Starting phenix.real_space_refine on Sun Nov 17 19:52:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/11_2024/8fte_29424.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/11_2024/8fte_29424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/11_2024/8fte_29424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/11_2024/8fte_29424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/11_2024/8fte_29424.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/11_2024/8fte_29424.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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 22 5.16 5 C 8998 2.51 5 N 2618 2.21 5 O 2926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14564 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "P" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "Q" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "V" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "W" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 9.96, per 1000 atoms: 0.68 Number of scatterers: 14564 At special positions: 0 Unit cell: (176.8, 178.16, 44.88, 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 22 16.00 O 2926 8.00 N 2618 7.00 C 8998 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 - 3.00 Amino acid : True - 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: 3.48 Conformation dependent library (CDL) restraints added in 2.1 seconds 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 22 sheets defined 42.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'B' and resid 126 through 146 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'C' and resid 126 through 146 Processing helix chain 'C' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'D' and resid 126 through 146 Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'E' and resid 126 through 146 Processing helix chain 'E' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 201 " --> pdb=" O LEU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'F' and resid 126 through 146 Processing helix chain 'F' and resid 187 through 201 removed outlier: 3.581A pdb=" N ALA F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA F 201 " --> pdb=" O LEU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'G' and resid 126 through 146 Processing helix chain 'G' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA G 193 " --> pdb=" O GLY G 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'H' and resid 126 through 146 Processing helix chain 'H' and resid 187 through 201 removed outlier: 3.581A pdb=" N ALA H 193 " --> pdb=" O GLY H 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 201 " --> pdb=" O LEU H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'I' and resid 126 through 146 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA I 193 " --> pdb=" O GLY I 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'J' and resid 126 through 146 Processing helix chain 'J' and resid 187 through 201 removed outlier: 3.579A pdb=" N ALA J 193 " --> pdb=" O GLY J 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA J 201 " --> pdb=" O LEU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 208 No H-bonds generated for 'chain 'J' and resid 206 through 208' Processing helix chain 'K' and resid 126 through 146 Processing helix chain 'K' and resid 187 through 201 removed outlier: 3.579A pdb=" N ALA K 193 " --> pdb=" O GLY K 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA K 201 " --> pdb=" O LEU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'L' and resid 126 through 146 Processing helix chain 'L' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA L 193 " --> pdb=" O GLY L 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA L 201 " --> pdb=" O LEU L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'M' and resid 126 through 146 Processing helix chain 'M' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA M 193 " --> pdb=" O GLY M 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA M 201 " --> pdb=" O LEU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 208 No H-bonds generated for 'chain 'M' and resid 206 through 208' Processing helix chain 'N' and resid 126 through 146 Processing helix chain 'N' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA N 193 " --> pdb=" O GLY N 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA N 201 " --> pdb=" O LEU N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 208 No H-bonds generated for 'chain 'N' and resid 206 through 208' Processing helix chain 'O' and resid 126 through 146 Processing helix chain 'O' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA O 193 " --> pdb=" O GLY O 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 208 No H-bonds generated for 'chain 'O' and resid 206 through 208' Processing helix chain 'P' and resid 126 through 146 Processing helix chain 'P' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA P 193 " --> pdb=" O GLY P 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 208 No H-bonds generated for 'chain 'P' and resid 206 through 208' Processing helix chain 'Q' and resid 126 through 146 Processing helix chain 'Q' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA Q 193 " --> pdb=" O GLY Q 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA Q 201 " --> pdb=" O LEU Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 208 No H-bonds generated for 'chain 'Q' and resid 206 through 208' Processing helix chain 'R' and resid 126 through 146 Processing helix chain 'R' and resid 187 through 201 removed outlier: 3.581A pdb=" N ALA R 193 " --> pdb=" O GLY R 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA R 201 " --> pdb=" O LEU R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 208 No H-bonds generated for 'chain 'R' and resid 206 through 208' Processing helix chain 'S' and resid 126 through 146 Processing helix chain 'S' and resid 187 through 201 removed outlier: 3.581A pdb=" N ALA S 193 " --> pdb=" O GLY S 