Starting phenix.real_space_refine on Tue Aug 6 18:52:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/08_2024/8rt5_19479.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/08_2024/8rt5_19479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/08_2024/8rt5_19479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/08_2024/8rt5_19479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/08_2024/8rt5_19479.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rt5_19479/08_2024/8rt5_19479.cif" } resolution = 2.69 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= 0.021 sd= 0.060 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 64 5.16 5 C 10928 2.51 5 N 3232 2.21 5 O 3232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 139": "OE1" <-> "OE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "B TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 109": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G ARG 144": "NH1" <-> "NH2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 71": "OD1" <-> "OD2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "K TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 71": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 139": "OE1" <-> "OE2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "N TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 71": "OD1" <-> "OD2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 109": "NH1" <-> "NH2" Residue "N ARG 113": "NH1" <-> "NH2" Residue "N TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 139": "OE1" <-> "OE2" Residue "P ARG 144": "NH1" <-> "NH2" Residue "Q TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 71": "OD1" <-> "OD2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q GLU 91": "OE1" <-> "OE2" Residue "Q TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 109": "NH1" <-> "NH2" Residue "Q ARG 113": "NH1" <-> "NH2" Residue "Q TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 139": "OE1" <-> "OE2" Residue "S ARG 144": "NH1" <-> "NH2" Residue "T TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 71": "OD1" <-> "OD2" Residue "T GLU 73": "OE1" <-> "OE2" Residue "T GLU 91": "OE1" <-> "OE2" Residue "T TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 109": "NH1" <-> "NH2" Residue "T ARG 113": "NH1" <-> "NH2" Residue "T TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 139": "OE1" <-> "OE2" Residue "u ARG 144": "NH1" <-> "NH2" Residue "v TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ASP 71": "OD1" <-> "OD2" Residue "v GLU 73": "OE1" <-> "OE2" Residue "v GLU 91": "OE1" <-> "OE2" Residue "v TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 109": "NH1" <-> "NH2" Residue "v ARG 113": "NH1" <-> "NH2" Residue "v TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 139": "OE1" <-> "OE2" Residue "V ARG 144": "NH1" <-> "NH2" Residue "W TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 71": "OD1" <-> "OD2" Residue "W GLU 73": "OE1" <-> "OE2" Residue "W GLU 91": "OE1" <-> "OE2" Residue "W TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W ARG 113": "NH1" <-> "NH2" Residue "W TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 139": "OE1" <-> "OE2" Residue "Y ARG 144": "NH1" <-> "NH2" Residue "Z TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 71": "OD1" <-> "OD2" Residue "Z GLU 73": "OE1" <-> "OE2" Residue "Z GLU 91": "OE1" <-> "OE2" Residue "Z TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 109": "NH1" <-> "NH2" Residue "Z ARG 113": "NH1" <-> "NH2" Residue "Z TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 139": "OE1" <-> "OE2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "c TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 71": "OD1" <-> "OD2" Residue "c GLU 73": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "c TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 109": "NH1" <-> "NH2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 139": "OE1" <-> "OE2" Residue "e ARG 144": "NH1" <-> "NH2" Residue "f TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 71": "OD1" <-> "OD2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f GLU 91": "OE1" <-> "OE2" Residue "f TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 109": "NH1" <-> "NH2" Residue "f ARG 113": "NH1" <-> "NH2" Residue "f TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 139": "OE1" <-> "OE2" Residue "h ARG 144": "NH1" <-> "NH2" Residue "i TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 71": "OD1" <-> "OD2" Residue "i GLU 73": "OE1" <-> "OE2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 109": "NH1" <-> "NH2" Residue "i ARG 113": "NH1" <-> "NH2" Residue "i TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 139": "OE1" <-> "OE2" Residue "k ARG 144": "NH1" <-> "NH2" Residue "l TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 71": "OD1" <-> "OD2" Residue "l GLU 73": "OE1" <-> "OE2" Residue "l GLU 91": "OE1" <-> "OE2" Residue "l TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 109": "NH1" <-> "NH2" Residue "l ARG 113": "NH1" <-> "NH2" Residue "l TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 139": "OE1" <-> "OE2" Residue "n ARG 144": "NH1" <-> "NH2" Residue "o TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 71": "OD1" <-> "OD2" Residue "o GLU 73": "OE1" <-> "OE2" Residue "o GLU 91": "OE1" <-> "OE2" Residue "o TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "o ARG 113": "NH1" <-> "NH2" Residue "o TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 139": "OE1" <-> "OE2" Residue "y ARG 144": "NH1" <-> "NH2" Residue "z TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 71": "OD1" <-> "OD2" Residue "z GLU 73": "OE1" <-> "OE2" Residue "z GLU 91": "OE1" <-> "OE2" Residue "z TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 109": "NH1" <-> "NH2" Residue "z ARG 113": "NH1" <-> "NH2" Residue "z TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17456 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "E" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "G" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "H" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "J" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "K" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "M" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "N" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "P" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "Q" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "S" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "T" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "u" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "v" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "V" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "W" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "Y" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "Z" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "b" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "c" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "e" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "f" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "h" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "i" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "k" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "l" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "n" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "o" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "y" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "z" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 942 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Time building chain proxies: 9.57, per 1000 atoms: 0.55 Number of scatterers: 17456 At special positions: 0 Unit cell: (167.519, 167.519, 67.221, 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 64 16.00 O 3232 8.00 N 3232 7.00 C 10928 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.83 Conformation dependent library (CDL) restraints added in 3.3 seconds 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4064 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 32 sheets defined 18.7% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 148 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 127 through 135 removed outlier: 3.573A pdb=" N GLN E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 148 Processing helix chain 'H' and resid 71 through 73 No H-bonds generated for 'chain 'H' and resid 71 through 73' Processing helix chain 'H' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN H 131 " --> pdb=" O TYR H 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 148 Processing helix chain 'K' and resid 71 through 73 No H-bonds generated for 'chain 'K' and resid 71 through 73' Processing helix chain 'K' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN K 131 " --> pdb=" O TYR K 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 148 Processing helix chain 'N' and resid 71 through 73 No H-bonds generated for 'chain 'N' and resid 71 through 73' Processing helix chain 'N' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN N 131 " --> pdb=" O TYR N 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 148 Processing helix chain 'Q' and resid 71 through 73 No H-bonds generated for 'chain 'Q' and resid 71 through 73' Processing helix chain 'Q' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN Q 131 " --> pdb=" O TYR Q 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 148 Processing helix chain 'T' and resid 71 through 73 No H-bonds generated for 'chain 'T' and resid 71 through 73' Processing helix chain 'T' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN T 131 " --> pdb=" O TYR T 127 " (cutoff:3.500A) Processing helix chain 'u' and resid 136 through 148 Processing helix chain 'v' and resid 71 through 73 No H-bonds generated for 'chain 'v' and resid 71 through 73' Processing helix chain 'v' and resid 127 through 135 removed outlier: 3.573A pdb=" N GLN v 131 " --> pdb=" O TYR v 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 148 Processing helix chain 'W' and resid 71 through 73 No H-bonds generated for 'chain 'W' and resid 71 through 73' Processing helix chain 'W' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN W 131 " --> pdb=" O TYR W 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 136 through 148 Processing helix chain 'Z' and resid 71 through 73 No H-bonds generated for 'chain 'Z' and resid 71 through 73' Processing helix chain 'Z' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN Z 131 " --> pdb=" O TYR Z 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 136 through 148 Processing helix chain 'c' and resid 71 through 73 No H-bonds generated for 'chain 'c' and resid 71 through 73' Processing helix chain 'c' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN c 131 " --> pdb=" O TYR c 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 148 Processing helix chain 'f' and resid 71 through 73 No H-bonds generated for 'chain 'f' and resid 71 through 73' Processing helix chain 'f' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN f 131 " --> pdb=" O TYR f 127 " (cutoff:3.500A) Processing helix chain 'h' and resid 136 through 148 Processing helix chain 'i' and resid 71 through 73 No H-bonds generated for 'chain 'i' and resid 71 through 73' Processing helix chain 'i' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN i 131 " --> pdb=" O TYR i 127 " (cutoff:3.500A) Processing helix chain 'k' and resid 136 through 148 Processing helix chain 'l' and resid 71 through 73 No H-bonds generated for 'chain 'l' and resid 71 through 73' Processing helix chain 'l' and resid 127 through 135 removed outlier: 3.573A pdb=" N GLN l 131 " --> pdb=" O TYR l 127 " (cutoff:3.500A) Processing helix chain 'n' and resid 136 through 148 Processing helix chain 'o' and resid 71 through 73 No H-bonds generated for 'chain 'o' and resid 71 through 73' Processing helix chain 'o' and resid 127 through 135 removed outlier: 3.572A pdb=" N GLN o 131 " --> pdb=" O TYR o 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 136 through 148 Processing helix chain 'z' and resid 71 through 73 No H-bonds generated for 'chain 'z' and resid 71 through 73' Processing helix chain 'z' and resid 127 through 135 removed outlier: 3.573A pdb=" N GLN z 131 " --> pdb=" O TYR z 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG B 34 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG B 126 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 36 " --> pdb=" O ARG B 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS B 55 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE B 125 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET B 57 " --> pdb=" O PHE B 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 48 Processing sheet with id=AA3, first strand: chain 'E' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG E 34 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG E 126 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL E 36 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS E 55 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE E 125 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET E 57 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 44 through 48 Processing sheet with id=AA5, first strand: chain 'H' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG H 34 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG H 126 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL H 36 " --> pdb=" O ARG H 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS H 55 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE H 125 " --> pdb=" O HIS H 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET H 57 " --> pdb=" O PHE H 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 44 through 48 Processing sheet with id=AA7, first strand: chain 'K' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG K 34 " --> pdb=" O ALA K 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG K 126 " --> pdb=" O ARG K 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL K 36 " --> pdb=" O ARG K 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS K 55 " --> pdb=" O LEU K 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE K 125 " --> pdb=" O HIS K 55 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N MET K 57 " --> pdb=" O PHE K 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 44 through 48 Processing sheet with id=AA9, first strand: chain 'N' and resid 25 through 26 removed outlier: 6.794A pdb=" N ARG N 34 " --> pdb=" O ALA N 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG N 126 " --> pdb=" O ARG N 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL N 36 " --> pdb=" O ARG N 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS N 55 " --> pdb=" O LEU N 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE N 125 " --> pdb=" O HIS N 55 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N MET N 57 " --> pdb=" O PHE N 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 44 through 48 Processing sheet with id=AB2, first strand: chain 'Q' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG Q 34 " --> pdb=" O ALA Q 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG Q 126 " --> pdb=" O ARG Q 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL Q 36 " --> pdb=" O ARG Q 126 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS Q 55 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE Q 125 " --> pdb=" O HIS Q 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET Q 57 " --> pdb=" O PHE Q 125 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 44 through 48 Processing sheet with id=AB4, first strand: chain 'T' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG T 34 " --> pdb=" O ALA T 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG T 126 " --> pdb=" O ARG T 34 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL T 36 " --> pdb=" O ARG T 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS T 55 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE T 125 " --> pdb=" O HIS T 55 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N MET T 57 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 44 through 48 Processing sheet with id=AB6, first strand: chain 'v' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG v 34 " --> pdb=" O ALA v 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG v 126 " --> pdb=" O ARG v 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL v 36 " --> pdb=" O ARG v 126 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS v 55 " --> pdb=" O LEU v 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE v 125 " --> pdb=" O HIS v 55 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N MET v 57 " --> pdb=" O PHE v 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'v' and resid 44 through 48 Processing sheet with id=AB8, first strand: chain 'W' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG W 34 " --> pdb=" O ALA W 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG W 126 " --> pdb=" O ARG W 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL W 36 " --> pdb=" O ARG W 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS W 55 " --> pdb=" O LEU W 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE W 125 " --> pdb=" O HIS W 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET W 57 " --> pdb=" O PHE W 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 44 through 48 Processing sheet with id=AC1, first strand: chain 'Z' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG Z 34 " --> pdb=" O ALA Z 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG Z 126 " --> pdb=" O ARG Z 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL Z 36 " --> pdb=" O ARG Z 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS Z 55 " --> pdb=" O LEU Z 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE Z 125 " --> pdb=" O HIS Z 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET Z 57 " --> pdb=" O PHE Z 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 44 through 48 Processing sheet with id=AC3, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG c 34 " --> pdb=" O ALA c 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG c 126 " --> pdb=" O ARG c 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL c 36 " --> pdb=" O ARG c 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS c 55 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE c 125 " --> pdb=" O HIS c 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET c 57 " --> pdb=" O PHE c 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 44 through 48 Processing sheet with id=AC5, first strand: chain 'f' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG f 34 " --> pdb=" O ALA f 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG f 126 " --> pdb=" O ARG f 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL f 36 " --> pdb=" O ARG f 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS f 55 " --> pdb=" O LEU f 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE f 125 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET f 57 " --> pdb=" O PHE f 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 44 through 48 Processing sheet with id=AC7, first strand: chain 'i' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG i 34 " --> pdb=" O ALA i 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG i 126 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL i 36 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS i 55 " --> pdb=" O LEU i 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE i 125 " --> pdb=" O HIS i 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET i 57 " --> pdb=" O PHE i 125 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'i' and resid 44 through 48 Processing sheet with id=AC9, first strand: chain 'l' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG l 34 " --> pdb=" O ALA l 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG l 126 " --> pdb=" O ARG l 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL l 36 " --> pdb=" O ARG l 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS l 55 " --> pdb=" O LEU l 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE l 125 " --> pdb=" O HIS l 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET l 57 " --> pdb=" O PHE l 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'l' and resid 44 through 48 Processing sheet with id=AD2, first strand: chain 'o' and resid 25 through 26 removed outlier: 6.796A pdb=" N ARG o 34 " --> pdb=" O ALA o 124 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ARG o 126 " --> pdb=" O ARG o 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL o 36 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS o 55 " --> pdb=" O LEU o 123 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N PHE o 125 " --> pdb=" O HIS o 55 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N MET o 57 " --> pdb=" O PHE o 125 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'o' and resid 44 through 48 Processing sheet with id=AD4, first strand: chain 'z' and resid 25 through 26 removed outlier: 6.795A pdb=" N ARG z 34 " --> pdb=" O ALA z 124 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ARG z 126 " --> pdb=" O ARG z 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL z 36 " --> pdb=" O ARG z 126 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS z 55 " --> pdb=" O LEU z 123 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE z 125 " --> pdb=" O HIS z 55 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N MET z 57 " --> pdb=" O PHE z 125 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'z' and resid 44 through 48 640 hydrogen bonds defined for protein. 