Starting phenix.real_space_refine on Thu Feb 15 00:58:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3n_4405/02_2024/6i3n_4405.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3n_4405/02_2024/6i3n_4405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3n_4405/02_2024/6i3n_4405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3n_4405/02_2024/6i3n_4405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3n_4405/02_2024/6i3n_4405.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i3n_4405/02_2024/6i3n_4405.pdb" } resolution = 3.1 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= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 6721 2.51 5 N 1898 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M ARG 28": "NH1" <-> "NH2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "J ARG 28": "NH1" <-> "NH2" Residue "K ARG 28": "NH1" <-> "NH2" Residue "H ARG 28": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "G ARG 28": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10660 Number of models: 1 Model: "" Number of chains: 13 Chain: "M" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 820 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.76, per 1000 atoms: 0.54 Number of scatterers: 10660 At special positions: 0 Unit cell: (83.74, 83.74, 126.14, 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 39 16.00 O 2002 8.00 N 1898 7.00 C 6721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'M' and resid 21 through 25 Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.510A pdb=" N SER M 34 " --> pdb=" O ARG M 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU M 50 " --> pdb=" O ASP M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 65 Processing helix chain 'M' and resid 69 through 78 Processing helix chain 'M' and resid 85 through 96 Processing helix chain 'M' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU M 103 " --> pdb=" O ASP M 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE M 109 " --> pdb=" O LEU M 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU M 110 " --> pdb=" O GLY M 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 25 Processing helix chain 'I' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER I 34 " --> pdb=" O ARG I 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE I 36 " --> pdb=" O ARG I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 54 removed outlier: 3.532A pdb=" N LEU I 50 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 65 Processing helix chain 'I' and resid 69 through 78 Processing helix chain 'I' and resid 85 through 96 Processing helix chain 'I' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU I 104 " --> pdb=" O ASP I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU I 110 " --> pdb=" O GLY I 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 25 Processing helix chain 'J' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER J 34 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU J 50 " --> pdb=" O ASP J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 65 Processing helix chain 'J' and resid 69 through 78 Processing helix chain 'J' and resid 85 through 96 Processing helix chain 'J' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU J 103 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU J 104 " --> pdb=" O ASP J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE J 109 " --> pdb=" O LEU J 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU J 110 " --> pdb=" O GLY J 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 25 Processing helix chain 'K' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER K 34 " --> pdb=" O ARG K 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE K 36 " --> pdb=" O ARG K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU K 50 " --> pdb=" O ASP K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 65 Processing helix chain 'K' and resid 69 through 78 Processing helix chain 'K' and resid 85 through 96 Processing helix chain 'K' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU K 103 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU K 104 " --> pdb=" O ASP K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE K 109 " --> pdb=" O LEU K 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU K 110 " --> pdb=" O GLY K 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 25 Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER H 34 " --> pdb=" O ARG H 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU H 50 " --> pdb=" O ASP H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 65 Processing helix chain 'H' and resid 69 through 78 Processing helix chain 'H' and resid 85 through 96 