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA S 201 " --> pdb=" O LEU S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 208 No H-bonds generated for 'chain 'S' and resid 206 through 208' Processing helix chain 'T' and resid 126 through 146 Processing helix chain 'T' and resid 187 through 201 removed outlier: 3.579A pdb=" N ALA T 193 " --> pdb=" O GLY T 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA T 201 " --> pdb=" O LEU T 197 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 208 No H-bonds generated for 'chain 'T' and resid 206 through 208' Processing helix chain 'V' and resid 126 through 146 Processing helix chain 'V' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA V 193 " --> pdb=" O GLY V 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA V 201 " --> pdb=" O LEU V 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 208 No H-bonds generated for 'chain 'V' and resid 206 through 208' Processing helix chain 'W' and resid 126 through 146 Processing helix chain 'W' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA W 193 " --> pdb=" O GLY W 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA W 201 " --> pdb=" O LEU W 197 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 208 No H-bonds generated for 'chain 'W' and resid 206 through 208' Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER A 152 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 179 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 154 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 173 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER B 152 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 179 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 154 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B 173 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER C 152 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR C 179 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 154 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 173 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER D 152 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR D 179 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 154 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 173 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER E 152 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR E 179 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 154 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 173 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER F 152 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR F 179 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG F 154 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER F 173 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER G 152 " --> pdb=" O THR G 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR G 179 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 154 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER G 173 " --> pdb=" O ALA G 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER H 152 " --> pdb=" O THR H 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR H 179 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG H 154 " --> pdb=" O THR H 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER H 173 " --> pdb=" O ALA H 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER I 152 " --> pdb=" O THR I 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR I 179 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG I 154 " --> pdb=" O THR I 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER I 173 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER J 152 " --> pdb=" O THR J 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR J 179 " --> pdb=" O SER J 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG J 154 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER J 173 " --> pdb=" O ALA J 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER K 152 " --> pdb=" O THR K 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR K 179 " --> pdb=" O SER K 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG K 154 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER K 173 " --> pdb=" O ALA K 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER L 152 " --> pdb=" O THR L 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR L 179 " --> pdb=" O SER L 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 154 " --> pdb=" O THR L 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER L 173 " --> pdb=" O ALA L 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER M 152 " --> pdb=" O THR M 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR M 179 " --> pdb=" O SER M 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG M 154 " --> pdb=" O THR M 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER M 173 " --> pdb=" O ALA M 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER N 152 " --> pdb=" O THR N 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR N 179 " --> pdb=" O SER N 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG N 154 " --> pdb=" O THR N 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER N 173 " --> pdb=" O ALA N 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER O 152 " --> pdb=" O THR O 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR O 179 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG O 154 " --> pdb=" O THR O 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER O 173 " --> pdb=" O ALA O 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER P 152 " --> pdb=" O THR P 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR P 179 " --> pdb=" O SER P 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG P 154 " --> pdb=" O THR P 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER P 173 " --> pdb=" O ALA P 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER Q 152 " --> pdb=" O THR Q 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR Q 179 " --> pdb=" O SER Q 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG Q 154 " --> pdb=" O THR Q 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER Q 173 " --> pdb=" O ALA Q 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER R 152 " --> pdb=" O THR R 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR R 179 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG R 154 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER R 173 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER S 152 " --> pdb=" O THR S 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR S 179 " --> pdb=" O SER S 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG S 154 " --> pdb=" O THR S 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER S 173 " --> pdb=" O ALA S 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER T 152 " --> pdb=" O THR T 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR T 179 " --> pdb=" O SER T 152 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG T 154 " --> pdb=" O THR T 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER T 173 " --> pdb=" O ALA T 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER V 152 " --> pdb=" O THR V 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR V 179 " --> pdb=" O SER V 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG V 154 " --> pdb=" O THR V 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER V 173 " --> pdb=" O ALA V 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER W 152 " --> pdb=" O THR W 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR W 179 " --> pdb=" O SER W 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG W 154 " --> pdb=" O THR W 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER W 173 " --> pdb=" O ALA W 158 " (cutoff:3.500A) 749 hydrogen bonds defined for protein. 2247 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.00 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5038 1.34 - 1.46: 1946 1.46 - 1.57: 7734 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 14762 Sorted by residual: bond pdb=" N ASN C 209 " pdb=" CA ASN C 209 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.33e-02 5.65e+03 7.26e+00 bond pdb=" CA ASN C 209 " pdb=" C ASN C 209 " ideal model delta sigma weight residual 1.522 1.532 -0.011 1.31e-02 5.83e+03 6.77e-01 bond pdb=" C ASN C 209 " pdb=" O ASN C 209 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.39e-02 5.18e+03 6.50e-01 bond pdb=" C GLU P 181 " pdb=" N PRO P 182 " ideal model delta sigma weight residual 1.332 1.342 -0.010 1.30e-02 5.92e+03 6.01e-01 bond pdb=" C GLU O 181 " pdb=" N PRO O 182 " ideal model delta sigma weight residual 1.332 1.341 -0.010 1.30e-02 5.92e+03 5.77e-01 ... (remaining 14757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 18188 0.91 - 1.81: 1518 1.81 - 2.72: 309 2.72 - 3.62: 115 3.62 - 4.53: 22 Bond angle restraints: 20152 Sorted by residual: angle pdb=" N ARG W 154 " pdb=" CA ARG W 154 " pdb=" C ARG W 154 " ideal model delta sigma weight residual 107.80 111.01 -3.21 1.73e+00 3.34e-01 3.44e+00 angle pdb=" N ARG M 154 " pdb=" CA ARG M 154 " pdb=" C ARG M 154 " ideal model delta sigma weight residual 107.80 110.99 -3.19 1.73e+00 3.34e-01 3.41e+00 angle pdb=" N ARG J 154 " pdb=" CA ARG J 154 " pdb=" C ARG J 154 " ideal model delta sigma weight residual 107.80 110.99 -3.19 1.73e+00 3.34e-01 3.41e+00 angle pdb=" N ARG K 154 " pdb=" CA ARG K 154 " pdb=" C ARG K 154 " ideal model delta sigma weight residual 107.80 110.99 -3.19 1.73e+00 3.34e-01 3.41e+00 angle pdb=" N ARG D 154 " pdb=" CA ARG D 154 " pdb=" C ARG D 154 " ideal model delta sigma weight residual 107.80 110.99 -3.19 1.73e+00 3.34e-01 3.40e+00 ... (remaining 20147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.58: 7943 11.58 - 23.15: 638 23.15 - 34.73: 205 34.73 - 46.30: 80 46.30 - 57.88: 88 Dihedral angle restraints: 8954 sinusoidal: 3190 harmonic: 5764 Sorted by residual: dihedral pdb=" CA GLN W 190 " pdb=" C GLN W 190 " pdb=" N ILE W 191 " pdb=" CA ILE W 191 " ideal model delta harmonic sigma weight residual 180.00 165.02 14.98 0 5.00e+00 4.00e-02 8.97e+00 dihedral pdb=" CA GLN N 190 " pdb=" C GLN N 190 " pdb=" N ILE N 191 " pdb=" CA ILE N 191 " ideal model delta harmonic sigma weight residual 180.00 165.03 14.97 0 5.00e+00 4.00e-02 8.97e+00 dihedral pdb=" CA GLN B 190 " pdb=" C GLN B 190 " pdb=" N ILE B 191 " pdb=" CA ILE B 191 " ideal model delta harmonic sigma weight residual 180.00 165.03 14.97 0 5.00e+00 4.00e-02 8.97e+00 ... (remaining 8951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1344 0.024 - 0.047: 621 0.047 - 0.071: 325 0.071 - 0.095: 195 0.095 - 0.118: 45 Chirality restraints: 2530 Sorted by residual: chirality pdb=" CA VAL D 213 " pdb=" N VAL D 213 " pdb=" C VAL D 213 " pdb=" CB VAL D 213 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA VAL P 213 " pdb=" N VAL P 213 " pdb=" C VAL P 213 " pdb=" CB VAL P 213 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA VAL H 213 " pdb=" N VAL H 213 " pdb=" C VAL H 213 " pdb=" CB VAL H 213 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 2527 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 171 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO J 172 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO J 172 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 172 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 171 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO N 172 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO N 172 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO N 172 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 171 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO D 172 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " -0.016 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1559 2.74 - 3.28: 14713 3.28 - 3.82: 22183 3.82 - 4.36: 24609 4.36 - 4.90: 40535 Nonbonded interactions: 103599 Sorted by model