pp30) REVERT: R 45 GLU cc_start: 0.9179 (pp20) cc_final: 0.8737 (pp20) REVERT: R 60 VAL cc_start: 0.8757 (p) cc_final: 0.8513 (p) REVERT: T 26 LEU cc_start: 0.9380 (tp) cc_final: 0.9136 (tp) REVERT: T 101 GLU cc_start: 0.8371 (tp30) cc_final: 0.8046 (mp0) REVERT: U 14 GLU cc_start: 0.9210 (tp30) cc_final: 0.8639 (tp30) REVERT: U 95 PHE cc_start: 0.9397 (m-80) cc_final: 0.9175 (m-10) REVERT: V 52 VAL cc_start: 0.8376 (m) cc_final: 0.8056 (m) REVERT: W 27 TYR cc_start: 0.9450 (m-80) cc_final: 0.9235 (m-80) REVERT: W 39 GLU cc_start: 0.9378 (mp0) cc_final: 0.9148 (mp0) REVERT: W 76 TYR cc_start: 0.9179 (t80) cc_final: 0.8954 (t80) REVERT: X 24 ARG cc_start: 0.8978 (mpt180) cc_final: 0.8529 (mmt-90) REVERT: X 26 LEU cc_start: 0.9466 (tp) cc_final: 0.9204 (tp) REVERT: X 103 LEU cc_start: 0.9084 (mt) cc_final: 0.8783 (mt) outliers start: 8 outliers final: 5 residues processed: 526 average time/residue: 0.3118 time to fit residues: 246.8728 Evaluate side-chains 375 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 370 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 205 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN C 90 ASN ** F 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 ASN M 43 ASN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN U 90 ASN ** W 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18933 Z= 0.281 Angle : 0.716 9.522 25761 Z= 0.377 Chirality : 0.042 0.154 3051 Planarity : 0.006 0.071 3249 Dihedral : 4.606 23.664 2601 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.16 % Allowed : 6.21 % Favored : 93.64 % 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: 0.31 (0.17), residues: 2322 helix: 0.87 (0.13), residues: 1461 sheet: -0.50 (0.29), residues: 276 loop : -0.92 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 117 HIS 0.007 0.002 HIS D 95 PHE 0.029 0.002 PHE K 95 TYR 0.032 0.003 TYR W 61 ARG 0.020 0.001 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 460 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 TYR cc_start: 0.7278 (m-80) cc_final: 0.6891 (m-80) REVERT: B 79 THR cc_start: 0.9408 (p) cc_final: 0.9068 (p) REVERT: B 103 LEU cc_start: 0.9493 (mt) cc_final: 0.9127 (mp) REVERT: C 80 GLU cc_start: 0.9219 (pt0) cc_final: 0.8536 (pt0) REVERT: D 24 ARG cc_start: 0.8894 (mpt180) cc_final: 0.8513 (mmt-90) REVERT: D 28 THR cc_start: 0.8784 (m) cc_final: 0.8344 (m) REVERT: D 77 PHE cc_start: 0.9475 (m-10) cc_final: 0.9166 (m-80) REVERT: D 80 THR cc_start: 0.9426 (p) cc_final: 0.9161 (p) REVERT: D 118 LEU cc_start: 0.9721 (mp) cc_final: 0.9491 (pp) REVERT: F 38 TYR cc_start: 0.8907 (m-80) cc_final: 0.8610 (m-10) REVERT: F 116 ASP cc_start: 0.8525 (m-30) cc_final: 0.8059 (p0) REVERT: G 82 TYR cc_start: 0.8558 (m-80) cc_final: 0.8261 (m-80) REVERT: H 119 ARG cc_start: 0.8804 (tpm170) cc_final: 0.8552 (tpm170) REVERT: J 75 LEU cc_start: 0.9725 (mm) cc_final: 0.9515 (mm) REVERT: K 7 MET cc_start: 0.8974 (ptp) cc_final: 0.8772 (ptp) REVERT: K 14 GLU cc_start: 0.9060 (tp30) cc_final: 0.8262 (tp30) REVERT: K 19 ASN cc_start: 0.8855 (m-40) cc_final: 0.8505 (m110) REVERT: K 22 THR cc_start: 0.9351 (p) cc_final: 0.9131 (p) REVERT: K 39 GLU cc_start: 0.9469 (mp0) cc_final: 0.9194 (mp0) REVERT: L 39 LEU cc_start: 0.9661 (mm) cc_final: 0.9317 (pp) REVERT: L 73 TYR cc_start: 0.8874 (m-80) cc_final: 0.8538 (m-80) REVERT: P 108 ILE cc_start: 0.8806 (pt) cc_final: 0.8466 (mp) REVERT: Q 95 PHE cc_start: 0.9430 (m-80) cc_final: 0.9119 (m-80) REVERT: R 25 LEU cc_start: 0.9539 (mm) cc_final: 0.9333 (mm) REVERT: R 45 GLU cc_start: 0.9262 (pp20) cc_final: 0.8857 (pp20) REVERT: R 66 LYS cc_start: 0.9550 (mmmt) cc_final: 0.9308 (mmmm) REVERT: R 75 LEU cc_start: 0.9681 (mt) cc_final: 0.9460 (mt) REVERT: T 26 LEU cc_start: 0.9518 (tp) cc_final: 0.9267 (tp) REVERT: U 14 GLU cc_start: 0.9250 (tp30) cc_final: 0.8762 (tp30) REVERT: U 95 PHE cc_start: 0.9452 (m-80) cc_final: 0.9101 (m-10) REVERT: V 52 VAL cc_start: 0.8219 (m) cc_final: 0.7903 (m) REVERT: V 103 