Starting phenix.real_space_refine on Fri Mar 15 07:14:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/03_2024/6ofg_20045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/03_2024/6ofg_20045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/03_2024/6ofg_20045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/03_2024/6ofg_20045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/03_2024/6ofg_20045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ofg_20045/03_2024/6ofg_20045.pdb" } resolution = 2.9 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= 0.001 sd= 0.010 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: 3 Type Number sf(0) Gaussians C 6930 2.51 5 N 1818 2.21 5 O 2232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 80": "NH1" <-> "NH2" Residue "Q ARG 80": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "L ARG 80": "NH1" <-> "NH2" Residue "M ARG 80": "NH1" <-> "NH2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "O ARG 80": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "I ARG 80": "NH1" <-> "NH2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10980 Number of models: 1 Model: "" Number of chains: 18 Chain: "P" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "R" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "K" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "M" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "N" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "O" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "G" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "H" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "I" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "J" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "A" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "E" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Time building chain proxies: 5.97, per 1000 atoms: 0.54 Number of scatterers: 10980 At special positions: 0 Unit cell: (90.915, 90.915, 147.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2232 8.00 N 1818 7.00 C 6930 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: 3.93 Conformation dependent library (CDL) restraints added in 1.8 seconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 91.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'P' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE P 16 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP P 17 " --> pdb=" O SER P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA P 36 " --> pdb=" O ASP P 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS P 37 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA P 74 " --> pdb=" O ASP P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE Q 16 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP Q 17 " --> pdb=" O SER Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA Q 36 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA Q 74 " --> pdb=" O ASP Q 70 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 80 No H-bonds generated for 'chain 'Q' and resid 78 through 80' Processing helix chain 'R' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE R 16 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR R 28 " --> pdb=" O GLN R 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 36 " --> pdb=" O ASP R 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA R 74 " --> pdb=" O ASP R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 80 No H-bonds generated for 'chain 'R' and resid 78 through 80' Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE K 16 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP K 17 " --> pdb=" O SER K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA K 36 " --> pdb=" O ASP K 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS K 37 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA K 74 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 80 No H-bonds generated for 'chain 'K' and resid 78 through 80' Processing helix chain 'L' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE L 16 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP L 17 " --> pdb=" O SER L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA L 36 " --> pdb=" O ASP L 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS L 37 " --> pdb=" O LYS L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA L 74 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 80 No H-bonds generated for 'chain 'L' and resid 78 through 80' Processing helix chain 'M' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE M 16 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP M 17 " --> pdb=" O SER M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 36 " --> pdb=" O ASP M 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA M 74 " --> pdb=" O ASP M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 80 No H-bonds generated for 'chain 'M' and resid 78 through 80' Processing helix chain 'N' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE N 16 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS N 37 " --> pdb=" O LYS N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA N 74 " --> pdb=" O ASP N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 80 No H-bonds generated for 'chain 'N' and resid 78 through 80' Processing helix chain 'O' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE O 16 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA O 36 " --> pdb=" O ASP O 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS O 37 " --> pdb=" O LYS O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA O 74 " --> pdb=" O ASP O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 80 No H-bonds generated for 'chain 'O' and resid 78 through 80' Processing helix chain 'F' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP F 17 " --> pdb=" O SER F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA F 74 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 80 No H-bonds generated for 'chain 'F' and resid 78 through 80' Processing helix chain 'G' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA G 36 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'H' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP H 17 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA H 74 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 80 No H-bonds generated for 'chain 'H' and resid 78 through 80' Processing helix chain 'I' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 80 No H-bonds generated for 'chain 'I' and resid 78 through 80' Processing helix chain 'J' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE J 16 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP J 17 " --> pdb=" O SER J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA J 36 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'A' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'B' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE B 16 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 36 " --> pdb=" O ASP B 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA B 74 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'C' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE C 16 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 17 " --> pdb=" O SER C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 36 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 77 removed outlier: 3.562A pdb=" N ALA C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'D' and resid 7 through 20 removed outlier: 3.580A pdb=" N PHE D 16 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 removed outlier: 3.662A pdb=" N THR D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.579A pdb=" N PHE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP E 17 " --> pdb=" O SER E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 37 removed outlier: 3.663A pdb=" N THR E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS E 37 " --> pdb=" O LYS E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 77 removed outlier: 3.563A pdb=" N ALA E 74 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' 900 hydrogen bonds defined for protein. 2700 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: 2.98 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 1962 1.29 - 1.35: 1674 1.35 - 1.41: 1087 1.41 - 1.48: 1689 1.48 - 1.54: 4766 Bond restraints: 11178 Sorted by residual: bond pdb=" CB GLU O 53 " pdb=" CG GLU O 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLU D 53 " pdb=" CG GLU D 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB GLU K 53 " pdb=" CG GLU K 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB GLU Q 53 " pdb=" CG GLU Q 53 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.57e+00 ... (remaining 11173 not shown) Histogram of bond angle deviations from ideal: 102.69 - 108.91: 639 108.91 - 115.13: 6183 115.13 - 121.36: 6049 121.36 - 127.58: 2249 127.58 - 133.80: 90 Bond angle restraints: 15210 Sorted by residual: angle pdb=" C VAL M 20 " pdb=" N ASP M 21 " pdb=" CA ASP M 21 " ideal model delta sigma weight residual 121.81 117.26 4.55 1.83e+00 2.99e-01 6.17e+00 angle pdb=" C VAL H 20 " pdb=" N ASP H 21 " pdb=" CA ASP H 21 " ideal model delta sigma weight residual 121.81 117.29 4.52 1.83e+00 2.99e-01 6.09e+00 angle pdb=" C VAL O 20 " pdb=" N ASP O 21 " pdb=" CA ASP O 21 " ideal model delta sigma weight residual 121.81 117.30 4.51 1.83e+00 2.99e-01 6.07e+00 angle pdb=" C VAL G 20 " pdb=" N ASP G 21 " pdb=" CA ASP G 21 " ideal model delta sigma weight residual 121.81 117.32 4.49 1.83e+00 2.99e-01 6.03e+00 angle pdb=" C VAL R 20 " pdb=" N ASP R 21 " pdb=" CA ASP R 21 " ideal model delta sigma weight residual 121.81 117.32 4.49 1.83e+00 2.99e-01 6.03e+00 ... (remaining 15205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 6534 14.84 - 29.68: 180 29.68 - 44.52: 54 44.52 - 59.37: 0 59.37 - 74.21: 18 Dihedral angle restraints: 6786 sinusoidal: 2592 harmonic: 4194 Sorted by residual: dihedral pdb=" CA GLY N 19 " pdb=" C GLY N 19 " pdb=" N VAL N 20 " pdb=" CA VAL N 20 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLY H 19 " pdb=" C