Processing helix chain 'H' and resid 99 through 105 removed outlier: 3.659A pdb=" N LEU H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 26 through 38 removed outlier: 3.510A pdb=" N SER L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE L 36 " --> pdb=" O ARG L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 54 removed outlier: 3.532A pdb=" N LEU L 50 " --> pdb=" O ASP L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 65 Processing helix chain 'L' and resid 69 through 78 Processing helix chain 'L' and resid 85 through 96 Processing helix chain 'L' and resid 99 through 105 removed outlier: 3.659A pdb=" N LEU L 103 " --> pdb=" O ASP L 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU L 104 " --> pdb=" O ASP L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE L 109 " --> pdb=" O LEU L 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU L 110 " --> pdb=" O GLY L 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 69 through 78 Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 99 through 105 removed outlier: 3.657A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE B 109 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 25 Processing helix chain 'F' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER F 34 " --> pdb=" O ARG F 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE F 36 " --> pdb=" O ARG F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'F' and resid 69 through 78 Processing helix chain 'F' and resid 85 through 96 Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.657A pdb=" N LEU F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 110 " --> pdb=" O GLY F 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 36 " --> pdb=" O ARG C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU C 50 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 69 through 78 Processing helix chain 'C' and resid 85 through 96 Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.657A pdb=" N LEU C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU C 104 " --> pdb=" O ASP C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 25 Processing helix chain 'D' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER D 34 " --> pdb=" O ARG D 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 36 " --> pdb=" O ARG D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 65 Processing helix chain 'D' and resid 69 through 78 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.510A pdb=" N SER A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 121 removed outlier: 3.632A pdb=" N ILE A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 25 Processing helix chain 'E' and resid 26 through 38 removed outlier: 3.510A pdb=" N SER E 34 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE E 36 " --> pdb=" O ARG E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'E' and resid 69 through 78 Processing helix chain 'E' and resid 85 through 96 Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU E 104 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 110 " --> pdb=" O GLY E 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.511A pdb=" N SER G 34 " --> pdb=" O ARG G 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 54 removed outlier: 3.531A pdb=" N LEU G 50 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'G' and resid 69 through 78 Processing helix chain 'G' and resid 85 through 96 Processing helix chain 'G' and resid 99 through 105 removed outlier: 3.658A pdb=" N LEU G 103 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 121 removed outlier: 3.633A pdb=" N ILE G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU G 110 " --> pdb=" O GLY G 106 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1638 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: 2.67 Time building geometry restraints manager: 4.40 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: 3653 1.34 - 1.46: 1579 1.46 - 1.57: 5506 1.57 - 1.69: 0 1.69 - 1.80: 65 Bond restraints: 10803 Sorted by residual: bond pdb=" SD MET J 54 " pdb=" CE MET J 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.10e+00 bond pdb=" SD MET A 54 " pdb=" CE MET A 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" SD MET I 54 " pdb=" CE MET I 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.07e+00 bond pdb=" SD MET H 54 " pdb=" CE MET H 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.06e+00 bond pdb=" SD MET E 54 " pdb=" CE MET E 54 " ideal model delta sigma weight residual 1.791 1.755 0.036 2.50e-02 1.60e+03 2.06e+00 ... (remaining 10798 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.58: 286 106.58 - 113.44: 5875 113.44 - 120.30: 4504 120.30 - 127.15: 