LEU cc_start: 0.9789 (mt) cc_final: 0.9584 (mt) REVERT: V 104 VAL cc_start: 0.9636 (m) cc_final: 0.9423 (p) REVERT: W 39 GLU cc_start: 0.9423 (mp0) cc_final: 0.9174 (mp0) REVERT: W 61 TYR cc_start: 0.8926 (m-80) cc_final: 0.8641 (m-80) REVERT: X 24 ARG cc_start: 0.9111 (mpt180) cc_final: 0.8450 (mmt-90) REVERT: X 26 LEU cc_start: 0.9481 (tp) cc_final: 0.9235 (tp) REVERT: X 103 LEU cc_start: 0.9124 (mt) cc_final: 0.8808 (mt) outliers start: 3 outliers final: 1 residues processed: 462 average time/residue: 0.3194 time to fit residues: 225.5927 Evaluate side-chains 354 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 197 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN G 43 ASN I 43 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN K 77 ASN M 43 ASN Q 43 ASN U 43 ASN W 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18933 Z= 0.195 Angle : 0.665 10.110 25761 Z= 0.336 Chirality : 0.041 0.194 3051 Planarity : 0.005 0.069 3249 Dihedral : 4.391 23.066 2601 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.10 % Allowed : 5.89 % Favored : 94.00 % 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: 0.61 (0.17), residues: 2322 helix: 1.17 (0.14), residues: 1449 sheet: -0.55 (0.27), residues: 300 loop : -0.85 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 117 HIS 0.004 0.001 HIS D 95 PHE 0.025 0.002 PHE K 95 TYR 0.027 0.002 TYR W 61 ARG 0.012 0.001 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 480 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 ARG cc_start: 0.9105 (mpt180) cc_final: 0.8095 (mmt-90) REVERT: B 25 LEU cc_start: 0.9722 (mm) cc_final: 0.9393 (mm) REVERT: B 57 VAL cc_start: 0.8900 (t) cc_final: 0.8573 (m) REVERT: B 101 GLU cc_start: 0.8896 (tp30) cc_final: 0.8688 (tp30) REVERT: B 103 LEU cc_start: 0.9541 (mt) cc_final: 0.9263 (mp) REVERT: C 31 LEU cc_start: 0.9659 (pp) cc_final: 0.9439 (mt) REVERT: C 49 LEU cc_start: 0.9503 (tt) cc_final: 0.9149 (mt) REVERT: D 24 ARG cc_start: 0.8868 (mpt180) cc_final: 0.8529 (mmt-90) REVERT: D 26 LEU cc_start: 0.9675 (tp) cc_final: 0.9463 (tp) REVERT: D 28 THR cc_start: 0.8714 (m) cc_final: 0.8253 (m) REVERT: D 77 PHE cc_start: 0.9454 (m-10) cc_final: 0.9138 (m-80) REVERT: D 80 THR cc_start: 0.9374 (p) cc_final: 0.9110 (p) REVERT: D 94 ARG cc_start: 0.9115 (tpm170) cc_final: 0.8845 (tpm170) REVERT: D 118 LEU cc_start: 0.9702 (mp) cc_final: 0.9466 (pp) REVERT: D 119 ARG cc_start: 0.9273 (tpt170) cc_final: 0.8815 (tpm170) REVERT: F 38 TYR cc_start: 0.8763 (m-80) cc_final: 0.8531 (m-10) REVERT: F 102 CYS cc_start: 0.8188 (t) cc_final: 0.7943 (t) REVERT: F 116 ASP cc_start: 0.8505 (m-30) cc_final: 0.8030 (p0) REVERT: G 61 TYR cc_start: 0.7998 (m-80) cc_final: 0.7706 (m-80) REVERT: G 82 TYR cc_start: 0.8553 (m-80) cc_final: 0.8300 (m-80) REVERT: H 22 ASP cc_start: 0.8507 (t0) cc_final: 0.8293 (t0) REVERT: I 27 TYR cc_start: 0.9004 (m-10) cc_final: 0.8301 (m-10) REVERT: J 20 THR cc_start: 0.6766 (t) cc_final: 0.6541 (t) REVERT: K 14 GLU cc_start: 0.9010 (tp30) cc_final: 0.7928 (tp30) REVERT: K 19 ASN cc_start: 0.8586 (m-40) cc_final: 0.8348 (t0) REVERT: K 22 THR cc_start: 0.9325 (p) cc_final: 0.8497 (p) REVERT: K 39 GLU cc_start: 0.9487 (mp0) cc_final: 0.9215 (mp0) REVERT: K 68 ASP cc_start: 0.8334 (t0) cc_final: 0.8049 (t0) REVERT: L 39 LEU cc_start: 0.9607 (mm) cc_final: 0.9323 (pp) REVERT: L 73 TYR cc_start: 0.8870 (m-80) cc_final: 0.8336 (m-80) REVERT: L 75 LEU cc_start: 0.9652 (mt) cc_final: 0.9320 (mt) REVERT: L 77 PHE cc_start: 0.9210 (m-80) cc_final: 0.8784 (m-80) REVERT: M 112 LEU cc_start: 0.9493 (mt) cc_final: 0.9262 (mt) REVERT: P 108 ILE cc_start: 0.8892 (pt) cc_final: 0.8478 (mp) REVERT: Q 24 ILE cc_start: 0.9843 (mm) cc_final: 0.9622 (mm) REVERT: R 25 LEU cc_start: 0.9567 (mm) cc_final: 0.9344 (mm) REVERT: R 29 THR cc_start: 0.7481 (t) cc_final: 0.7212 (m) REVERT: R 45 GLU cc_start: 0.9222 (pp20) cc_final: 0.8803 (pp20) REVERT: R 66 LYS cc_start: 0.9522 (mmmt) cc_final: 0.9260 (mmmm) REVERT: T 26 