GLY H 19 " pdb=" N VAL H 20 " pdb=" CA VAL H 20 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLY D 19 " pdb=" C GLY D 19 " pdb=" N VAL D 20 " pdb=" CA VAL D 20 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 6783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.020: 425 0.020 - 0.040: 694 0.040 - 0.059: 305 0.059 - 0.079: 184 0.079 - 0.099: 120 Chirality restraints: 1728 Sorted by residual: chirality pdb=" CA PRO D 38 " pdb=" N PRO D 38 " pdb=" C PRO D 38 " pdb=" CB PRO D 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.44e-01 chirality pdb=" CA PRO L 38 " pdb=" N PRO L 38 " pdb=" C PRO L 38 " pdb=" CB PRO L 38 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.44e-01 chirality pdb=" CA PRO B 41 " pdb=" N PRO B 41 " pdb=" C PRO B 41 " pdb=" CB PRO B 41 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.38e-01 ... (remaining 1725 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 20 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C VAL A 20 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL A 20 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 21 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 20 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C VAL N 20 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL N 20 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP N 21 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 20 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C VAL G 20 " 0.023 2.00e-02 2.50e+03 pdb=" O VAL G 20 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP G 21 " -0.008 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3286 2.79 - 3.32: 10703 3.32 - 3.85: 18136 3.85 - 4.37: 23422 4.37 - 4.90: 38800 Nonbonded interactions: 94347 Sorted by model distance: nonbonded pdb=" OD1 ASP K 17 " pdb=" OH TYR K 57 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP Q 17 " pdb=" OH TYR Q 57 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP G 17 " pdb=" OH TYR G 57 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP C 17 " pdb=" OH TYR C 57 " model vdw 2.263 2.440 nonbonded pdb=" OD1 ASP D 17 " pdb=" OH TYR D 57 " model vdw 2.263 2.440 ... (remaining 94342 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' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.920 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 30.340 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 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:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.008 0.040 11178 Z= 0.480 Angle : 0.750 4.546 15210 Z= 0.406 Chirality : 0.043 0.099 1728 Planarity : 0.005 0.030 1998 Dihedral : 10.039 74.208 4050 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -6.09 (0.10), residues: 1368 helix: -3.76 (0.06), residues: 1170 sheet: None (None), residues: 0 loop : -3.57 (0.31), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP N 5 PHE 0.012 0.002 PHE M 79 TYR 0.011 0.003 TYR Q 57 ARG 0.002 0.001 ARG F 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 33 LYS cc_start: 0.8552 (mttt) cc_final: 0.8324 (mttm) REVERT: N 28 THR cc_start: 0.8841 (m) cc_final: 0.8033 (m) REVERT: N 29 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7477 (mt-10) REVERT: N 32 ASP cc_start: 0.7471 (m-30) cc_final: 0.7138 (m-30) REVERT: O 10 ASP cc_start: 0.8938 (m-30) cc_final: 0.8720 (m-30) REVERT: A 37 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7090 (tttp) REVERT: A 66 LYS cc_start: 0.8971 (tptp) cc_final: 0.7623 (tppt) REVERT: A 72 ASP cc_start: 0.8867 (m-30) cc_final: 0.8639 (m-30) REVERT: B 66 LYS cc_start: 0.9050 (tptp) cc_final: 0.7748 (tppt) REVERT: D 72 ASP cc_start: 0.8868 (m-30) cc_final: 0.8613 (m-30) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 1.0093 time to fit residues: 388.6412 Evaluate side-chains 242 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN Q 78 ASN R 61 GLN K 61 GLN K 63 ASN K 77 GLN K 78 ASN L 55 ASN L 61 GLN L 77 GLN M 55 ASN M 61 GLN N 55 ASN N 61 GLN O 55 ASN O 61 GLN F 61 GLN F 78 ASN G 61 GLN G 77 GLN G 78 ASN H 61 GLN H 78 ASN I 61 GLN J 61 GLN A 59 ASN A 61 GLN B 61 GLN C 61 GLN D 61 GLN E 63 ASN E 77 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 11178 Z= 0.161 Angle : 0.469 3.554 15210 Z= 0.263 Chirality : 0.033 0.112 1728 Planarity : 0.005 0.027 1998 Dihedral : 4.168 21.190 1512 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.68 % Allowed : 14.87 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.18), residues: 1368 helix: -0.03 (0.11), residues: 1224 sheet: None (None), residues: 0 loop : -3.11 (0.45), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 5 PHE 0.006 0.001 PHE B 16 TYR 0.010 0.001 TYR E 57 ARG 0.001 0.000 ARG B 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 266 time to evaluate : 1.297 Fit side-chains REVERT: P 59 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.8009 (t0) REVERT: Q 32 ASP cc_start: 0.7717 (m-30) cc_final: 0.7338 (m-30) REVERT: K 59 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8154 (m-40) REVERT: K 69 