3843 127.15 - 134.01: 104 Bond angle restraints: 14612 Sorted by residual: angle pdb=" C LEU A 37 " pdb=" N ASN A 38 " pdb=" CA ASN A 38 " ideal model delta sigma weight residual 122.65 117.65 5.00 1.60e+00 3.91e-01 9.75e+00 angle pdb=" C LEU I 37 " pdb=" N ASN I 38 " pdb=" CA ASN I 38 " ideal model delta sigma weight residual 122.65 117.65 5.00 1.60e+00 3.91e-01 9.75e+00 angle pdb=" C LEU J 37 " pdb=" N ASN J 38 " pdb=" CA ASN J 38 " ideal model delta sigma weight residual 122.65 117.66 4.99 1.60e+00 3.91e-01 9.74e+00 angle pdb=" C LEU C 37 " pdb=" N ASN C 38 " pdb=" CA ASN C 38 " ideal model delta sigma weight residual 122.65 117.67 4.98 1.60e+00 3.91e-01 9.70e+00 angle pdb=" C LEU B 37 " pdb=" N ASN B 38 " pdb=" CA ASN B 38 " ideal model delta sigma weight residual 122.65 117.68 4.97 1.60e+00 3.91e-01 9.65e+00 ... (remaining 14607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.43: 6215 14.43 - 28.86: 301 28.86 - 43.29: 140 43.29 - 57.72: 0 57.72 - 72.14: 26 Dihedral angle restraints: 6682 sinusoidal: 2808 harmonic: 3874 Sorted by residual: dihedral pdb=" CA PHE E 36 " pdb=" C PHE E 36 " pdb=" N LEU E 37 " pdb=" CA LEU E 37 " ideal model delta harmonic sigma weight residual -180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA PHE L 36 " pdb=" C PHE L 36 " pdb=" N LEU L 37 " pdb=" CA LEU L 37 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PHE H 36 " pdb=" C PHE H 36 " pdb=" N LEU H 37 " pdb=" CA LEU H 37 " ideal model delta harmonic sigma weight residual 180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 6679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 945 0.039 - 0.078: 561 0.078 - 0.118: 138 0.118 - 0.157: 33 0.157 - 0.196: 13 Chirality restraints: 1690 Sorted by residual: chirality pdb=" CA ASN M 38 " pdb=" N ASN M 38 " pdb=" C ASN M 38 " pdb=" CB ASN M 38 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA ASN H 38 " pdb=" N ASN H 38 " pdb=" C ASN H 38 " pdb=" CB ASN H 38 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA ASN F 38 " pdb=" N ASN F 38 " pdb=" C ASN F 38 " pdb=" CB ASN F 38 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.56e-01 ... (remaining 1687 not shown) Planarity restraints: 1898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 81 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO G 82 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 82 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 82 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 81 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO H 82 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 82 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 82 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG M 81 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO M 82 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO M 82 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO M 82 " 0.028 5.00e-02 4.00e+02 ... (remaining 1895 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3976 2.91 - 3.41: 11047 3.41 - 3.90: 16996 3.90 - 4.40: 20180 4.40 - 4.90: 33209 Nonbonded interactions: 85408 Sorted by model distance: nonbonded pdb=" OH TYR B 58 " pdb=" OD1 ASP E 76 " model vdw 2.410 2.440 nonbonded pdb=" OD1 ASP D 76 " pdb=" OH TYR A 58 " model vdw 2.411 2.440 nonbonded pdb=" ND2 ASN K 26 " pdb=" OE2 GLU H 52 " model vdw 2.419 2.520 nonbonded pdb=" OH TYR I 58 " pdb=" OD1 ASP L 76 " model vdw 2.428 2.440 nonbonded pdb=" OD1 ASP K 76 " pdb=" OH TYR H 58 " model vdw 2.432 2.440 ... (remaining 85403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 2.900 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.450 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 10803 Z= 0.459 Angle : 1.055 7.112 14612 Z= 0.577 Chirality : 0.052 0.196 1690 Planarity : 0.006 0.049 1898 Dihedral : 11.331 72.145 4160 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.28 (0.16), residues: 1313 helix: -3.60 (0.10), residues: 1027 sheet: None (None), residues: 0 loop : -1.86 (0.31), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP B 78 PHE 0.010 0.002 PHE H 36 TYR 0.010 0.003 TYR I 116 ARG 0.012 0.002 ARG K 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: I 119 LYS cc_start: 0.7860 (tttt) cc_final: 0.7576 (ttpp) REVERT: J 27 MET cc_start: 0.9075 (mmm) cc_final: 0.8746 (mmt) REVERT: K 27 MET cc_start: 0.9106 (mmm) cc_final: 0.8778 (mmm) REVERT: K 60 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6956 (mm-30) REVERT: H 103 LEU cc_start: 0.8592 (tt) cc_final: 0.8317 (mt) REVERT: L 39 VAL cc_start: 0.9145 (t) cc_final: 0.8942 (p) REVERT: B 27 MET cc_start: 0.8838 (mmm) cc_final: 0.8622 (mmp) REVERT: F 99 ASP cc_start: 0.8211 (m-30) cc_final: 0.7960 (m-30) REVERT: F 119 LYS cc_start: 0.8336 (tttt) cc_final: 0.7952 (ttpp) REVERT: C 27 MET cc_start: 0.8640 (mmm) cc_final: 0.8127 (mmp) REVERT: C 119 LYS cc_start: 0.7846 (tttt) cc_final: 0.7554 (ttpp) REVERT: A 27 MET cc_start: 0.8912 (mmm) cc_final: 0.8645 (mmp) REVERT: A 73 ARG cc_start: 0.8796 (mmp80) cc_final: 0.8401 (mmp-170) REVERT: A 76 ASP cc_start: 0.8210 (m-30) cc_final: 0.7642 (m-30) REVERT: G 53 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6974 (mm-30) REVERT: G 119 LYS cc_start: 0.8197 (tttt) cc_final: 0.7796 (tttm) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.3709 time to fit residues: 192.6866 Evaluate side-chains 328 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 0.0570 chunk 33 optimal weight: 0.0370 chunk 66 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 79 GLN J 42 GLN K 79 GLN B 42 GLN B 63 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10803 Z= 0.132 Angle : 0.530 5.878 14612 Z= 0.272 Chirality : 0.036 0.124 1690 Planarity : 0.004 0.032 1898 Dihedral : 5.072 16.651 1482 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.95 % Allowed : 8.05 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.20), residues: 1313 helix: -1.17 (0.14), residues: 975 sheet: None (None), residues: 0 loop : -1.39 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 78 PHE 0.006 0.001 PHE I 56 TYR 0.006 0.001 TYR F 116 ARG 0.006 0.000 ARG L 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 332 time to evaluate : 1.198 Fit side-chains REVERT: M 94 THR cc_start: 0.9261 (m) cc_final: 0.9056 (m) REVERT: J 27 MET cc_start: 0.8876 (mmm) cc_final: 0.8657 (mmt) REVERT: K 62 ARG cc_start: 0.9231 (mmm160) cc_final: 0.9026 (mmm-85) REVERT: K 67 GLN cc_start: 0.7895 (pt0) cc_final: 0.7615 (pt0) REVERT: H 46 ASP cc_start: 0.8118 (p0) cc_final: 0.7840 (p0) REVERT: H 103 LEU cc_start: 0.8610 (tt) cc_final: 0.8319 (mt) REVERT: L 119 LYS cc_start: 0.7745 (tttt) cc_final: 0.7187 (tttm) REVERT: B 27 MET cc_start: 0.8645 (mmm) cc_final: 0.8338 (mmp) REVERT: B 31 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7273 (ttt-90) REVERT: B 99 ASP cc_start: 0.7751 (m-30) cc_final: 0.7545 (m-30) REVERT: F 38 ASN cc_start: 0.7671 (p0) cc_final: 0.7381 (p0) REVERT: F 60 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6991 (mm-30) REVERT: F 76 ASP cc_start: 0.8201 (m-30) cc_final: 0.7844 (m-30) REVERT: F 99 ASP cc_start: 0.8072 (m-30) cc_final: 0.7842 (m-30) REVERT: F 119 LYS cc_start: 0.8186 (tttt) cc_final: 0.7897 (ttpp) REVERT: C 27 MET cc_start: 0.8347 (mmm) cc_final: 0.7944 (mmp) REVERT: C 62 ARG cc_start: 0.8948 (mmm160) cc_final: 0.8550 (mmm160) REVERT: C 119 LYS cc_start: 0.7884 (tttt) cc_final: 0.7566 (ttpp) REVERT: D 38 ASN cc_start: 0.7751 (p0) cc_final: 0.7458 (p0) REVERT: D 42 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7973 (mm-40) REVERT: D 103 LEU cc_start: 0.8852 (tp) cc_final: 0.8527 (mp) REVERT: A 27 MET cc_start: 0.8624 (mmm) cc_final: 0.8303 (mmp) REVERT: A 76 ASP cc_start: 0.8059 (m-30) cc_final: 0.7772 (m-30) REVERT: E 42 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: G 27 MET cc_start: 0.8606 (mmm) cc_final: 0.8324 (mmt) REVERT: G 38 ASN cc_start: 0.7860 (p0) cc_final: 0.7630 (p0) REVERT: G 53 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6989 (mm-30) REVERT: G 112 ASP cc_start: 0.8431 (m-30) cc_final: 0.8116 (m-30) REVERT: G 119 LYS cc_start: 0.8224 (tttt) cc_final: 0.7766 (tttm) outliers start: 22 outliers final: 11 residues processed: 338 average time/residue: 0.3251 time to fit residues: 142.7538 Evaluate side-chains 323 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 311 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 127 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 79 GLN B 63 GLN B 67 GLN ** F 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10803 Z= 0.248 Angle : 0.572 5.703 14612 Z= 0.290 Chirality : 0.040 0.127 1690 Planarity : 0.004 0.030 1898 Dihedral : 4.923 17.405 1482 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.03 % Allowed : 11.76 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1313 helix: 0.17 (0.16), residues: 975 sheet: None (None), residues: 0 loop : -0.95 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 78 PHE 0.011 0.001 PHE G 36 TYR 0.012 0.002 TYR A 58 ARG 0.004 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 322 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: I 60 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8017 (mt-10) REVERT: J 27 MET cc_start: 0.8911 (mmm) cc_final: 0.8597 (mmt) REVERT: H 103 LEU cc_start: 0.8720 (tt) cc_final: 0.8459 (mt) REVERT: B 42 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6752 (tm-30) REVERT: B 99 ASP cc_start: 0.7581 (m-30) cc_final: 0.7340 (m-30) REVERT: F 76 ASP cc_start: 0.8180 (m-30) cc_final: 0.7962 (m-30) REVERT: F 79 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7447 (tp40) REVERT: F 115 LYS cc_start: 0.8266 (mttt) cc_final: 0.7811 (mttt) REVERT: F 119 LYS cc_start: 0.8375 (tttt) cc_final: 0.7950 (ttpp) REVERT: C 27 MET cc_start: 0.8567 (mmm) cc_final: 0.8101 (mmp) REVERT: C 119 LYS cc_start: 0.8129 (tttt) cc_final: 0.7810 (tmmt) REVERT: D 38 ASN cc_start: 0.7850 (p0) cc_final: 0.7613 (p0) REVERT: D 42 GLN cc_start: 0.8358 (tp40) cc_final: 0.8108 (mm-40) REVERT: A 27 MET cc_start: 0.8676 (mmm) cc_final: 0.8301 (mmp) REVERT: A 76 ASP cc_start: 0.8140 (m-30) cc_final: 0.7838 (m-30) REVERT: E 42 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: G 27 MET cc_start: 0.8688 (mmm) cc_final: 0.8401 (mmt) REVERT: G 38 ASN cc_start: 0.7792 (p0) cc_final: 0.7559 (p0) REVERT: G 119 LYS cc_start: 0.8421 (tttt) cc_final: 0.8144 (ttpt) outliers start: 23 outliers final: 15 residues processed: 331 average time/residue: 0.3493 time to fit residues: 150.8700 Evaluate side-chains 329 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 312 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN K 79 GLN L 79 GLN F 79 GLN A 63 GLN E 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10803 Z= 0.222 Angle : 0.536 5.721 14612 Z= 0.271 Chirality : 0.039 0.128 1690 Planarity : 0.004 0.030 1898 Dihedral : 4.722 17.963 1482 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.03 % Allowed : 14.06 % Favored : 83.91 % 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: 1.00 (0.22), residues: 1313 helix: 1.40 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -1.01 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 78 PHE 0.008 0.001 PHE G 36 TYR 0.010 0.002 TYR E 116 ARG 0.003 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 316 time to evaluate : 1.263 Fit side-chains REVERT: I 31 ARG cc_start: 0.8004 (mtm110) cc_final: 0.7721 (mtm-85) REVERT: I 60 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7946 (mt-10) REVERT: J 27 MET cc_start: 0.8902 (mmm) cc_final: 0.8545 (mmt) REVERT: H 42 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: H 103 LEU cc_start: 0.8737 (tt) cc_final: 0.8488 (mt) REVERT: B 31 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7421 (ttt-90) REVERT: B 42 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.6591 (tm-30) REVERT: B 99 ASP cc_start: 0.7611 (m-30) cc_final: 0.7365 (m-30) REVERT: F 31 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7217 (mtm-85) REVERT: F 76 ASP cc_start: 0.8148 (m-30) cc_final: 0.7928 (m-30) REVERT: F 115 LYS cc_start: 0.8208 (mttt) cc_final: 0.7788 (mttt) REVERT: F 119 LYS cc_start: 0.8464 (tttt) cc_final: 0.8065 (ttpp) REVERT: C 27 MET cc_start: 0.8587 (mmm) cc_final: 0.8125 (mmp) REVERT: C 119 LYS cc_start: 0.8159 (tttt) cc_final: 0.7814 (tmmt) REVERT: A 27 MET cc_start: 0.8717 (mmm) cc_final: 0.8384 (mmp) REVERT: A 42 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7990 (mm-40) REVERT: A 76 ASP cc_start: 0.8152 (m-30) cc_final: 0.7851 (m-30) REVERT: E 42 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: G 119 LYS cc_start: 0.8421 (tttt) cc_final: 0.8121 (ttpt) outliers start: 23 outliers final: 16 residues processed: 325 average time/residue: 0.3126 time to fit residues: 130.2875 Evaluate side-chains 332 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 312 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN I 79 GLN K 79 GLN L 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10803 Z= 0.157 Angle : 0.497 6.521 14612 Z= 0.250 Chirality : 0.038 0.117 1690 Planarity : 0.003 0.029 1898 Dihedral : 4.479 17.720 1482 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.30 % Allowed : 14.94 % Favored : 82.76 % 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: 1.55 (0.23), residues: 1313 helix: 1.86 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.92 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 78 PHE 0.006 0.001 PHE G 36 TYR 0.007 0.001 TYR A 58 ARG 0.004 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 317 time to evaluate : 1.147 Fit side-chains REVERT: M 94 THR cc_start: 0.9210 (m) cc_final: 0.8993 (m) REVERT: I 31 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7722 (mtm-85) REVERT: J 27 MET cc_start: 0.8880 (mmm) cc_final: 0.8508 (mmt) REVERT: K 67 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: H 42 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: H 46 ASP cc_start: 0.8262 (p0) cc_final: 0.7964 (p0) REVERT: H 103 LEU cc_start: 0.8756 (tt) cc_final: 0.8481 (mt) REVERT: B 99 ASP cc_start: 0.7531 (m-30) cc_final: 0.7291 (m-30) REVERT: F 31 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7188 (mtm-85) REVERT: F 76 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: F 119 LYS cc_start: 0.8460 (tttt) cc_final: 0.8060 (ttpp) REVERT: C 27 MET cc_start: 0.8550 (mmm) cc_final: 0.8118 (mmp) REVERT: C 119 LYS cc_start: 0.8123 (tttt) cc_final: 0.7794 (tmmt) REVERT: A 27 MET cc_start: 0.8720 (mmm) cc_final: 0.8381 (mmp) REVERT: A 42 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7956 (mm-40) REVERT: A 73 ARG cc_start: 0.8773 (mmp80) cc_final: 0.8465 (mmp-170) REVERT: A 76 ASP cc_start: 0.8124 (m-30) cc_final: 0.7634 (m-30) REVERT: E 42 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: G 119 LYS cc_start: 0.8367 (tttt) cc_final: 0.7891 (tttm) outliers start: 26 outliers final: 19 residues processed: 326 average time/residue: 0.3046 time to fit residues: 127.8370 Evaluate side-chains 335 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN I 79 GLN K 79 GLN L 79 GLN F 79 GLN F 120 GLN C 38 ASN E 67 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10803 Z= 0.207 Angle : 0.520 7.017 14612 Z= 0.261 Chirality : 0.039 0.125 1690 Planarity : 0.004 0.031 1898 Dihedral : 4.475 18.003 1482 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.65 % Allowed : 15.03 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.23), residues: 1313 helix: 1.99 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 78 PHE 0.007 0.001 PHE G 36 TYR 0.009 0.002 TYR A 58 ARG 0.004 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 316 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: M 94 THR cc_start: 0.9220 (m) cc_final: 0.8985 (m) REVERT: I 31 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7728 (mtm-85) REVERT: J 27 MET cc_start: 0.8892 (mmm) cc_final: 0.8511 (mmt) REVERT: J 88 ARG cc_start: 0.8650 (tpt170) cc_final: 0.8416 (tpt170) REVERT: K 67 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: H 42 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: H 103 LEU cc_start: 0.8748 (tt) cc_final: 0.8481 (mt) REVERT: L 119 LYS cc_start: 0.8134 (tttt) cc_final: 0.7738 (tmtt) REVERT: B 99 ASP cc_start: 0.7567 (m-30) cc_final: 0.7321 (m-30) REVERT: B 119 LYS cc_start: 0.8607 (tmmt) cc_final: 0.8388 (ttpp) REVERT: F 31 ARG cc_start: 0.7550 (mtm110) cc_final: 0.7187 (mtm-85) REVERT: F 76 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: F 115 LYS cc_start: 0.8137 (mttt) cc_final: 0.7805 (mttt) REVERT: F 119 LYS cc_start: 0.8482 (tttt) cc_final: 0.8123 (ttpp) REVERT: C 27 MET cc_start: 0.8598 (mmm) cc_final: 0.8150 (mmp) REVERT: C 38 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7993 (p0) REVERT: C 119 LYS cc_start: 0.8078 (tttt) cc_final: 0.7739 (tmmt) REVERT: A 27 MET cc_start: 0.8736 (mmm) cc_final: 0.8372 (mmp) REVERT: A 42 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7954 (mm-40) REVERT: A 76 ASP cc_start: 0.8159 (m-30) cc_final: 0.7862 (m-30) REVERT: E 42 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: E 53 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6986 (mm-30) REVERT: G 119 LYS cc_start: 0.8447 (tttt) cc_final: 0.7975 (tttm) outliers start: 30 outliers final: 22 residues processed: 326 average time/residue: 0.3015 time to fit residues: 127.3466 Evaluate side-chains 342 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 314 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 125 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 79 GLN I 79 GLN L 79 GLN F 120 GLN C 38 ASN E 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10803 Z= 0.135 Angle : 0.488 7.210 14612 Z= 0.244 Chirality : 0.037 0.120 1690 Planarity : 0.003 0.030 1898 Dihedral : 4.303 18.108 1482 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.21 % Allowed : 16.09 % Favored : 81.70 % 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: 1.96 (0.23), residues: 1313 helix: 2.21 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.88 (0.24), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 78 PHE 0.005 0.001 PHE G 36 TYR 0.006 0.001 TYR E 58 ARG 0.005 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 318 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: M 94 THR cc_start: 0.9177 (m) cc_final: 0.8941 (m) REVERT: I 31 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7724 (mtm-85) REVERT: J 27 MET cc_start: 0.8875 (mmm) cc_final: 0.8485 (mmt) REVERT: J 88 ARG cc_start: 0.8545 (tpt170) cc_final: 0.8305 (tpt170) REVERT: H 42 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7570 (tm-30) REVERT: H 103 LEU cc_start: 0.8742 (tt) cc_final: 0.8464 (mt) REVERT: L 119 LYS cc_start: 0.8100 (tttt) cc_final: 0.7714 (tmtt) REVERT: B 31 