LEU cc_start: 0.9520 (tp) cc_final: 0.9268 (tp) REVERT: U 14 GLU cc_start: 0.9211 (tp30) cc_final: 0.8661 (tp30) REVERT: U 61 TYR cc_start: 0.9203 (m-80) cc_final: 0.8512 (m-80) REVERT: U 95 PHE cc_start: 0.9399 (m-80) cc_final: 0.8962 (m-10) REVERT: V 28 THR cc_start: 0.8749 (m) cc_final: 0.8430 (m) REVERT: V 104 VAL cc_start: 0.9626 (m) cc_final: 0.9419 (p) REVERT: W 33 LYS cc_start: 0.8760 (tttt) cc_final: 0.8548 (ttpt) REVERT: W 61 TYR cc_start: 0.8830 (m-80) cc_final: 0.8601 (m-80) REVERT: W 97 LYS cc_start: 0.9568 (mtpt) cc_final: 0.9222 (mmmt) REVERT: X 24 ARG cc_start: 0.9103 (mpt180) cc_final: 0.8557 (mmt-90) REVERT: X 26 LEU cc_start: 0.9423 (tp) cc_final: 0.9171 (tp) REVERT: X 66 LYS cc_start: 0.7380 (mmpt) cc_final: 0.7093 (mmmt) REVERT: X 103 LEU cc_start: 0.9085 (mt) cc_final: 0.8790 (mm) outliers start: 2 outliers final: 0 residues processed: 481 average time/residue: 0.3070 time to fit residues: 223.0119 Evaluate side-chains 376 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 152 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN G 43 ASN I 43 ASN I 77 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18933 Z= 0.215 Angle : 0.673 9.188 25761 Z= 0.345 Chirality : 0.041 0.172 3051 Planarity : 0.005 0.055 3249 Dihedral : 4.401 23.942 2601 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.26 % Allowed : 5.53 % Favored : 94.21 % 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: 0.48 (0.17), residues: 2322 helix: 1.08 (0.14), residues: 1440 sheet: -0.59 (0.28), residues: 276 loop : -0.89 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 117 HIS 0.004 0.001 HIS F 95 PHE 0.026 0.002 PHE K 95 TYR 0.038 0.003 TYR I 48 ARG 0.010 0.001 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 454 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.9289 (m-10) cc_final: 0.8759 (m-80) REVERT: B 24 ARG cc_start: 0.8987 (mpt180) cc_final: 0.8249 (mmt-90) REVERT: B 28 THR cc_start: 0.8156 (m) cc_final: 0.7676 (m) REVERT: B 57 VAL cc_start: 0.8920 (t) cc_final: 0.8615 (m) REVERT: B 80 THR cc_start: 0.9137 (p) cc_final: 0.8925 (p) REVERT: B 81 ARG cc_start: 0.8647 (ptt-90) cc_final: 0.7761 (ptt90) REVERT: B 101 GLU cc_start: 0.8911 (tp30) cc_final: 0.8700 (tp30) REVERT: B 103 LEU cc_start: 0.9557 (mt) cc_final: 0.9277 (mp) REVERT: C 31 LEU cc_start: 0.9683 (pp) cc_final: 0.9468 (mt) REVERT: C 49 LEU cc_start: 0.9529 (tt) cc_final: 0.9305 (mt) REVERT: D 26 LEU cc_start: 0.9704 (tp) cc_final: 0.9473 (tp) REVERT: D 28 THR cc_start: 0.8779 (m) cc_final: 0.8535 (m) REVERT: D 80 THR cc_start: 0.9303 (p) cc_final: 0.9083 (p) REVERT: D 94 ARG cc_start: 0.9192 (tpm170) cc_final: 0.8852 (tpp-160) REVERT: D 104 VAL cc_start: 0.9688 (m) cc_final: 0.9436 (p) REVERT: D 118 LEU cc_start: 0.9659 (mp) cc_final: 0.9428 (pp) REVERT: F 116 ASP cc_start: 0.8489 (m-30) cc_final: 0.8031 (p0) REVERT: G 7 MET cc_start: 0.8734 (ppp) cc_final: 0.8431 (ppp) REVERT: G 61 TYR cc_start: 0.8124 (m-80) cc_final: 0.7720 (m-80) REVERT: H 101 GLU cc_start: 0.8775 (tp30) cc_final: 0.8418 (tp30) REVERT: H 103 LEU cc_start: 0.9364 (mt) cc_final: 0.9022 (mt) REVERT: J 20 THR cc_start: 0.6945 (t) cc_final: 0.6701 (t) REVERT: J 95 HIS cc_start: 0.4981 (t70) cc_final: 0.4742 (t70) REVERT: K 14 GLU cc_start: 0.9071 (tp30) cc_final: 0.7997 (tp30) REVERT: K 22 THR cc_start: 0.9180 (p) cc_final: 0.8591 (p) REVERT: K 39 GLU cc_start: 0.9461 (mp0) cc_final: 0.9208 (mp0) REVERT: K 68 ASP cc_start: 0.8384 (t0) cc_final: 0.8099 (t0) REVERT: L 39 LEU cc_start: 0.9648 (mm) cc_final: 0.9385 (pp) REVERT: L 73 TYR cc_start: 0.8849 (m-80) cc_final: 0.8196 (m-80) REVERT: L 75 LEU cc_start: 0.9621 (mt) cc_final: 0.9303 (mt) REVERT: L 77 PHE cc_start: 0.9250 (m-80) cc_final: 0.8904 (m-80) REVERT: M 112 LEU cc_start: 0.9544 (mt) cc_final: 0.9315 (mt) REVERT: P 108 ILE cc_start: 0.8849 (pt) cc_final: 0.8366 (mp) REVERT: Q 24 ILE cc_start: 0.9830 (mm) cc_final: 0.9621 (mm) REVERT: R 25 LEU cc_start: 0.9591 (mm) cc_final: 0.9359 (mm) REVERT: R 29 THR cc_start: 0.7400 (t) cc_final: 0.7187 (m) REVERT: R 45 GLU cc_start: 0.9234 (pp20) cc_final: 0.8823 (pp20) REVERT: R 46 LYS cc_start: 0.9045 (pttp) cc_final: 0.8843 (pttm) REVERT: R 64 ASN cc_start: 0.9290 (p0) cc_final: 0.9086 (p0) REVERT: R 66 LYS cc_start: 0.9539 (mmmt) cc_final: 0.9279 (mmmm) REVERT: T 26 LEU cc_start: 0.9528 (tp) cc_final: 0.9287 (tp) REVERT: U 14 GLU cc_start: 0.9238 (tp30) cc_final: 0.8708 (tp30) REVERT: U 61 TYR cc_start: 0.9213 (m-80) cc_final: 0.8566 (m-80) REVERT: U 95 PHE cc_start: 0.9417 (m-80) cc_final: 0.8955 (m-10) REVERT: V 28 THR cc_start: 0.8766 (m) cc_final: 0.8365 (m) REVERT: V 104 VAL cc_start: 0.9641 (m) cc_final: 0.9431 (p) REVERT: W 33 LYS cc_start: 0.8828 (tttt) cc_final: 0.8489 (ttpt) REVERT: W 61 TYR cc_start: 0.8820 (m-80) cc_final: 0.8590 (m-80) REVERT: W 97 LYS cc_start: 0.9567 (mtpt) cc_final: 0.9246 (mmmt) REVERT: X 24 ARG cc_start: 0.9141 (mpt180) cc_final: 0.8553 (mmt-90) REVERT: X 26 LEU cc_start: 0.9476 (tp) cc_final: 0.9250 (tp) REVERT: X 103 LEU cc_start: 0.9094 (mt) cc_final: 0.8792 (mt) outliers start: 5 outliers final: 1 residues processed: 458 average time/residue: 0.3053 time to fit residues: 211.6520 Evaluate side-chains 365 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 220 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18933 Z= 0.221 Angle : 0.675 10.463 25761 Z= 0.345 Chirality : 0.041 0.180 3051 Planarity : 0.005 0.071 3249 Dihedral : 4.404 21.918 2601 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.17), residues: 2322 helix: 1.20 (0.14), residues: 1416 sheet: -0.77 (0.27), residues: 300 loop : -0.62 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 117 HIS 0.003 0.001 HIS X 95 PHE 0.015 0.002 PHE Q 95 TYR 0.050 0.003 TYR Q 48 ARG 0.014 0.001 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 448 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.9256 (m-10) cc_final: 0.8755 (m-80) REVERT: B 57 VAL cc_start: 0.8897 (t) cc_final: 0.8575 (m) REVERT: B 81 ARG cc_start: 0.8621 (ptt-90) cc_final: 0.8362 (ptt90) REVERT: C 49 LEU cc_start: 0.9520 (tt) cc_final: 0.9305 (mt) REVERT: D 22 ASP cc_start: 0.7978 (t0) cc_final: 0.7468 (t0) REVERT: D 26 LEU cc_start: 0.9703 (tp) cc_final: 0.9491 (tp) REVERT: D 28 THR cc_start: 0.8749 (m) cc_final: 0.8489 (m) REVERT: D 80 THR cc_start: 0.9235 (p) cc_final: 0.8966 (p) REVERT: D 94 ARG cc_start: 0.9257 (tpm170) cc_final: 0.8758 (tpm170) REVERT: D 104 VAL cc_start: 0.9692 (m) cc_final: 0.9449 (p) REVERT: D 118 LEU cc_start: 0.9648 (mp) cc_final: 0.9421 (pp) REVERT: F 85 ASP cc_start: 0.9261 (m-30) cc_final: 0.8978 (t70) REVERT: F 116 ASP cc_start: 0.8502 (m-30) cc_final: 0.8038 (p0) REVERT: G 7 MET cc_start: 0.8792 (ppp) cc_final: 0.8533 (ppp) REVERT: G 61 TYR cc_start: 0.8246 (m-80) cc_final: 0.7910 (m-80) REVERT: H 103 LEU cc_start: 0.9325 (mt) cc_final: 0.9120 (mt) REVERT: K 14 GLU cc_start: 0.8991 (tp30) cc_final: 0.8185 (tp30) REVERT: K 19 ASN cc_start: 0.8686 (t0) cc_final: 0.8486 (m-40) REVERT: K 39 GLU cc_start: 0.9433 (mp0) cc_final: 0.9188 (mp0) REVERT: K 68 ASP cc_start: 0.8435 (t0) cc_final: 0.8117 (t0) REVERT: L 39 LEU cc_start: 0.9656 (mm) cc_final: 0.9425 (pp) REVERT: L 73 TYR cc_start: 0.8960 (m-80) cc_final: 0.8333 (m-80) REVERT: L 75 LEU cc_start: 0.9658 (mt) cc_final: 0.9407 (mt) REVERT: L 77 PHE cc_start: 0.9227 (m-80) cc_final: 0.8920 (m-80) REVERT: M 112 LEU cc_start: 0.9560 (mt) cc_final: 0.9291 (mt) REVERT: N 48 LEU cc_start: 0.9295 (tp) cc_final: 0.9079 (tp) REVERT: N 74 ARG cc_start: 0.9474 (tpt90) cc_final: 0.9245 (mmm-85) REVERT: P 108 ILE cc_start: 0.8872 (pt) cc_final: 0.8404 (mp) REVERT: R 45 GLU cc_start: 0.9246 (pp20) cc_final: 0.8847 (pp20) REVERT: R 64 ASN cc_start: 0.9353 (p0) cc_final: 0.9130 (p0) REVERT: R 66 LYS cc_start: 0.9543 (mmmt) cc_final: 0.9258 (mmmm) REVERT: T 26 LEU cc_start: 0.9520 (tp) cc_final: 0.9276 (tp) REVERT: U 14 GLU cc_start: 0.9277 (tp30) cc_final: 0.8777 (tp30) REVERT: U 61 TYR cc_start: 