distance: nonbonded pdb=" NH1 ARG D 154 " pdb=" NH2 ARG E 142 " model vdw 2.203 3.200 nonbonded pdb=" NH1 ARG H 154 " pdb=" NH2 ARG I 142 " model vdw 2.208 3.200 nonbonded pdb=" NH1 ARG M 154 " pdb=" NH2 ARG N 142 " model vdw 2.220 3.200 nonbonded pdb=" NH1 ARG T 154 " pdb=" NH2 ARG V 142 " model vdw 2.220 3.200 nonbonded pdb=" NH1 ARG V 154 " pdb=" NH2 ARG W 142 " model vdw 2.221 3.200 ... (remaining 103594 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.150 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.790 Find NCS groups from input model: 0.600 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: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4932 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14762 Z= 0.189 Angle : 0.627 4.530 20152 Z= 0.375 Chirality : 0.039 0.118 2530 Planarity : 0.004 0.029 2640 Dihedral : 12.353 57.877 5214 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.56 % Allowed : 13.89 % Favored : 80.56 % 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: 0.06 (0.20), residues: 1958 helix: 1.95 (0.19), residues: 770 sheet: -1.10 (0.26), residues: 440 loop : -1.24 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 196 PHE 0.001 0.001 PHE K 126 TYR 0.004 0.001 TYR C 132 ARG 0.001 0.000 ARG H 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 423 time to evaluate : 1.552 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: B 176 VAL cc_start: 0.7465 (t) cc_final: 0.7176 (m) REVERT: D 160 PRO cc_start: 0.5619 (Cg_exo) cc_final: 0.5317 (Cg_endo) REVERT: F 220 LEU cc_start: 0.7565 (mt) cc_final: 0.5267 (tt) REVERT: I 220 LEU cc_start: 0.6616 (mt) cc_final: 0.6401 (mt) REVERT: J 177 THR cc_start: 0.6018 (p) cc_final: 0.5793 (p) REVERT: K 159 MET cc_start: 0.6754 (mmt) cc_final: 0.5976 (mmp) REVERT: M 159 MET cc_start: 0.6271 (mmt) cc_final: 0.5476 (mmm) REVERT: N 159 MET cc_start: 0.6330 (mmt) cc_final: 0.5560 (mmm) REVERT: O 159 MET cc_start: 0.5642 (mmt) cc_final: 0.5000 (mmp) REVERT: P 159 MET cc_start: 0.4903 (mmt) cc_final: 0.4684 (mmm) REVERT: Q 147 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6379 (tm) REVERT: T 129 GLN cc_start: 0.5664 (mm-40) cc_final: 0.4997 (mm110) REVERT: V 129 GLN cc_start: 0.6458 (mm-40) cc_final: 0.5916 (mp10) outliers start: 88 outliers final: 21 residues processed: 463 average time/residue: 0.3069 time to fit residues: 197.1169 Evaluate side-chains 254 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 0.0470 chunk 80 optimal weight: 0.0020 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.0040 chunk 115 optimal weight: 2.9990 chunk 179 optimal weight: 0.0370 overall best weight: 0.0976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 156 HIS A 222 GLN B 156 HIS B 222 GLN C 156 HIS C 209 ASN C 222 GLN D 156 HIS D 222 GLN E 156 HIS E 222 GLN F 156 HIS F 222 GLN G 156 HIS G 222 GLN H 222 GLN I 222 GLN J 222 GLN K 222 GLN M 222 GLN N 222 GLN O 222 GLN P 156 HIS P 222 GLN Q 156 HIS Q 222 GLN R 156 HIS R 222 GLN S 156 HIS S 222 GLN T 156 HIS T 222 GLN V 156 HIS V 222 GLN W 156 HIS W 222 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5094 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14762 Z= 0.166 Angle : 0.617 10.113 20152 Z= 0.282 Chirality : 0.041 0.134 2530 Planarity : 0.005 0.047 2640 Dihedral : 6.129 56.781 2156 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.76 % Allowed : 13.26 % Favored : 79.99 % 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: 0.98 (0.21), residues: 1958 helix: 2.40 (0.19), residues: 770 sheet: -0.21 (0.28), residues: 440 loop : -0.66 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 156 PHE 0.019 0.001 PHE V 126 TYR 0.005 0.001 TYR B 132 ARG 0.015 0.001 ARG N 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 290 time to evaluate : 1.828 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: C 212 LEU cc_start: 0.5414 (OUTLIER) cc_final: 0.5139 (tp) REVERT: C 220 LEU cc_start: 0.7237 (mt) cc_final: 0.5540 (tt) REVERT: D 220 LEU cc_start: 0.7242 (mt) cc_final: 0.5129 (tt) REVERT: E 180 LEU cc_start: 0.3001 (tp) cc_final: 0.2781 (mp) REVERT: F 220 LEU cc_start: 0.7448 (mt) cc_final: 0.5287 (tt) REVERT: J 177 THR cc_start: 0.7037 (p) cc_final: 0.6662 (p) REVERT: K 142 ARG cc_start: 0.8180 (mmp80) cc_final: 0.6867 (ttp80) REVERT: K 159 MET cc_start: 0.6375 (mmt) cc_final: 0.5536 (mmp) REVERT: M 159 MET cc_start: 0.6434 (mmt) cc_final: 0.5708 (mmm) REVERT: N 142 ARG cc_start: 0.7686 (tpp-160) cc_final: 0.7458 (tpp-160) REVERT: N 150 VAL cc_start: 0.5556 (OUTLIER) cc_final: 0.5265 (m) REVERT: N 159 MET cc_start: 0.6610 (mmt) cc_final: 0.5834 (mmm) REVERT: O 159 MET cc_start: 0.6226 (mmt) cc_final: 0.5802 (mmm) REVERT: O 180 LEU cc_start: 0.5095 (tp) cc_final: 0.4742 (mp) REVERT: P 159 MET cc_start: 0.5391 (mmt) cc_final: 0.5012 (mmm) REVERT: P 180 LEU cc_start: 0.4875 (tp) cc_final: 0.4555 (mp) REVERT: R 147 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6925 (tm) REVERT: V 147 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7223 (tm) outliers start: 107 outliers final: 50 residues processed: 359 average time/residue: 0.2808 time to fit residues: 144.9938 Evaluate side-chains 293 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 239 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 194 optimal weight: 0.0070 chunk 160 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS E 209 ASN F 209 ASN G 209 ASN H 156 HIS H 209 ASN I 156 HIS I 209 ASN J 156 HIS J 209 ASN K 125 GLN K 156 HIS K 209 ASN L 156 HIS L 209 ASN M 156 HIS M 209 ASN N 156 HIS N 196 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14762 Z= 0.223 Angle : 0.665 10.499 20152 Z= 0.312 Chirality : 0.042 0.282 2530 Planarity : 0.005 0.040 2640 Dihedral : 5.935 52.197 2138 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 7.51 % Allowed : 14.33 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1958 helix: 2.27 (0.19), residues: 748 sheet: -0.47 (0.27), residues: 440 loop : -0.75 