1680 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: 5.31 Time building geometry restraints manager: 7.51 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: 5962 1.34 - 1.45: 2802 1.45 - 1.57: 8884 1.57 - 1.68: 16 1.68 - 1.80: 128 Bond restraints: 17792 Sorted by residual: bond pdb=" CG PRO M 137 " pdb=" CD PRO M 137 " ideal model delta sigma weight residual 1.503 1.439 0.064 3.40e-02 8.65e+02 3.49e+00 bond pdb=" CG PRO S 137 " pdb=" CD PRO S 137 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.46e+00 bond pdb=" CG PRO u 137 " pdb=" CD PRO u 137 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.45e+00 bond pdb=" CG PRO Y 137 " pdb=" CD PRO Y 137 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.45e+00 bond pdb=" CG PRO V 137 " pdb=" CD PRO V 137 " ideal model delta sigma weight residual 1.503 1.440 0.063 3.40e-02 8.65e+02 3.45e+00 ... (remaining 17787 not shown) Histogram of bond angle deviations from ideal: 98.36 - 104.98: 304 104.98 - 111.59: 7561 111.59 - 118.20: 5212 118.20 - 124.82: 10762 124.82 - 131.43: 177 Bond angle restraints: 24016 Sorted by residual: angle pdb=" CA PRO J 137 " pdb=" N PRO J 137 " pdb=" CD PRO J 137 " ideal model delta sigma weight residual 112.00 105.72 6.28 1.40e+00 5.10e-01 2.01e+01 angle pdb=" CA PRO e 137 " pdb=" N PRO e 137 " pdb=" CD PRO e 137 " ideal model delta sigma weight residual 112.00 105.73 6.27 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO n 137 " pdb=" N PRO n 137 " pdb=" CD PRO n 137 " ideal model delta sigma weight residual 112.00 105.74 6.26 1.40e+00 5.10e-01 2.00e+01 angle pdb=" CA PRO b 137 " pdb=" N PRO b 137 " pdb=" CD PRO b 137 " ideal model delta sigma weight residual 112.00 105.75 6.25 1.40e+00 5.10e-01 1.99e+01 angle pdb=" CA PRO P 137 " pdb=" N PRO P 137 " pdb=" CD PRO P 137 " ideal model delta sigma weight residual 112.00 105.75 6.25 1.40e+00 5.10e-01 1.99e+01 ... (remaining 24011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 9744 15.06 - 30.12: 816 30.12 - 45.17: 144 45.17 - 60.23: 64 60.23 - 75.29: 16 Dihedral angle restraints: 10784 sinusoidal: 4464 harmonic: 6320 Sorted by residual: dihedral pdb=" CG ARG N 34 " pdb=" CD ARG N 34 " pdb=" NE ARG N 34 " pdb=" CZ ARG N 34 " ideal model delta sinusoidal sigma weight residual 90.00 130.80 -40.80 2 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CG ARG o 34 " pdb=" CD ARG o 34 " pdb=" NE ARG o 34 " pdb=" CZ ARG o 34 " ideal model delta sinusoidal sigma weight residual 90.00 130.80 -40.80 2 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CG ARG Z 34 " pdb=" CD ARG Z 34 " pdb=" NE ARG Z 34 " pdb=" CZ ARG Z 34 " ideal model delta sinusoidal sigma weight residual 90.00 130.79 -40.79 2 1.50e+01 4.44e-03 9.11e+00 ... (remaining 10781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1383 0.033 - 0.066: 757 0.066 - 0.098: 271 0.098 - 0.131: 165 0.131 - 0.164: 16 Chirality restraints: 2592 Sorted by residual: chirality pdb=" CA PRO e 137 " pdb=" N PRO e 137 " pdb=" C PRO e 137 " pdb=" CB PRO e 137 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA PRO A 137 " pdb=" N PRO A 137 " pdb=" C PRO A 137 " pdb=" CB PRO A 137 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA PRO Y 137 " pdb=" N PRO Y 137 " pdb=" C PRO Y 137 " pdb=" CB PRO Y 137 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 2589 not shown) Planarity restraints: 3152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 136 " -0.070 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO S 137 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO S 137 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO S 137 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR k 136 " 0.070 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO k 137 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO k 137 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO k 137 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 136 " 0.070 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO G 137 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO G 137 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 137 " 0.056 5.00e-02 4.00e+02 ... (remaining 3149 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 150 2.57 - 3.15: 13482 3.15 - 3.74: 27234 3.74 - 4.32: 40468 4.32 - 4.90: 67458 Nonbonded interactions: 148792 Sorted by model distance: nonbonded pdb=" NZ LYS i 87 " pdb=" O MET k 145 " model vdw 1.988 3.120 nonbonded pdb=" NZ LYS l 87 " pdb=" O MET n 145 " model vdw 2.112 3.120 nonbonded pdb=" NZ LYS T 87 " pdb=" O MET u 145 " model vdw 2.115 3.120 nonbonded pdb=" NH1 ARG n 144 " pdb=" OD2 ASP o 71 " model vdw 2.120 3.120 nonbonded pdb=" NZ LYS Q 87 " pdb=" O MET S 145 " model vdw 2.166 3.120 ... (remaining 148787 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'b' selection = chain 'e' selection = chain 'h' selection = chain 'k' selection = chain 'n' selection = chain 'u' selection = chain 'y' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' selection = chain 'f' selection = chain 'i' selection = chain 'l' selection = chain 'o' selection = chain 'v' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 47.350 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 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 : 0.007 0.079 17792 Z= 0.465 Angle : 0.789 7.478 24016 Z= 0.466 Chirality : 0.050 0.164 2592 Planarity : 0.008 0.102 3152 Dihedral : 12.352 75.289 6720 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2080 helix: 2.22 (0.26), residues: 320 sheet: 0.52 (0.16), residues: 880 loop : -0.75 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS Q 83 PHE 0.009 0.002 PHE f 77 TYR 0.014 0.002 TYR l 127 ARG 0.009 0.001 ARG G 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 776 time to evaluate : 2.089 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: A 136 THR cc_start: 0.7681 (t) cc_final: 0.7428 (t) REVERT: h 136 THR cc_start: 0.7747 (t) cc_final: 0.7356 (t) REVERT: l 129 ASP cc_start: 0.6701 (p0) cc_final: 0.6495 (p0) REVERT: n 136 THR cc_start: 0.6566 (t) cc_final: 0.6033 (t) outliers start: 0 outliers final: 3 residues processed: 776 average time/residue: 1.2156 time to fit residues: 1051.7621 Evaluate side-chains 608 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 605 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain W residue 114 ASN Chi-restraints excluded: chain c residue 114 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 174 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: B 94 ASN E 89 GLN E 94 ASN H 94 ASN N 94 ASN Q 89 GLN Q 94 ASN T 94 ASN v 94 ASN W 45 GLN W 89 GLN Z 89 GLN Z 94 ASN c 94 ASN f 94 ASN i 94 ASN l 89 GLN l 94 ASN o 94 ASN z 94 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17792 Z= 0.284 Angle : 0.670 7.422 24016 Z= 0.349 Chirality : 0.048 0.182 2592 Planarity : 0.005 0.044 3152 Dihedral : 4.348 15.311 2502 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.50 % Allowed : 16.34 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2080 helix: 2.62 (0.26), residues: 320 sheet: 0.68 (0.16), residues: 864 loop : -0.69 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 83 PHE 0.010 0.001 PHE v 77 TYR 0.017 0.001 TYR S 138 ARG 0.008 0.001 ARG c 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 650 time to evaluate : 2.048 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: D 136 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7568 (t) REVERT: D 140 LEU cc_start: 0.7404 (mp) cc_final: 0.7024 (mp) REVERT: M 135 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7799 (ttpt) REVERT: M 143 GLU cc_start: 0.5607 (tp30) cc_final: 0.5354 (tp30) outliers start: 82 outliers final: 18 residues processed: 677 average time/residue: 1.0543 time to fit residues: 808.3894 Evaluate side-chains 595 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 576 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain T residue 114 ASN Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain W residue 57 MET Chi-restraints excluded: chain W residue 71 ASP Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain c residue 114 ASN Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain i residue 71 ASP Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain l residue 122 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 94 ASN Q 45 GLN Q 89 GLN ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 ASN Z 89 GLN ** l 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 17792 Z= 0.467 Angle : 0.685 6.723 24016 Z= 0.359 Chirality : 0.050 0.213 2592 Planarity : 0.004 0.038 3152 Dihedral : 4.349 28.536 2498 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 4.71 % Allowed : 19.46 % Favored : 75.82 % 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: 0.76 (0.18), residues: 2080 helix: 2.82 (0.25), residues: 320 sheet: 0.65 (0.16), residues: 896 loop : -0.51 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS i 55 PHE 0.014 0.002 PHE f 77 TYR 0.013 0.001 TYR Z 127 ARG 0.004 0.001 ARG v 109 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 593 time to evaluate : 2.057 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: A 140 LEU cc_start: 0.7581 (mm) cc_final: 0.7085 (mm) REVERT: M 140 LEU cc_start: 0.7671 (mm) cc_final: 0.7277 (mm) REVERT: S 143 GLU cc_start: 0.5735 (tp30) cc_final: 0.5282 (tp30) REVERT: h 142 ARG cc_start: 0.7283 (mtp85) cc_final: 0.6959 (mtp85) REVERT: k 135 LYS cc_start: 0.8108 (mttt) cc_final: 0.7534 (ttpt) outliers start: 86 outliers final: 31 residues processed: 621 average time/residue: 1.1681 time to fit residues: 815.0073 Evaluate side-chains 568 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 537 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 ASN Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain u residue 151 THR Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 114 ASN Chi-restraints excluded: chain c residue 114 ASN Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain h residue 151 THR Chi-restraints excluded: chain i residue 114 ASN Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 151 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 GLN E 89 GLN v 89 GLN ** W 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17792 Z= 0.269 Angle : 0.658 7.267 24016 Z= 0.345 Chirality : 0.049 0.196 2592 Planarity : 0.003 0.027 3152 Dihedral : 4.287 28.266 2498 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.84 % Allowed : 20.83 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2080 helix: 2.74 (0.26), residues: 320 sheet: 0.60 (0.17), residues: 864 loop : -0.59 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS c 55 PHE 0.010 0.002 PHE v 77 TYR 0.016 0.001 TYR V 138 ARG 0.004 0.000 ARG Z 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 603 time to evaluate : 2.404 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: b 135 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.7150 (ttmm) outliers start: 70 outliers final: 25 residues processed: 631 average time/residue: 1.1069 time to fit residues: 786.9903 Evaluate side-chains 561 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 535 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 143 GLU Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain v residue 92 LEU Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain b residue 135 LYS Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 114 ASN Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain l residue 57 MET Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain y residue 136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 2 optimal weight: 0.0770 chunk 138 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN Q 89 GLN T 89 GLN v 89 GLN v 131 GLN f 131 GLN o 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17792 Z= 0.272 Angle : 0.693 10.068 24016 Z= 0.363 Chirality : 0.050 0.288 2592 Planarity : 0.003 0.033 3152 Dihedral : 4.341 25.910 2498 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 4.11 % Allowed : 22.53 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2080 helix: 2.43 (0.28), residues: 320 sheet: 0.37 (0.16), residues: 944 loop : -0.55 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS l 55 PHE 0.010 0.002 PHE v 77 TYR 0.020 0.001 TYR k 138 ARG 0.005 0.000 ARG l 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 586 time to evaluate : 2.147 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: A 143 GLU cc_start: 0.5700 (tp30) cc_final: 0.5301 (tp30) REVERT: S 143 GLU cc_start: 0.6053 (tp30) cc_final: 0.5808 (tp30) REVERT: b 135 LYS cc_start: 0.7334 (OUTLIER) cc_final: 0.7028 (ttmm) outliers start: 75 outliers final: 36 residues processed: 611 average time/residue: 1.0786 time to fit residues: 744.3070 Evaluate side-chains 571 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 534 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain K residue 57 MET Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 89 GLN Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 114 ASN Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain b residue 135 LYS Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 114 ASN Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain e residue 151 THR Chi-restraints excluded: chain h residue 151 THR Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain z residue 57 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 89 GLN Q 111 GLN Z 89 GLN f 89 GLN z 89 GLN z 131 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17792 Z= 0.289 Angle : 0.727 11.789 24016 Z= 0.379 Chirality : 0.051 0.324 2592 Planarity : 0.003 0.033 3152 Dihedral : 4.416 25.442 2498 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 3.56 % Allowed : 24.78 % Favored : 71.66 % 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: 0.53 (0.19), residues: 2080 helix: 2.24 (0.29), residues: 320 sheet: 0.48 (0.16), residues: 912 loop : -0.46 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS f 55 PHE 0.011 0.002 PHE v 77 TYR 0.017 0.001 TYR J 138 ARG 0.005 0.000 ARG l 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 567 time to evaluate : 1.909 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: b 135 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6857 (ttmm) outliers start: 65 outliers final: 32 residues processed: 592 average time/residue: 1.1432 time to fit residues: 761.3795 Evaluate side-chains 549 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 516 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 MET Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain N residue 57 MET Chi-restraints excluded: chain N residue 130 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 120 MET Chi-restraints excluded: chain Q residue 130 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain u residue 135 LYS Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain W residue 130 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 114 ASN Chi-restraints excluded: chain Z residue 120 MET Chi-restraints excluded: chain b residue 135 LYS Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain c residue 130 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain h residue 151 THR Chi-restraints excluded: chain i residue 130 THR Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 185 optimal weight: 0.0270 chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 overall best weight: 0.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 131 GLN W 89 GLN Z 45 GLN f 89 GLN i 45 GLN l 45 GLN l 89 GLN o 45 GLN z 89 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17792 Z= 0.230 Angle : 0.766 11.272 24016 Z= 0.394 Chirality : 0.052 0.312 2592 Planarity : 0.003 0.055 3152 Dihedral : 4.398 17.760 2496 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.19 % Allowed : 27.58 % Favored : 70.23 % 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: 0.50 (0.19), residues: 2080 helix: 2.14 (0.29), residues: 320 sheet: 0.41 (0.16), residues: 912 loop : -0.37 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS z 55 PHE 0.010 0.001 PHE o 77 TYR 0.011 0.001 TYR b 138 ARG 0.013 0.000 ARG e 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 586 time to evaluate : 2.152 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 outliers start: 