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.7790 (tptm) REVERT: L 33 LYS cc_start: 0.8532 (mttt) cc_final: 0.8278 (mttm) REVERT: N 28 THR cc_start: 0.8824 (m) cc_final: 0.7973 (m) REVERT: N 29 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7377 (mt-10) REVERT: N 32 ASP cc_start: 0.7512 (m-30) cc_final: 0.7183 (m-30) REVERT: O 32 ASP cc_start: 0.7668 (m-30) cc_final: 0.7441 (m-30) REVERT: F 11 ASP cc_start: 0.8292 (m-30) cc_final: 0.8090 (m-30) REVERT: H 59 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8210 (t0) REVERT: I 59 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7840 (t0) REVERT: J 59 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7986 (t0) REVERT: J 69 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8431 (tttm) REVERT: A 37 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7108 (tttp) REVERT: B 66 LYS cc_start: 0.8981 (tptp) cc_final: 0.7796 (tppt) REVERT: B 69 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8274 (tptm) REVERT: B 72 ASP cc_start: 0.8648 (m-30) cc_final: 0.8428 (m-30) REVERT: C 53 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7079 (mm-30) REVERT: C 72 ASP cc_start: 0.8708 (m-30) cc_final: 0.8396 (m-30) REVERT: D 49 SER cc_start: 0.8860 (p) cc_final: 0.8648 (m) REVERT: E 72 ASP cc_start: 0.8892 (m-30) cc_final: 0.8610 (m-30) outliers start: 43 outliers final: 22 residues processed: 286 average time/residue: 0.8725 time to fit residues: 275.0976 Evaluate side-chains 259 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 229 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 59 ASN Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 59 ASN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 22 ASN Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN Q 78 ASN K 77 GLN L 61 GLN L 77 GLN M 61 GLN N 61 GLN O 61 GLN ** O 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN F 77 GLN F 78 ASN G 61 GLN G 77 GLN G 78 ASN H 61 GLN I 55 ASN I 61 GLN J 55 ASN J 61 GLN J 78 ASN A 78 ASN B 61 GLN C 61 GLN D 77 GLN E 61 GLN E 77 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 11178 Z= 0.144 Angle : 0.421 3.356 15210 Z= 0.230 Chirality : 0.033 0.102 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.700 18.796 1512 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.27 % Allowed : 14.62 % Favored : 81.11 % 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: 2.38 (0.21), residues: 1368 helix: 2.06 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.78 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 5 PHE 0.004 0.001 PHE A 79 TYR 0.010 0.001 TYR E 57 ARG 0.001 0.000 ARG G 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 267 time to evaluate : 1.343 Fit side-chains REVERT: P 59 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.8024 (t0) REVERT: Q 32 ASP cc_start: 0.7763 (m-30) cc_final: 0.7394 (m-30) REVERT: K 53 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7712 (mm-30) REVERT: K 59 ASN cc_start: 0.8462 (OUTLIER) cc_final: 0.8149 (m-40) REVERT: K 69 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.7875 (tptm) REVERT: L 24 GLN cc_start: 0.8065 (mp10) cc_final: 0.7175 (tp-100) REVERT: L 33 LYS cc_start: 0.8572 (mttt) cc_final: 0.8302 (mttm) REVERT: M 69 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.7863 (tptm) REVERT: N 28 THR cc_start: 0.8829 (m) cc_final: 0.8175 (m) REVERT: N 32 ASP cc_start: 0.7580 (m-30) cc_final: 0.6907 (m-30) REVERT: N 59 ASN cc_start: 0.8375 (t0) cc_final: 0.8040 (t0) REVERT: N 69 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.7255 (tptm) REVERT: O 32 ASP cc_start: 0.7513 (m-30) cc_final: 0.7174 (m-30) REVERT: O 69 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.7362 (ttmt) REVERT: F 10 ASP cc_start: 0.8938 (m-30) cc_final: 0.8636 (m-30) REVERT: F 11 ASP cc_start: 0.8292 (m-30) cc_final: 0.8043 (m-30) REVERT: F 53 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7603 (mm-30) REVERT: F 69 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8051 (tttm) REVERT: G 72 ASP cc_start: 0.8692 (m-30) cc_final: 0.8420 (m-30) REVERT: H 53 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7767 (mm-30) REVERT: I 15 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7937 (tttt) REVERT: I 59 ASN cc_start: 0.8305 (OUTLIER) cc_final: 0.7853 (t0) REVERT: J 15 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8059 (tttt) REVERT: J 59 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8063 (t0) REVERT: J 69 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8444 (tttm) REVERT: A 37 LYS cc_start: 0.8458 (ttmt) cc_final: 0.7177 (tttp) REVERT: B 72 ASP cc_start: 0.8647 (m-30) cc_final: 0.8431 (m-30) REVERT: C 53 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7305 (mm-30) REVERT: C 72 ASP cc_start: 0.8725 (m-30) cc_final: 0.8445 (m-30) REVERT: E 15 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8059 (mtpt) REVERT: E 22 ASN cc_start: 0.7881 (p0) cc_final: 0.7653 (p0) REVERT: E 59 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7815 (t0) REVERT: E 72 ASP cc_start: 0.8811 (m-30) cc_final: 0.8555 (m-30) outliers start: 