0.9229 (m-80) cc_final: 0.8590 (m-80) REVERT: U 95 PHE cc_start: 0.9450 (m-80) cc_final: 0.8989 (m-10) REVERT: V 28 THR cc_start: 0.8665 (m) cc_final: 0.8221 (m) REVERT: V 52 VAL cc_start: 0.8343 (m) cc_final: 0.8126 (m) REVERT: W 8 TYR cc_start: 0.8671 (t80) cc_final: 0.8423 (t80) REVERT: W 33 LYS cc_start: 0.8868 (tttt) cc_final: 0.8549 (ttpt) REVERT: W 61 TYR cc_start: 0.8825 (m-80) cc_final: 0.8604 (m-80) REVERT: X 24 ARG cc_start: 0.9127 (mpt180) cc_final: 0.8604 (mmt-90) REVERT: X 26 LEU cc_start: 0.9506 (tp) cc_final: 0.9275 (tp) REVERT: X 103 LEU cc_start: 0.9092 (mt) cc_final: 0.8858 (mt) outliers start: 1 outliers final: 0 residues processed: 449 average time/residue: 0.3027 time to fit residues: 206.4470 Evaluate side-chains 358 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.6241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18933 Z= 0.222 Angle : 0.699 9.608 25761 Z= 0.359 Chirality : 0.042 0.193 3051 Planarity : 0.005 0.071 3249 Dihedral : 4.429 23.687 2601 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 0.24 (0.17), residues: 2322 helix: 0.95 (0.13), residues: 1440 sheet: -0.90 (0.27), residues: 300 loop : -1.05 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 117 HIS 0.004 0.001 HIS F 95 PHE 0.029 0.002 PHE K 95 TYR 0.043 0.002 TYR B 38 ARG 0.014 0.001 ARG B 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 452 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.9290 (m-10) cc_final: 0.8768 (m-80) REVERT: B 57 VAL cc_start: 0.8904 (t) cc_final: 0.8558 (m) REVERT: B 81 ARG cc_start: 0.8657 (ptt-90) cc_final: 0.8348 (ptt90) REVERT: D 22 ASP cc_start: 0.7811 (t0) cc_final: 0.7396 (t0) REVERT: D 26 LEU cc_start: 0.9752 (tp) cc_final: 0.9462 (tp) REVERT: D 28 THR cc_start: 0.8901 (m) cc_final: 0.8425 (m) REVERT: D 80 THR cc_start: 0.9149 (p) cc_final: 0.8898 (p) REVERT: D 104 VAL cc_start: 0.9704 (m) cc_final: 0.9494 (p) REVERT: D 118 LEU cc_start: 0.9655 (mp) cc_final: 0.9442 (pp) REVERT: F 102 CYS cc_start: 0.8313 (t) cc_final: 0.7592 (t) REVERT: F 116 ASP cc_start: 0.8482 (m-30) cc_final: 0.8035 (p0) REVERT: G 7 MET cc_start: 0.8859 (ppp) cc_final: 0.8569 (ppp) REVERT: G 61 TYR cc_start: 0.8328 (m-10) cc_final: 0.7926 (m-80) REVERT: H 63 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8164 (mm-30) REVERT: J 20 THR cc_start: 0.7112 (t) cc_final: 0.6868 (t) REVERT: J 48 LEU cc_start: 0.9406 (mm) cc_final: 0.8507 (tp) REVERT: K 14 GLU cc_start: 0.9132 (tp30) cc_final: 0.8196 (tp30) REVERT: K 19 ASN cc_start: 0.8876 (t0) cc_final: 0.8452 (t0) REVERT: K 39 GLU cc_start: 0.9452 (mp0) cc_final: 0.9205 (mp0) REVERT: K 68 ASP cc_start: 0.8466 (t0) cc_final: 0.8139 (t0) REVERT: L 39 LEU cc_start: 0.9675 (mm) cc_final: 0.9431 (pp) REVERT: L 73 TYR cc_start: 0.8987 (m-80) cc_final: 0.8359 (m-80) REVERT: L 75 LEU cc_start: 0.9636 (mt) cc_final: 0.9379 (mt) REVERT: L 77 PHE cc_start: 0.9318 (m-80) cc_final: 0.8914 (m-80) REVERT: L 87 LEU cc_start: 0.9622 (tt) cc_final: 0.9347 (pp) REVERT: M 112 LEU cc_start: 0.9585 (mt) cc_final: 0.9382 (mt) REVERT: N 45 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8785 (mm-30) REVERT: N 48 LEU cc_start: 0.9366 (tp) cc_final: 0.9106 (tp) REVERT: N 74 ARG cc_start: 0.9442 (tpt90) cc_final: 0.9240 (mmm-85) REVERT: N 75 LEU cc_start: 0.9538 (mm) cc_final: 0.9266 (mm) REVERT: P 108 ILE cc_start: 0.8858 (pt) cc_final: 0.8401 (mp) REVERT: R 45 GLU cc_start: 0.9242 (pp20) cc_final: 0.8861 (pp20) REVERT: R 64 ASN cc_start: 0.9410 (p0) cc_final: 0.9152 (p0) REVERT: R 66 LYS cc_start: 0.9544 (mmmt) cc_final: 0.9257 (mmmm) REVERT: R 80 THR cc_start: 0.9271 (p) cc_final: 0.9050 (p) REVERT: T 26 LEU cc_start: 0.9550 (tp) cc_final: 0.9286 (tp) REVERT: U 14 GLU cc_start: 0.9199 (tp30) cc_final: 0.8746 (tp30) REVERT: U 61 TYR cc_start: 0.9248 (m-80) cc_final: 0.8810 (m-80) REVERT: U 95 PHE cc_start: 0.9428 (m-80) cc_final: 0.8976 (m-10) REVERT: V 52 VAL cc_start: 0.8425 (m) cc_final: 0.8120 (m) REVERT: W 8 TYR cc_start: 0.8652 (t80) cc_final: 0.8439 (t80) REVERT: W 61 TYR cc_start: 0.8882 (m-10) cc_final: 0.8589 (m-80) REVERT: X 24 ARG cc_start: 0.9148 (mpt180) cc_final: 0.8580 (mmt-90) REVERT: X 73 TYR cc_start: 0.8479 (m-80) cc_final: 0.7842 (m-80) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.3107 time to fit residues: 211.9724 Evaluate side-chains 350 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 66 optimal weight: 30.0000 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 139 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 172 optimal weight: 0.0970 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.6430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18933 Z= 0.198 Angle : 0.702 10.245 25761 Z= 0.352 Chirality : 0.042 0.200 3051 Planarity : 0.005 0.062 3249 Dihedral : 4.368 21.472 2601 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: 0.23 (0.17), residues: 2322 helix: 0.98 (0.14), residues: 1440 sheet: -0.96 (0.27), residues: 300 loop : -1.14 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 90 HIS 0.002 0.001 HIS D 95 PHE 0.022 0.002 PHE K 95 TYR 0.043 0.002 TYR C 48 ARG 0.018 0.001 ARG V 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 456 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 TYR cc_start: 0.9058 (t80) cc_final: 0.8847 (t80) REVERT: A 82 TYR cc_start: 0.9278 (m-10) cc_final: 0.8757 (m-80) REVERT: B 52 VAL cc_start: 0.8982 (m) cc_final: 0.8690 (m) REVERT: B 57 VAL cc_start: 0.8832 (t) cc_final: 0.8521 (m) REVERT: C 65 LEU cc_start: 0.9565 (pp) cc_final: 0.9172 (mt) REVERT: D 22 ASP cc_start: 0.7825 (t0) cc_final: 0.7484 (t0) REVERT: D 26 LEU cc_start: 0.9734 (tp) cc_final: 0.9509 (tp) REVERT: D 28 THR cc_start: 0.8934 (m) cc_final: 0.8246 (p) REVERT: D 80 THR cc_start: 0.9171 (p) cc_final: 0.8853 (p) REVERT: D 118 LEU cc_start: 0.9622 (mp) cc_final: 0.9405 (pp) REVERT: F 116 ASP cc_start: 0.8475 (m-30) cc_final: 0.8028 (p0) REVERT: G 7 MET cc_start: 0.8856 (ppp) cc_final: 0.8557 (ppp) REVERT: G 61 TYR cc_start: 0.8385 (m-10) cc_final: 0.7974 (m-80) REVERT: H 63 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8165 (mm-30) REVERT: H 103 LEU cc_start: 0.9305 (mt) cc_final: 0.9097 (mt) REVERT: H 119 ARG cc_start: 0.9069 (tpm170) cc_final: 0.8835 (mmp-170) REVERT: J 48 LEU cc_start: 0.9407 (mm) cc_final: 0.8581 (tp) REVERT: K 14 GLU cc_start: 0.8988 (tp30) cc_final: 0.7930 (tp30) REVERT: K 19 ASN cc_start: 0.8644 (t0) cc_final: 0.8210 (m-40) REVERT: K 39 GLU cc_start: 0.9447 (mp0) cc_final: 0.9203 (mp0) REVERT: K 68 ASP cc_start: 0.8454 (t0) cc_final: 0.8135 (t0) REVERT: L 39 LEU cc_start: 0.9674 (mm) cc_final: 0.9426 (pp) REVERT: L 73 TYR cc_start: 0.8953 (m-80) cc_final: 0.8232 (m-80) REVERT: L 75 LEU cc_start: 0.9604 (mt) cc_final: 0.9355 (mt) REVERT: L 77 PHE cc_start: 0.9296 (m-80) cc_final: 0.8938 (m-80) REVERT: L 87 LEU cc_start: 0.9618 (tt) cc_final: 0.9344 (pp) REVERT: M 7 MET cc_start: 0.9411 (mmp) cc_final: 0.9138 (mmt) REVERT: M 112 LEU cc_start: 0.9566 (mt) cc_final: 0.9355 (mt) REVERT: N 45 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8725 (mm-30) REVERT: N 74 ARG cc_start: 0.9467 (tpt90) cc_final: 0.9197 (mmm-85) REVERT: P 108 ILE cc_start: 0.8913 (pt) cc_final: 0.8521 (mp) REVERT: Q 68 ASP cc_start: 0.9080 (t0) cc_final: 0.8780 (t0) REVERT: R 29 THR cc_start: 0.7338 (t) cc_final: 0.7100 (m) REVERT: R 45 GLU cc_start: 0.9276 (pp20) cc_final: 0.8880 (pp20) REVERT: R 64 ASN cc_start: 0.9422 (p0) cc_final: 0.9163 (p0) REVERT: R 66 LYS cc_start: 0.9538 (mmmt) cc_final: 0.9241 (mmmm) REVERT: T 26 LEU cc_start: 0.9517 (tp) cc_final: 0.9297 (tp) REVERT: U 95 PHE cc_start: 0.9405 (m-80) cc_final: 0.8956 (m-10) REVERT: V 52 VAL cc_start: 0.8240 (m) cc_final: 0.8006 (m) REVERT: W 33 LYS cc_start: 0.8876 (tttt) cc_final: 0.8612 (ttpt) REVERT: W 61 TYR cc_start: 0.8865 (m-10) cc_final: 0.8583 (m-80) REVERT: X 24 ARG cc_start: 0.9121 (mpt180) cc_final: 0.8659 (mmt-90) REVERT: X 73 TYR cc_start: 0.8462 (m-80) cc_final: 0.7780 (m-80) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.2985 time to fit residues: 208.0325 Evaluate side-chains 353 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 204 optimal weight: 0.0870 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18933 Z= 0.263 Angle : 0.740 11.539 25761 Z= 0.381 Chirality : 0.043 0.199 3051 Planarity : 0.005 0.075 3249 Dihedral : 4.573 21.447 2601 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 28.