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS Q 196 PHE 0.009 0.001 PHE T 126 TYR 0.013 0.001 TYR A 132 ARG 0.009 0.001 ARG L 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 253 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: A 142 ARG cc_start: 0.7470 (tpp-160) cc_final: 0.7255 (mmp80) REVERT: A 147 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7357 (tm) REVERT: B 160 PRO cc_start: 0.6390 (Cg_endo) cc_final: 0.5793 (Cg_exo) REVERT: C 147 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7111 (tt) REVERT: F 209 ASN cc_start: 0.6322 (OUTLIER) cc_final: 0.5657 (t0) REVERT: H 209 ASN cc_start: 0.5795 (OUTLIER) cc_final: 0.5135 (t0) REVERT: I 140 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6649 (tt) REVERT: K 142 ARG cc_start: 0.8260 (mmp80) cc_final: 0.6890 (ttp80) REVERT: K 209 ASN cc_start: 0.5465 (OUTLIER) cc_final: 0.4716 (t0) REVERT: M 159 MET cc_start: 0.6793 (mmt) cc_final: 0.5914 (mmm) REVERT: N 159 MET cc_start: 0.7000 (mmt) cc_final: 0.5904 (mmp) REVERT: O 159 MET cc_start: 0.6946 (mmt) cc_final: 0.5953 (mmp) REVERT: O 180 LEU cc_start: 0.5182 (tp) cc_final: 0.4623 (mp) REVERT: P 129 GLN cc_start: 0.6431 (tm-30) cc_final: 0.6213 (tm-30) REVERT: P 142 ARG cc_start: 0.7658 (tpp-160) cc_final: 0.7351 (tpp80) REVERT: P 159 MET cc_start: 0.6292 (mmt) cc_final: 0.5644 (mmm) REVERT: P 180 LEU cc_start: 0.5230 (tp) cc_final: 0.5009 (mp) REVERT: Q 147 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7590 (tm) REVERT: Q 180 LEU cc_start: 0.5709 (tp) cc_final: 0.5093 (mp) REVERT: R 159 MET cc_start: 0.6817 (mmm) cc_final: 0.6600 (mmm) REVERT: R 181 GLU cc_start: 0.5408 (tp30) cc_final: 0.4802 (mt-10) REVERT: S 147 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7360 (tm) REVERT: S 154 ARG cc_start: 0.5891 (mpp-170) cc_final: 0.5076 (mpp-170) REVERT: S 159 MET cc_start: 0.6930 (mmm) cc_final: 0.6488 (mmp) REVERT: S 181 GLU cc_start: 0.4996 (tp30) cc_final: 0.4565 (mt-10) REVERT: T 147 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7374 (tm) REVERT: V 128 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6081 (tm-30) REVERT: V 147 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7143 (tm) outliers start: 119 outliers final: 68 residues processed: 335 average time/residue: 0.2747 time to fit residues: 134.9045 Evaluate side-chains 308 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 229 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 209 ASN Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 128 GLU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 93 optimal weight: 0.0070 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN I 209 ASN J 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14762 Z= 0.185 Angle : 0.615 11.483 20152 Z= 0.281 Chirality : 0.041 0.239 2530 Planarity : 0.004 0.034 2640 Dihedral : 5.564 52.506 2134 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.76 % Allowed : 16.41 % Favored : 76.83 % 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: 0.90 (0.21), residues: 1958 helix: 2.35 (0.19), residues: 748 sheet: -0.18 (0.27), residues: 440 loop : -0.66 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS R 196 PHE 0.005 0.001 PHE T 126 TYR 0.010 0.001 TYR B 132 ARG 0.008 0.000 ARG L 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 239 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7486 (tpp-160) cc_final: 0.7150 (mmt-90) REVERT: A 147 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7345 (tm) REVERT: A 209 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.4792 (t0) REVERT: B 160 PRO cc_start: 0.6806 (Cg_endo) cc_final: 0.6306 (Cg_exo) REVERT: B 209 ASN cc_start: 0.5932 (OUTLIER) cc_final: 0.4833 (t0) REVERT: C 147 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7036 (tt) REVERT: C 209 ASN cc_start: 0.6208 (OUTLIER) cc_final: 0.5014 (t0) REVERT: C 212 LEU cc_start: 0.5409 (OUTLIER) cc_final: 0.5184 (tp) REVERT: E 209 ASN cc_start: 0.5859 (OUTLIER) cc_final: 0.4828 (t0) REVERT: F 209 ASN cc_start: 0.6090 (OUTLIER) cc_final: 0.5232 (t0) REVERT: H 209 ASN cc_start: 0.6061 (OUTLIER) cc_final: 0.5126 (t0) REVERT: I 209 ASN cc_start: 0.6001 (OUTLIER) cc_final: 0.5225 (t0) REVERT: J 140 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7013 (mm) REVERT: J 209 ASN cc_start: 0.5429 (OUTLIER) cc_final: 0.4465 (t0) REVERT: K 142 ARG cc_start: 0.8207 (mmp80) cc_final: 0.6847 (ttp80) REVERT: K 159 MET cc_start: 0.7066 (mmt) cc_final: 0.5958 (mmp) REVERT: K 209 ASN cc_start: 0.5281 (OUTLIER) cc_final: 0.4143 (t0) REVERT: K 222 GLN cc_start: 0.7878 (mp-120) cc_final: 0.7640 (mp10) REVERT: M 159 MET cc_start: 0.6929 (mmt) cc_final: 0.6028 (mmm) REVERT: N 159 MET cc_start: 0.7142 (mmt) cc_final: 0.5985 (mmp) REVERT: N 181 GLU cc_start: 0.4194 (mt-10) cc_final: 0.3925 (mt-10) REVERT: O 159 MET cc_start: 0.6955 (mmt) cc_final: 0.5909 (mmp) REVERT: O 180 LEU cc_start: 0.5398 (tp) cc_final: 0.4727 (mp) REVERT: O 181 GLU cc_start: 0.3816 (mt-10) cc_final: 0.3607 (mt-10) REVERT: P 129 GLN cc_start: 0.6542 (tm-30) cc_final: 0.6322 (tm-30) REVERT: P 142 ARG cc_start: 0.7557 (tpp-160) cc_final: 0.7258 (tpp80) REVERT: P 159 MET cc_start: 0.6941 (mmt) cc_final: 0.6012 (mmm) REVERT: Q 180 LEU cc_start: 0.5901 (tp) cc_final: 0.5194 (mp) REVERT: R 159 MET cc_start: 0.7387 (mmm) cc_final: 0.7128 (mmm) REVERT: R 181 GLU cc_start: 0.5312 (tp30) cc_final: 0.4704 (mt-10) REVERT: S 159 MET cc_start: 0.6937 (mmm) cc_final: 0.6571 (mmp) REVERT: S 181 GLU cc_start: 0.5384 (tp30) cc_final: 0.5106 (mt-10) REVERT: V 147 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7204 (tm) outliers start: 107 outliers final: 71 residues processed: 307 average time/residue: 0.2452 time to fit residues: 112.5171 Evaluate side-chains 309 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 224 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 209 ASN Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 125 GLN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 