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7289 (ttt-90) REVERT: B 99 ASP cc_start: 0.7498 (m-30) cc_final: 0.7233 (m-30) REVERT: F 31 ARG cc_start: 0.7552 (mtm110) cc_final: 0.7152 (mtm-85) REVERT: F 76 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: F 115 LYS cc_start: 0.8119 (mttt) cc_final: 0.7782 (mttt) REVERT: C 27 MET cc_start: 0.8533 (mmm) cc_final: 0.8107 (mmp) REVERT: C 62 ARG cc_start: 0.8920 (mmm160) cc_final: 0.8667 (mmm160) REVERT: C 119 LYS cc_start: 0.8152 (tttt) cc_final: 0.7794 (ttpt) REVERT: D 42 GLN cc_start: 0.8368 (tp40) cc_final: 0.8104 (mm-40) REVERT: A 27 MET cc_start: 0.8753 (mmm) cc_final: 0.8381 (mmp) REVERT: A 42 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7861 (mm-40) REVERT: A 76 ASP cc_start: 0.8131 (m-30) cc_final: 0.7841 (m-30) REVERT: E 42 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: E 53 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6939 (mm-30) REVERT: G 119 LYS cc_start: 0.8396 (tttt) cc_final: 0.7931 (tttm) outliers start: 25 outliers final: 19 residues processed: 327 average time/residue: 0.3184 time to fit residues: 134.2234 Evaluate side-chains 332 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 309 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 79 GLN K 79 GLN L 79 GLN L 114 GLN C 38 ASN E 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10803 Z= 0.313 Angle : 0.575 6.172 14612 Z= 0.288 Chirality : 0.042 0.151 1690 Planarity : 0.004 0.038 1898 Dihedral : 4.600 18.557 1482 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.83 % Allowed : 15.56 % Favored : 81.61 % 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: 1.68 (0.23), residues: 1313 helix: 1.92 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.75 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 78 PHE 0.010 0.001 PHE G 36 TYR 0.013 0.003 TYR A 58 ARG 0.005 0.001 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 326 time to evaluate : 1.351 Fit side-chains REVERT: I 60 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8045 (mt-10) REVERT: I 119 LYS cc_start: 0.8213 (tttt) cc_final: 0.7947 (ttpt) REVERT: J 27 MET cc_start: 0.8936 (mmm) cc_final: 0.8528 (mmt) REVERT: J 88 ARG cc_start: 0.8652 (tpt170) cc_final: 0.8418 (tpt170) REVERT: K 67 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: H 42 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: H 103 LEU cc_start: 0.8798 (tt) cc_final: 0.8528 (mt) REVERT: B 99 ASP cc_start: 0.7636 (m-30) cc_final: 0.7385 (m-30) REVERT: B 119 LYS cc_start: 0.8678 (tmmt) cc_final: 0.8463 (ttpp) REVERT: F 31 ARG cc_start: 0.7598 (mtm110) cc_final: 0.7202 (mtm-85) REVERT: F 76 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: F 115 LYS cc_start: 0.8226 (mttt) cc_final: 0.7938 (mttt) REVERT: C 27 MET cc_start: 0.8609 (mmm) cc_final: 0.8165 (mmp) REVERT: C 119 LYS cc_start: 0.8197 (tttt) cc_final: 0.7858 (tmmt) REVERT: A 27 MET cc_start: 0.8777 (mmm) cc_final: 0.8429 (mmp) REVERT: A 42 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7982 (mm-40) REVERT: A 76 ASP cc_start: 0.8206 (m-30) cc_final: 0.7892 (m-30) REVERT: E 42 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7214 (tm-30) REVERT: G 119 LYS cc_start: 0.8412 (tttt) cc_final: 0.8044 (tttm) outliers start: 32 outliers final: 24 residues processed: 338 average time/residue: 0.3041 time to fit residues: 133.2733 Evaluate side-chains 350 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 321 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain L residue 48 THR Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 0.0770 chunk 120 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 76 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN M 79 GLN I 79 GLN K 79 GLN L 79 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10803 Z= 0.137 Angle : 0.499 6.041 14612 Z= 0.250 Chirality : 0.037 0.140 1690 Planarity : 0.004 0.041 1898 Dihedral : 4.332 18.942 1482 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.30 % Allowed : 17.06 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.23), residues: 1313 helix: 2.25 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.72 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 78 PHE 0.005 0.001 PHE I 36 TYR 0.006 0.001 TYR E 58 ARG 0.008 0.000 ARG E 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 314 time to evaluate : 1.395 Fit side-chains REVERT: M 94 THR cc_start: 0.9179 (m) cc_final: 0.8923 (m) REVERT: J 27 MET cc_start: 0.8927 (mmm) cc_final: 0.8691 (mmt) REVERT: J 88 ARG cc_start: 0.8573 (tpt170) cc_final: 0.8332 (tpt170) REVERT: H 42 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: H 103 LEU cc_start: 0.8726 (tt) cc_final: 0.8393 (mt) REVERT: L 