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 0.14 (0.17), residues: 2322 helix: 0.89 (0.13), residues: 1416 sheet: -1.16 (0.27), residues: 300 loop : -0.90 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 117 HIS 0.005 0.001 HIS D 95 PHE 0.015 0.002 PHE C 95 TYR 0.041 0.003 TYR W 48 ARG 0.017 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 TYR cc_start: 0.7256 (m-80) cc_final: 0.6994 (m-80) REVERT: B 57 VAL cc_start: 0.8924 (t) cc_final: 0.8689 (m) REVERT: B 103 LEU cc_start: 0.9214 (tp) cc_final: 0.8919 (mt) REVERT: C 65 LEU cc_start: 0.9591 (pp) cc_final: 0.9201 (mt) REVERT: D 28 THR cc_start: 0.9086 (m) cc_final: 0.8792 (m) REVERT: D 77 PHE cc_start: 0.9308 (m-10) cc_final: 0.9046 (m-80) REVERT: F 38 TYR cc_start: 0.8648 (m-80) cc_final: 0.8408 (m-80) REVERT: F 116 ASP cc_start: 0.8468 (m-30) cc_final: 0.8001 (p0) REVERT: G 7 MET cc_start: 0.8898 (ppp) cc_final: 0.8599 (ppp) REVERT: G 61 TYR cc_start: 0.8501 (m-10) cc_final: 0.8039 (m-80) REVERT: H 63 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8053 (mp0) REVERT: H 103 LEU cc_start: 0.9311 (mt) cc_final: 0.9099 (mt) REVERT: H 119 ARG cc_start: 0.9089 (tpm170) cc_final: 0.8858 (mmp-170) REVERT: J 48 LEU cc_start: 0.9462 (mm) cc_final: 0.8630 (tp) REVERT: K 14 GLU cc_start: 0.9041 (tp30) cc_final: 0.7953 (tp30) REVERT: K 19 ASN cc_start: 0.8699 (t0) cc_final: 0.8168 (t0) REVERT: K 22 THR cc_start: 0.9186 (p) cc_final: 0.8635 (p) REVERT: K 39 GLU cc_start: 0.9451 (mp0) cc_final: 0.9192 (mp0) REVERT: L 39 LEU cc_start: 0.9708 (mm) cc_final: 0.9463 (pp) REVERT: L 73 TYR cc_start: 0.9012 (m-80) cc_final: 0.8383 (m-80) REVERT: L 75 LEU cc_start: 0.9622 (mt) cc_final: 0.9410 (mt) REVERT: L 77 PHE cc_start: 0.9253 (m-80) cc_final: 0.8913 (m-80) REVERT: L 87 LEU cc_start: 0.9662 (tt) cc_final: 0.9410 (pp) REVERT: M 7 MET cc_start: 0.9468 (mmp) cc_final: 0.9165 (mmm) REVERT: P 108 ILE cc_start: 0.8982 (pt) cc_final: 0.8668 (mp) REVERT: R 45 GLU cc_start: 0.9310 (pp20) cc_final: 0.8974 (pp20) REVERT: R 66 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9293 (mmmm) REVERT: R 82 GLU cc_start: 0.9491 (pm20) cc_final: 0.9064 (pm20) REVERT: T 26 LEU cc_start: 0.9583 (tp) cc_final: 0.9345 (tp) REVERT: U 14 GLU cc_start: 0.9235 (tp30) cc_final: 0.8744 (tp30) REVERT: U 61 TYR cc_start: 0.9303 (m-80) cc_final: 0.8835 (m-80) REVERT: U 95 PHE cc_start: 0.9430 (m-80) cc_final: 0.8968 (m-10) REVERT: V 52 VAL cc_start: 0.8254 (m) cc_final: 0.7966 (m) REVERT: W 27 TYR cc_start: 0.9513 (m-80) cc_final: 0.9222 (m-80) REVERT: W 33 LYS cc_start: 0.8945 (tttt) cc_final: 0.8673 (ttpt) REVERT: X 24 ARG cc_start: 0.9012 (mpt180) cc_final: 0.8546 (mmt-90) REVERT: X 73 TYR cc_start: 0.8961 (m-80) cc_final: 0.8316 (m-80) outliers start: 0 outliers final: 0 residues processed: 430 average time/residue: 0.2862 time to fit residues: 190.1128 Evaluate side-chains 339 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 227 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 chunk 143 optimal weight: 9.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18933 Z= 0.281 Angle : 0.756 11.420 25761 Z= 0.390 Chirality : 0.044 0.218 3051 Planarity : 0.005 0.066 3249 Dihedral : 4.649 22.764 2601 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 29.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.01 (0.17), residues: 2322 helix: 0.79 (0.13), residues: 1404 sheet: -1.29 (0.26), residues: 300 loop : -0.97 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP V 117 HIS 0.005 0.001 HIS X 95 PHE 0.022 0.002 PHE K 95 TYR 0.034 0.003 TYR B 38 ARG 0.016 0.001 ARG V 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4644 Ramachandran restraints generated. 