chunk 132 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 0.0670 chunk 171 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 125 GLN J 222 GLN K 125 GLN O 209 ASN P 209 ASN S 209 ASN T 209 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5517 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14762 Z= 0.168 Angle : 0.618 11.312 20152 Z= 0.278 Chirality : 0.041 0.231 2530 Planarity : 0.004 0.035 2640 Dihedral : 5.360 53.700 2132 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 6.76 % Allowed : 17.55 % Favored : 75.69 % 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: 1.16 (0.21), residues: 1958 helix: 2.43 (0.19), residues: 748 sheet: 0.19 (0.28), residues: 440 loop : -0.53 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 218 PHE 0.004 0.001 PHE K 126 TYR 0.008 0.001 TYR B 132 ARG 0.007 0.000 ARG N 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 245 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7656 (tpp-160) cc_final: 0.7393 (mmt-90) REVERT: A 147 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7255 (tm) REVERT: A 209 ASN cc_start: 0.6271 (OUTLIER) cc_final: 0.4801 (t0) REVERT: C 147 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7191 (tt) REVERT: D 159 MET cc_start: 0.7615 (tpp) cc_final: 0.6877 (mmm) REVERT: E 209 ASN cc_start: 0.6576 (m-40) cc_final: 0.5871 (t0) REVERT: F 209 ASN cc_start: 0.6353 (m-40) cc_final: 0.5590 (t0) REVERT: H 140 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6330 (tt) REVERT: I 209 ASN cc_start: 0.5564 (OUTLIER) cc_final: 0.4650 (t0) REVERT: J 140 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6926 (mm) REVERT: K 142 ARG cc_start: 0.8205 (mmp80) cc_final: 0.6874 (ttp80) REVERT: K 159 MET cc_start: 0.7161 (mmt) cc_final: 0.6129 (mmp) REVERT: M 159 MET cc_start: 0.7000 (mmt) cc_final: 0.6071 (mmm) REVERT: N 159 MET cc_start: 0.7259 (mmt) cc_final: 0.6343 (mmm) REVERT: O 159 MET cc_start: 0.7074 (mmt) cc_final: 0.6334 (mmm) REVERT: O 180 LEU cc_start: 0.5302 (tp) cc_final: 0.4717 (mp) REVERT: P 159 MET cc_start: 0.6988 (mmt) cc_final: 0.6244 (mmm) REVERT: P 209 ASN cc_start: 0.6418 (OUTLIER) cc_final: 0.5807 (t0) REVERT: R 159 MET cc_start: 0.7397 (mmm) cc_final: 0.7148 (mmm) REVERT: R 181 GLU cc_start: 0.5389 (tp30) cc_final: 0.4840 (mt-10) REVERT: S 159 MET cc_start: 0.7045 (mmm) cc_final: 0.6741 (mmp) REVERT: S 181 GLU cc_start: 0.5405 (tp30) cc_final: 0.4890 (mt-10) REVERT: W 209 ASN cc_start: 0.6222 (OUTLIER) cc_final: 0.5345 (t0) outliers start: 107 outliers final: 75 residues processed: 311 average time/residue: 0.2329 time to fit residues: 109.7960 Evaluate side-chains 308 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 225 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 125 GLN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 112 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN F 209 ASN J 209 ASN K 125 GLN K 209 ASN K 222 GLN L 222 GLN P 209 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5572 moved from start: 0.6460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14762 Z= 0.186 Angle : 0.645 11.421 20152 Z= 0.289 Chirality : 0.042 0.216 2530 Planarity : 0.004 0.045 2640 Dihedral : 5.241 55.014 2128 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 7.26 % Allowed : 17.80 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.21), residues: 1958 helix: 2.38 (0.19), residues: 748 sheet: 0.45 (0.28), residues: 440 loop : -0.58 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS R 196 PHE 0.004 0.001 PHE Q 126 TYR 0.009 0.001 TYR B 132 ARG 0.007 0.000 ARG N 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 228 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7397 (tm) REVERT: A 209 ASN cc_start: 0.6328 (OUTLIER) cc_final: 0.4826 (t0) REVERT: B 209 ASN cc_start: 0.6068 (OUTLIER) cc_final: 0.5489 (t0) REVERT: D 159 MET cc_start: 0.7612 (tpp) cc_final: 0.7400 (mmm) REVERT: D 209 ASN cc_start: 0.6127 (OUTLIER) cc_final: 0.5077 (t0) REVERT: F 209 ASN cc_start: 0.6081 (m110) cc_final: 0.5171 (t0) REVERT: G 213 VAL cc_start: 0.5992 (p) cc_final: 0.5769 (t) REVERT: H 140 LEU cc_start: 0.6653 (OUTLIER) cc_final: 0.6336 (tt) REVERT: I 140 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6649 (tt) REVERT: J 154 ARG cc_start: 0.6100 (mtm-85) cc_final: 0.5740 (mtm-85) REVERT: J 209 ASN cc_start: 0.6086 (OUTLIER) cc_final: 0.5565 (t0) REVERT: K 140 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7097 (mm) REVERT: K 142 ARG cc_start: 0.8125 (mmp80) cc_final: 0.7105 (ttp80) REVERT: K 159 MET cc_start: 0.7107 (mmt) cc_final: 0.6126 (mmp) REVERT: M 159 MET cc_start: 0.7096 (mmt) cc_final: 0.6161 (mmm) REVERT: N 159 MET cc_start: 0.7380 (mmt) cc_final: 0.6444 (mmm) REVERT: O 159 MET cc_start: 0.7269 (mmt) cc_final: 0.6572 (mmm) REVERT: O 180 LEU cc_start: 0.5126 (tp) cc_final: 0.4571 (mp) REVERT: O 181 GLU cc_start: 0.4210 (mt-10) cc_final: 0.3958 (mt-10) REVERT: P 159 MET cc_start: 0.7124 (mmt) cc_final: 0.6338 (mmm) REVERT: P 209 ASN cc_start: 0.6478 (OUTLIER) cc_final: 0.5775 (t0) REVERT: R 159 MET cc_start: 0.7542 (mmm) cc_final: 0.7213 (mmm) REVERT: R 181 GLU cc_start: 0.5465 (tp30) cc_final: 0.5031 (mt-10) REVERT: R 209 ASN cc_start: 0.6223 (OUTLIER) cc_final: 0.5591 (m-40) REVERT: S 181 GLU cc_start: 0.5601 (tp30) cc_final: 0.5252 (mt-10) REVERT: W 159 MET cc_start: 0.7435 (tpp) cc_final: 0.6836 (mmm) REVERT: W 209 ASN cc_start: 0.6249 (OUTLIER) cc_final: 0.5876 (t0) outliers start: 115 outliers final: 77 residues processed: 310 average time/residue: 0.2326 time to fit residues: 109.9241 Evaluate side-chains 304 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 216 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 139 optimal weight: 0.0980 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 106 optimal weight: 0.0030 chunk 190 optimal weight: 0.8980 chunk 119 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN J 125 GLN J 209 ASN K 125 GLN L 222 GLN P 209 ASN V 209 