40 outliers final: 15 residues processed: 598 average time/residue: 1.0583 time to fit residues: 716.7394 Evaluate side-chains 542 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 527 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain Z residue 114 ASN Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 114 ASN Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain y residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 17792 Z= 0.355 Angle : 0.836 10.801 24016 Z= 0.429 Chirality : 0.055 0.337 2592 Planarity : 0.003 0.033 3152 Dihedral : 4.578 20.041 2496 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.36 % Allowed : 29.28 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 2080 helix: 1.93 (0.30), residues: 320 sheet: 0.39 (0.16), residues: 912 loop : -0.37 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 55 PHE 0.011 0.002 PHE c 77 TYR 0.014 0.001 TYR e 138 ARG 0.009 0.000 ARG e 147 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 538 time to evaluate : 2.187 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 outliers start: 43 outliers final: 18 residues processed: 557 average time/residue: 1.1697 time to fit residues: 738.9520 Evaluate side-chains 524 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 506 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 114 ASN Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain h residue 151 THR Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 0.0270 chunk 113 optimal weight: 0.4980 overall best weight: 2.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN H 111 GLN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17792 Z= 0.314 Angle : 0.896 12.419 24016 Z= 0.457 Chirality : 0.057 0.374 2592 Planarity : 0.003 0.027 3152 Dihedral : 4.695 20.711 2496 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.70 % Allowed : 30.98 % Favored : 67.32 % 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: 0.36 (0.19), residues: 2080 helix: 1.74 (0.30), residues: 320 sheet: 0.33 (0.16), residues: 912 loop : -0.33 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS o 55 PHE 0.011 0.001 PHE Q 77 TYR 0.011 0.001 TYR u 138 ARG 0.007 0.000 ARG e 147 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 544 time to evaluate : 2.058 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 outliers start: 31 outliers final: 18 residues processed: 555 average time/residue: 1.1191 time to fit residues: 700.3128 Evaluate side-chains 534 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 516 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 71 ASP Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain u residue 140 LEU Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 143 GLU Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 136 THR Chi-restraints excluded: chain y residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17792 Z= 0.368 Angle : 0.938 12.911 24016 Z= 0.481 Chirality : 0.058 0.357 2592 Planarity : 0.004 0.033 3152 Dihedral : 4.784 20.984 2496 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 0.99 % Allowed : 31.96 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2080 helix: 1.39 (0.31), residues: 320 sheet: 0.33 (0.16), residues: 912 loop : -0.34 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 55 PHE 0.012 0.002 PHE Q 77 TYR 0.014 0.001 TYR G 138 ARG 0.015 0.001 ARG V 147 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 524 time to evaluate : 2.096 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: c 120 MET cc_start: 0.5727 (tpp) cc_final: 0.5297 (tpt) outliers start: 18 outliers final: 19 residues processed: 531 average time/residue: 1.1016 time to fit residues: 660.1921 Evaluate side-chains 515 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 496 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain J residue 136 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain P residue 136 THR Chi-restraints excluded: chain Q residue 120 MET Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 151 THR Chi-restraints excluded: chain V residue 136 THR Chi-restraints excluded: chain Y residue 150 LEU Chi-restraints excluded: chain b residue 136 THR Chi-restraints excluded: chain e residue 136 THR Chi-restraints excluded: chain k residue 142 ARG Chi-restraints excluded: chain l residue 123 LEU Chi-restraints excluded: chain n residue 151 THR Chi-restraints excluded: chain y residue 140 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 133 optimal weight: 0.0270 overall best weight: 3.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.056690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.042875 restraints weight = 60508.909| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.98 r_work: 0.2534 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 17792 Z= 0.369 Angle : 0.961 13.151 24016 Z= 0.491 Chirality : 0.059 0.383 2592 Planarity : 0.004 0.074 3152 Dihedral : 4.845 22.357 2496 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 1.21 % Allowed : 32.73 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 2080 helix: 1.04 (0.30), residues: 320 sheet: 0.30 (0.16), residues: 912 loop : -0.35 (0.24), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 55 PHE 0.012 0.002 PHE Q 77 TYR 0.013 0.001 TYR u 138 ARG 0.015 0.001 ARG D 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10278.27 seconds wall clock time: 178 minutes 30.60 seconds (10710.60 seconds total)