2322 Oldfield, 0 Emsley, 2322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 18 ILE cc_start: 0.8835 (tp) cc_final: 0.8532 (mp) REVERT: B 28 THR cc_start: 0.8733 (m) cc_final: 0.8488 (m) REVERT: B 38 TYR cc_start: 0.7180 (m-80) cc_final: 0.6947 (m-80) REVERT: B 57 VAL cc_start: 0.8974 (t) cc_final: 0.8748 (m) REVERT: C 14 GLU cc_start: 0.9537 (tp30) cc_final: 0.9086 (tp30) REVERT: D 63 GLU cc_start: 0.9621 (tp30) cc_final: 0.9287 (tp30) REVERT: F 38 TYR cc_start: 0.8699 (m-80) cc_final: 0.8428 (m-80) REVERT: F 85 ASP cc_start: 0.9313 (m-30) cc_final: 0.9020 (t70) REVERT: F 116 ASP cc_start: 0.8515 (m-30) cc_final: 0.8056 (p0) REVERT: G 7 MET cc_start: 0.8900 (ppp) cc_final: 0.8680 (ppp) REVERT: G 61 TYR cc_start: 0.8471 (m-10) cc_final: 0.8052 (m-80) REVERT: H 63 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8353 (mp0) REVERT: H 116 ASP cc_start: 0.9301 (m-30) cc_final: 0.8842 (p0) REVERT: J 48 LEU cc_start: 0.9367 (mm) cc_final: 0.8651 (tp) REVERT: K 14 GLU cc_start: 0.9106 (tp30) cc_final: 0.8014 (tp30) REVERT: K 19 ASN cc_start: 0.8752 (t0) cc_final: 0.8203 (t0) REVERT: K 22 THR cc_start: 0.9199 (p) cc_final: 0.8636 (p) REVERT: K 39 GLU cc_start: 0.9459 (mp0) cc_final: 0.9207 (mp0) REVERT: L 39 LEU cc_start: 0.9719 (mm) cc_final: 0.9505 (pp) REVERT: L 73 TYR cc_start: 0.8994 (m-80) cc_final: 0.8382 (m-80) REVERT: L 77 PHE cc_start: 0.9306 (m-80) cc_final: 0.8938 (m-80) REVERT: M 7 MET cc_start: 0.9515 (mmp) cc_final: 0.9229 (mmm) REVERT: N 45 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8827 (mm-30) REVERT: N 46 LYS cc_start: 0.9147 (ptpt) cc_final: 0.8736 (ptmt) REVERT: N 48 LEU cc_start: 0.9488 (tp) cc_final: 0.9018 (mm) REVERT: N 54 ILE cc_start: 0.8552 (tt) cc_final: 0.8335 (mm) REVERT: N 84 LEU cc_start: 0.9474 (mt) cc_final: 0.9198 (mt) REVERT: P 108 ILE cc_start: 0.9039 (pt) cc_final: 0.8837 (mp) REVERT: Q 95 PHE cc_start: 0.9388 (m-10) cc_final: 0.9160 (m-80) REVERT: R 38 TYR cc_start: 0.6144 (m-80) cc_final: 0.5420 (m-80) REVERT: R 45 GLU cc_start: 0.9337 (pp20) cc_final: 0.9026 (pp20) REVERT: R 66 LYS cc_start: 0.9575 (mmmt) cc_final: 0.9304 (mmmm) REVERT: T 26 LEU cc_start: 0.9613 (tp) cc_final: 0.9380 (tp) REVERT: U 14 GLU cc_start: 0.9260 (tp30) cc_final: 0.8766 (tp30) REVERT: U 61 TYR cc_start: 0.9321 (m-80) cc_final: 0.8862 (m-80) REVERT: U 95 PHE cc_start: 0.9434 (m-80) cc_final: 0.8990 (m-10) REVERT: V 52 VAL cc_start: 0.8177 (m) cc_final: 0.7897 (m) REVERT: X 24 ARG cc_start: 0.8954 (mpt180) cc_final: 0.8401 (mmt-90) REVERT: X 73 TYR cc_start: 0.8998 (m-80) cc_final: 0.8433 (m-80) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.2824 time to fit residues: 181.4108 Evaluate side-chains 324 residues out of total 1917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 ASN M 43 ASN Q 43 ASN U 43 ASN ** X 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.053049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.039233 restraints weight = 118977.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.040575 restraints weight = 82421.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.041591 restraints weight = 61559.527| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.7183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18933 Z= 0.214 Angle : 0.727 11.084 25761 Z= 0.366 Chirality : 0.043 0.207 3051 Planarity : 0.005 0.064 3249 Dihedral : 4.537 22.205 2601 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.17), residues: 2322 helix: 0.84 (0.14), residues: 1428 sheet: -1.24 (0.27), residues: 300 loop : -1.23 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 117 HIS 0.002 0.001 HIS L 95 PHE 0.013 0.002 PHE C 95 TYR 0.034 0.003 TYR B 38 ARG 0.014 0.001 ARG V 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4338.83 seconds wall clock time: 80 minutes 23.93 seconds (4823.93 seconds total)