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 moved from start: 0.6682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14762 Z= 0.156 Angle : 0.640 11.890 20152 Z= 0.279 Chirality : 0.041 0.203 2530 Planarity : 0.004 0.028 2640 Dihedral : 5.117 56.487 2128 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.50 % Allowed : 19.32 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.22), residues: 1958 helix: 2.52 (0.19), residues: 748 sheet: 0.81 (0.29), residues: 440 loop : -0.46 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 196 PHE 0.006 0.001 PHE K 126 TYR 0.010 0.001 TYR V 132 ARG 0.007 0.000 ARG N 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 230 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6261 (OUTLIER) cc_final: 0.4853 (t0) REVERT: D 147 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6499 (tt) REVERT: D 209 ASN cc_start: 0.6000 (OUTLIER) cc_final: 0.4797 (t0) REVERT: F 209 ASN cc_start: 0.6013 (m110) cc_final: 0.5150 (t0) REVERT: G 154 ARG cc_start: 0.6512 (mtm-85) cc_final: 0.6043 (mpp-170) REVERT: H 140 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6300 (tt) REVERT: I 140 LEU cc_start: 0.7000 (OUTLIER) cc_final: 0.6744 (tt) REVERT: J 154 ARG cc_start: 0.6124 (mtm-85) cc_final: 0.5788 (mtm-85) REVERT: J 209 ASN cc_start: 0.5438 (OUTLIER) cc_final: 0.4785 (t0) REVERT: K 126 PHE cc_start: 0.5046 (t80) cc_final: 0.4787 (t80) REVERT: K 140 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7205 (mm) REVERT: K 142 ARG cc_start: 0.8103 (mmp80) cc_final: 0.7099 (ttp80) REVERT: K 159 MET cc_start: 0.7105 (mmt) cc_final: 0.6119 (mmp) REVERT: M 159 MET cc_start: 0.7091 (mmt) cc_final: 0.6168 (mmm) REVERT: N 159 MET cc_start: 0.7448 (mmt) cc_final: 0.6570 (mmm) REVERT: O 159 MET cc_start: 0.7252 (mmt) cc_final: 0.6209 (mmp) REVERT: O 180 LEU cc_start: 0.5068 (tp) cc_final: 0.4575 (mp) REVERT: P 159 MET cc_start: 0.7111 (mmt) cc_final: 0.6336 (mmm) REVERT: P 209 ASN cc_start: 0.6544 (OUTLIER) cc_final: 0.6161 (t0) REVERT: Q 129 GLN cc_start: 0.6623 (tp-100) cc_final: 0.5644 (mm110) REVERT: R 159 MET cc_start: 0.7670 (mmm) cc_final: 0.7444 (mmm) REVERT: R 181 GLU cc_start: 0.5359 (tp30) cc_final: 0.5043 (mt-10) REVERT: R 209 ASN cc_start: 0.6186 (OUTLIER) cc_final: 0.5552 (m-40) REVERT: S 159 MET cc_start: 0.6519 (mmp) cc_final: 0.6203 (mmm) REVERT: S 181 GLU cc_start: 0.5447 (tp30) cc_final: 0.5146 (mt-10) REVERT: W 159 MET cc_start: 0.7455 (tpp) cc_final: 0.6925 (mmm) REVERT: W 209 ASN cc_start: 0.6456 (OUTLIER) cc_final: 0.6255 (t0) outliers start: 103 outliers final: 78 residues processed: 308 average time/residue: 0.2446 time to fit residues: 112.8839 Evaluate side-chains 306 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 218 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 125 GLN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 121 optimal weight: 0.0980 chunk 130 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 0.0060 chunk 150 optimal weight: 1.9990 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 209 ASN K 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14762 Z= 0.151 Angle : 0.641 11.960 20152 Z= 0.278 Chirality : 0.041 0.216 2530 Planarity : 0.004 0.031 2640 Dihedral : 5.025 57.763 2128 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 6.25 % Allowed : 19.70 % Favored : 74.05 % 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: 1.65 (0.22), residues: 1958 helix: 2.58 (0.19), residues: 748 sheet: 1.05 (0.30), residues: 440 loop : -0.39 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 196 PHE 0.003 0.000 PHE M 126 TYR 0.008 0.001 TYR V 132 ARG 0.009 0.000 ARG M 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 229 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6241 (OUTLIER) cc_final: 0.4819 (t0) REVERT: B 209 ASN cc_start: 0.5722 (OUTLIER) cc_final: 0.5305 (t0) REVERT: E 159 MET cc_start: 0.7658 (mmm) cc_final: 0.7087 (mmm) REVERT: F 209 ASN cc_start: 0.6014 (m110) cc_final: 0.5141 (t0) REVERT: H 140 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6281 (tt) REVERT: J 154 ARG cc_start: 0.6027 (mtm-85) cc_final: 0.5675 (mtm-85) REVERT: J 209 ASN cc_start: 0.5608 (OUTLIER) cc_final: 0.4992 (t0) REVERT: K 140 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7062 (mm) REVERT: K 142 ARG cc_start: 0.8090 (mmp80) cc_final: 0.7098 (ttp80) REVERT: K 159 MET cc_start: 0.7097 (mmt) cc_final: 0.6138 (mmp) REVERT: L 140 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6841 (mm) REVERT: M 159 MET cc_start: 0.7109 (mmt) cc_final: 0.6189 (mmm) REVERT: N 159 MET cc_start: 0.7449 (mmt) cc_final: 0.6573 (mmm) REVERT: O 159 MET cc_start: 0.7255 (mmt) cc_final: 0.6218 (mmp) REVERT: O 180 LEU cc_start: 0.4914 (tp) cc_final: 0.4402 (mp) REVERT: P 159 MET cc_start: 0.7216 (mmt) cc_final: 0.6398 (mmm) REVERT: R 159 MET cc_start: 0.7666 (mmm) cc_final: 0.7439 (mmm) REVERT: R 181 GLU cc_start: 0.5325 (tp30) cc_final: 0.5040 (mt-10) REVERT: S 159 MET cc_start: 0.6403 (mmp) cc_final: 0.5989 (mmm) REVERT: S 181 GLU cc_start: 0.5586 (tp30) cc_final: 0.5217 (mt-10) REVERT: W 159 MET cc_start: 0.7474 (tpp) cc_final: 0.6964 (mmm) outliers start: 99 outliers final: 77 residues processed: 301 average time/residue: 0.2587 time to fit residues: 116.4818 Evaluate side-chains 307 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 224 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 125 GLN Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.0570 chunk 166 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 160 optimal weight: 0.4980 chunk 168 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN E 209 ASN K 125 GLN P 209 ASN R 209 ASN T 196 HIS W 156 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5613 moved from start: 0.7218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14762 Z= 0.186 Angle : 0.697 11.858 20152 Z= 0.305 Chirality : 0.042 0.275 2530 Planarity : 0.004 0.081 2640 Dihedral : 5.006 59.173 2124 