32 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7805 (mmm160) REVERT: L 119 LYS cc_start: 0.8164 (tttt) cc_final: 0.7779 (tmmt) REVERT: B 31 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7288 (ttt-90) REVERT: B 99 ASP cc_start: 0.7450 (m-30) cc_final: 0.7142 (m-30) REVERT: F 31 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7175 (mtm-85) REVERT: F 76 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: F 115 LYS cc_start: 0.8208 (mttt) cc_final: 0.7906 (mttt) REVERT: C 27 MET cc_start: 0.8522 (mmm) cc_final: 0.8099 (mmp) REVERT: C 119 LYS cc_start: 0.8269 (tttt) cc_final: 0.7943 (tmmt) REVERT: D 114 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7998 (mm-40) REVERT: A 27 MET cc_start: 0.8750 (mmm) cc_final: 0.8399 (mmp) REVERT: A 73 ARG cc_start: 0.8883 (mmp80) cc_final: 0.8482 (mmp-170) REVERT: E 42 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: G 119 LYS cc_start: 0.8439 (tttt) cc_final: 0.8048 (tttm) outliers start: 26 outliers final: 21 residues processed: 322 average time/residue: 0.3127 time to fit residues: 129.7339 Evaluate side-chains 333 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 309 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 79 GLN Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain F residue 76 ASP Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.6980 chunk 58 optimal weight: 0.0670 chunk 85 optimal weight: 3.9990 chunk 129 optimal weight: 0.0370 chunk 119 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN I 79 GLN K 79 GLN L 79 GLN F 67 GLN F 79 GLN E 67 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10803 Z= 0.131 Angle : 0.498 7.528 14612 Z= 0.248 Chirality : 0.037 0.122 1690 Planarity : 0.003 0.040 1898 Dihedral : 4.181 18.385 1482 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.21 % Allowed : 16.98 % Favored : 80.81 % 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: 2.22 (0.23), residues: 1313 helix: 2.39 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.72 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 78 PHE 0.004 0.001 PHE I 36 TYR 0.005 0.001 TYR E 58 ARG 0.009 0.000 ARG E 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 307 time to evaluate : 1.273 Fit side-chains REVERT: M 94 THR cc_start: 0.9168 (m) cc_final: 0.8917 (m) REVERT: J 27 MET cc_start: 0.8923 (mmm) cc_final: 0.8678 (mmt) REVERT: H 42 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: H 103 LEU cc_start: 0.8701 (tt) cc_final: 0.8371 (mt) REVERT: L 32 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7829 (mmm160) REVERT: B 31 ARG cc_start: 0.7937 (mtm-85) cc_final: 0.7255 (ttt-90) REVERT: B 99 ASP cc_start: 0.7440 (m-30) cc_final: 0.7163 (m-30) REVERT: F 115 LYS cc_start: 0.8192 (mttt) cc_final: 0.7891 (mttt) REVERT: C 27 MET cc_start: 0.8525 (mmm) cc_final: 0.8128 (mmp) REVERT: C 119 LYS cc_start: 0.8227 (tttt) cc_final: 0.7900 (ttpt) REVERT: A 27 MET cc_start: 0.8746 (mmm) cc_final: 0.8397 (mmp) REVERT: A 73 ARG cc_start: 0.8850 (mmp80) cc_final: 0.8473 (mmp-170) REVERT: E 42 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: G 114 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7767 (mm-40) REVERT: G 119 LYS cc_start: 0.8377 (tttt) cc_final: 0.7906 (tttm) outliers start: 25 outliers final: 18 residues processed: 317 average time/residue: 0.3022 time to fit residues: 124.0055 Evaluate side-chains 325 residues out of total 1144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 305 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 26 ASN Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain H residue 42 GLN Chi-restraints excluded: chain H residue 117 ILE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 0.0060 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 67 GLN M 79 GLN J 63 GLN J 67 GLN J 79 GLN K 79 GLN L 79 GLN E 67 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109159 restraints weight = 12465.862| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.56 r_work: 0.3058 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10803 Z= 0.244 Angle : 0.548 7.262 14612 Z= 0.272 Chirality : 0.040 0.141 1690 Planarity : 0.004 0.038 1898 Dihedral : 4.358 17.813 1482 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.21 % Allowed : 16.71 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.23), residues: 1313 helix: 2.14 (0.18), residues: 910 sheet: None (None), residues: 0 loop : -0.70 (0.25), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 78 PHE 0.007 0.001 PHE G 36 TYR 0.013 0.002 TYR A 58 ARG 0.009 0.000 ARG E 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3009.63 seconds wall clock time: 54 minutes 37.61 seconds (3277.61 seconds total)