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.12 % Allowed : 20.20 % Favored : 73.67 % 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: 1.36 (0.22), residues: 1958 helix: 2.33 (0.19), residues: 748 sheet: 0.95 (0.29), residues: 440 loop : -0.58 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS W 156 PHE 0.005 0.001 PHE M 126 TYR 0.008 0.001 TYR A 132 ARG 0.009 0.000 ARG N 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 226 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6463 (OUTLIER) cc_final: 0.4918 (t0) REVERT: B 209 ASN cc_start: 0.5878 (OUTLIER) cc_final: 0.5335 (t0) REVERT: D 209 ASN cc_start: 0.6160 (OUTLIER) cc_final: 0.5331 (t0) REVERT: E 159 MET cc_start: 0.7726 (mmm) cc_final: 0.7188 (mmm) REVERT: F 209 ASN cc_start: 0.5819 (m110) cc_final: 0.4949 (t0) REVERT: H 140 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5993 (tt) REVERT: I 154 ARG cc_start: 0.6517 (mtm-85) cc_final: 0.6175 (mpp-170) REVERT: J 209 ASN cc_start: 0.6886 (OUTLIER) cc_final: 0.5968 (t0) REVERT: K 142 ARG cc_start: 0.8100 (mmp80) cc_final: 0.7113 (ttp80) REVERT: K 159 MET cc_start: 0.7044 (mmt) cc_final: 0.6128 (mmp) REVERT: M 131 ASN cc_start: 0.6916 (t0) cc_final: 0.6656 (m-40) REVERT: M 159 MET cc_start: 0.7163 (mmt) cc_final: 0.6274 (mmm) REVERT: N 159 MET cc_start: 0.7534 (mmt) cc_final: 0.6645 (mmm) REVERT: O 159 MET cc_start: 0.7262 (mmt) cc_final: 0.6597 (mmm) REVERT: O 180 LEU cc_start: 0.4640 (tp) cc_final: 0.4127 (mp) REVERT: P 159 MET cc_start: 0.7281 (mmt) cc_final: 0.6433 (mmm) REVERT: Q 129 GLN cc_start: 0.6601 (tp-100) cc_final: 0.5665 (mm110) REVERT: R 159 MET cc_start: 0.7653 (mmm) cc_final: 0.7397 (mmm) REVERT: S 181 GLU cc_start: 0.5667 (tp30) cc_final: 0.5350 (mt-10) REVERT: W 159 MET cc_start: 0.7636 (tpp) cc_final: 0.7426 (mmm) outliers start: 97 outliers final: 80 residues processed: 300 average time/residue: 0.2537 time to fit residues: 115.9166 Evaluate side-chains 299 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 214 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 89 optimal weight: 0.0370 chunk 130 optimal weight: 0.0470 chunk 197 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 16 optimal weight: 0.1980 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 124 optimal weight: 0.0980 overall best weight: 0.1956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 125 GLN T 196 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 0.7317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14762 Z= 0.154 Angle : 0.686 12.776 20152 Z= 0.295 Chirality : 0.042 0.269 2530 Planarity : 0.004 0.038 2640 Dihedral : 4.809 59.383 2124 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.80 % Allowed : 21.72 % Favored : 73.48 % 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: 1.74 (0.22), residues: 1958 helix: 2.50 (0.19), residues: 748 sheet: 1.27 (0.29), residues: 440 loop : -0.27 (0.28), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 196 PHE 0.002 0.000 PHE S 126 TYR 0.016 0.001 TYR S 132 ARG 0.009 0.000 ARG N 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 229 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6383 (OUTLIER) cc_final: 0.4940 (t0) REVERT: B 209 ASN cc_start: 0.5785 (OUTLIER) cc_final: 0.5381 (t0) REVERT: D 209 ASN cc_start: 0.5779 (OUTLIER) cc_final: 0.5212 (t0) REVERT: E 159 MET cc_start: 0.7830 (mmm) cc_final: 0.7239 (mmm) REVERT: F 209 ASN cc_start: 0.5810 (m110) cc_final: 0.5074 (t0) REVERT: H 140 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5954 (tt) REVERT: K 142 ARG cc_start: 0.8199 (mmp80) cc_final: 0.7134 (ttp80) REVERT: K 159 MET cc_start: 0.6998 (mmt) cc_final: 0.6134 (mmp) REVERT: L 140 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6900 (mm) REVERT: M 131 ASN cc_start: 0.6895 (t0) cc_final: 0.6638 (m-40) REVERT: M 159 MET cc_start: 0.7114 (mmt) cc_final: 0.6249 (mmm) REVERT: N 159 MET cc_start: 0.7481 (mmt) cc_final: 0.6586 (mmm) REVERT: O 159 MET cc_start: 0.7248 (mmt) cc_final: 0.6238 (mmp) REVERT: O 180 LEU cc_start: 0.4609 (tp) cc_final: 0.4095 (mp) REVERT: P 159 MET cc_start: 0.7234 (mmt) cc_final: 0.6407 (mmm) REVERT: Q 129 GLN cc_start: 0.6590 (tp-100) cc_final: 0.5618 (mm110) REVERT: S 181 GLU cc_start: 0.5703 (tp30) cc_final: 0.5372 (mt-10) REVERT: W 159 MET cc_start: 0.7643 (tpp) cc_final: 0.7288 (mmm) outliers start: 76 outliers final: 67 residues processed: 286 average time/residue: 0.2410 time to fit residues: 105.0549 Evaluate side-chains 293 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 221 THR Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 144 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.0030 chunk 157 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5714 r_free = 0.5714 target = 0.307748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5664 r_free = 0.5664 target = 0.297206 restraints weight = 18327.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5681 r_free = 0.5681 target = 0.299362 restraints weight = 12952.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5694 r_free = 0.5694 target = 0.300922 restraints weight = 9683.079| |-----------------------------------------------------------------------------| r_work (final): 0.5682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.7377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14762 Z= 0.195 Angle : 0.696 12.227 20152 Z= 0.305 Chirality : 0.042 0.260 2530 Planarity : 0.004 0.084 2640 Dihedral : 4.856 59.301 2124 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.49 % Allowed : 21.15 % 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: 1.67 (0.22), residues: 1958 helix: 2.41 (0.19), residues: 748 sheet: 1.25 (0.29), residues: 440 loop : -0.29 (0.28), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 196 PHE 0.004 0.001 PHE M 126 TYR 0.017 0.001 TYR S 132 ARG 0.010 0.001 ARG S 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3295.33 seconds wall clock time: 61 minutes 11.81 seconds (3671.81 seconds total)