50 outliers final: 26 residues processed: 296 average time/residue: 0.9365 time to fit residues: 304.5090 Evaluate side-chains 276 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 238 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 59 ASN Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 59 ASN Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 15 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 GLN R 61 GLN K 61 GLN K 63 ASN K 77 GLN L 61 GLN L 77 GLN M 61 GLN N 61 GLN F 61 GLN F 77 GLN F 78 ASN G 77 GLN I 61 GLN I 77 GLN J 61 GLN J 77 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 11178 Z= 0.188 Angle : 0.437 3.429 15210 Z= 0.236 Chirality : 0.034 0.106 1728 Planarity : 0.003 0.020 1998 Dihedral : 3.672 18.184 1512 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.62 % Allowed : 13.93 % Favored : 81.45 % 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: 3.34 (0.22), residues: 1368 helix: 2.69 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.48 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 5 PHE 0.006 0.001 PHE K 68 TYR 0.012 0.001 TYR D 57 ARG 0.002 0.000 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 247 time to evaluate : 1.263 Fit side-chains REVERT: Q 32 ASP cc_start: 0.7794 (m-30) cc_final: 0.7464 (m-30) REVERT: K 53 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7890 (mm-30) REVERT: K 59 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8137 (m-40) REVERT: K 69 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.7884 (tptm) REVERT: L 24 GLN cc_start: 0.7990 (mp10) cc_final: 0.7151 (tp-100) REVERT: L 33 LYS cc_start: 0.8574 (mttt) cc_final: 0.8312 (mttm) REVERT: M 50 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8712 (mptt) REVERT: M 69 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.7835 (tptm) REVERT: N 29 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7420 (mt-10) REVERT: N 32 ASP cc_start: 0.7614 (m-30) cc_final: 0.7168 (m-30) REVERT: N 59 ASN cc_start: 0.8422 (t0) cc_final: 0.8128 (t0) REVERT: N 69 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.7175 (tptm) REVERT: O 32 ASP cc_start: 0.7540 (m-30) cc_final: 0.7262 (m-30) REVERT: O 69 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.7365 (tttt) REVERT: F 10 ASP cc_start: 0.8919 (m-30) cc_final: 0.8659 (m-30) REVERT: F 53 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7545 (mm-30) REVERT: F 69 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8031 (tttm) REVERT: G 72 ASP cc_start: 0.8708 (m-30) cc_final: 0.8465 (m-30) REVERT: H 53 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7888 (mm-30) REVERT: H 69 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.7949 (tttm) REVERT: I 10 ASP cc_start: 0.8962 (m-30) cc_final: 0.8758 (m-30) REVERT: I 59 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7843 (t0) REVERT: I 77 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: J 15 LYS cc_start: 0.8495 (ttmm) cc_final: 0.7930 (tttt) REVERT: J 59 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8052 (t0) REVERT: J 69 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8514 (tttm) REVERT: A 37 LYS cc_start: 0.8483 (ttmt) cc_final: 0.7214 (tttp) REVERT: B 69 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8424 (tptm) REVERT: C 53 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7291 (mm-30) REVERT: C 72 ASP cc_start: 0.8744 (m-30) cc_final: 0.8420 (m-30) REVERT: D 53 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7280 (mm-30) REVERT: E 59 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7741 (t0) REVERT: E 72 ASP cc_start: 0.8788 (m-30) cc_final: 0.8552 (m-30) outliers start: 54 outliers final: 31 residues processed: 283 average time/residue: 0.8958 time to fit residues: 279.0767 Evaluate side-chains 284 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 239 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 50 LYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 59 ASN Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 77 GLN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN R 61 GLN K 61 GLN L 77 GLN M 61 GLN N 61 GLN F 61 GLN F 77 GLN F 78 ASN G 77 GLN H 61 GLN I 77 GLN J 61 GLN J 77 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 11178 Z= 0.143 Angle : 0.402 3.283 15210 Z= 0.218 Chirality : 0.033 0.101 1728 Planarity : 0.003 0.020 1998 Dihedral : 3.480 16.395 1512 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.79 % Allowed : 13.68 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.92 (0.22), residues: 1368 helix: 3.09 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.47 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 5 PHE 0.004 0.001 PHE O 68 TYR 0.010 0.001 TYR D 57 ARG 0.001 0.000 ARG J 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 249 time to evaluate : 1.327 Fit side-chains REVERT: Q 32 ASP cc_start: 0.7779 (m-30) cc_final: 0.7420 (m-30) REVERT: K 53 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7832 (mm-30) REVERT: K 59 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8166 (m-40) REVERT: K 69 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.7846 (tptm) REVERT: L 24 GLN cc_start: 0.7945 (mp10) cc_final: 0.7165 (tp-100) REVERT: L 33 LYS cc_start: 0.8557 (mttt) cc_final: 0.8288 (mttm) REVERT: M 50 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8646 (mptt) REVERT: M 69 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.7862 (tptm) REVERT: N 29 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7448 (mt-10) REVERT: N 32 ASP cc_start: 0.7680 (m-30) cc_final: 0.7321 (m-30) REVERT: N 59 ASN cc_start: 0.8379 (t0) cc_final: 0.8081 (t0) REVERT: N 69 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.7171 (tptm) REVERT: O 32 ASP cc_start: 0.7503 (m-30) cc_final: 0.7265 (m-30) REVERT: O 69 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.7355 (tttt) REVERT: F 10 ASP cc_start: 0.8909 (m-30) cc_final: 0.8657 (m-30) REVERT: F 53 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7618 (mm-30) REVERT: F 69 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8003 (tttm) REVERT: G 72 ASP cc_start: 0.8705 (m-30) cc_final: 0.8437 (m-30) REVERT: H 53 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7894 (mm-30) REVERT: H 59 ASN cc_start: 0.8442 (m-40) cc_final: 0.8206 (t0) REVERT: H 69 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.7922 (tttm) REVERT: I 10 ASP cc_start: 0.8987 (m-30) cc_final: 0.8765 (m-30) REVERT: I 59 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7875 (t0) REVERT: J 15 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8004 (tttt) REVERT: J 59 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8078 (t0) REVERT: J 69 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8502 (tttm) REVERT: A 32 ASP cc_start: 0.7402 (m-30) cc_final: 0.6869 (m-30) REVERT: A 37 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7195 (tttp) REVERT: B 69 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8345 (tptm) REVERT: C 72 ASP cc_start: 0.8719 (m-30) cc_final: 0.8433 (m-30) REVERT: D 53 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7561 (mm-30) REVERT: E 59 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7727 (t0) REVERT: E 72 ASP cc_start: 0.8727 (m-30) cc_final: 0.8526 (m-30) outliers start: 56 outliers final: 36 residues processed: 289 average time/residue: 0.9348 time to fit residues: 296.7074 Evaluate side-chains 287 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 238 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 50 LYS Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 59 ASN Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN L 61 GLN L 77 GLN M 61 GLN N 61 GLN F 61 GLN F 77 GLN F 78 ASN G 77 GLN H 61 GLN I 77 GLN J 61 GLN J 77 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 11178 Z= 0.144 Angle : 0.397 3.331 15210 Z= 0.214 Chirality : 0.033 0.101 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.401 15.439 1512 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.38 % Allowed : 13.50 % Favored : 81.11 % 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: 4.29 (0.22), residues: 1368 helix: 3.34 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.46 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 5 PHE 0.005 0.001 PHE K 68 TYR 0.010 0.001 TYR D 57 ARG 0.001 0.000 ARG J 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 245 time to evaluate : 1.306 Fit side-chains REVERT: Q 32 ASP cc_start: 0.7778 (m-30) cc_final: 0.7418 (m-30) REVERT: K 53 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7824 (mm-30) REVERT: K 59 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8165 (m-40) REVERT: K 69 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.7847 (tptm) REVERT: L 24 GLN cc_start: 0.7928 (mp10) cc_final: 0.7150 (tp-100) REVERT: L 33 LYS cc_start: 0.8552 (mttt) cc_final: 0.8276 (mttm) REVERT: M 50 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8745 (mptt) REVERT: M 69 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.7852 (tptm) REVERT: N 59 ASN cc_start: 0.8376 (t0) cc_final: 0.8110 (t0) REVERT: N 69 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7733 (tptm) REVERT: O 32 ASP cc_start: 0.7472 (m-30) cc_final: 0.7183 (m-30) REVERT: O 69 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.7364 (tttt) REVERT: F 10 ASP cc_start: 0.8866 (m-30) cc_final: 0.8620 (m-30) REVERT: F 53 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7614 (mm-30) REVERT: F 69 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.7947 (tttm) REVERT: G 72 ASP cc_start: 0.8701 (m-30) cc_final: 0.8435 (m-30) REVERT: H 53 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7888 (mm-30) REVERT: H 57 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.7330 (t80) REVERT: H 59 ASN cc_start: 0.8465 (m-40) cc_final: 0.8237 (t0) REVERT: H 69 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.7920 (tttm) REVERT: I 10 ASP cc_start: 0.8982 (m-30) cc_final: 0.8775 (m-30) REVERT: I 53 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7837 (mm-30) REVERT: I 59 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7831 (t0) REVERT: J 15 LYS cc_start: 0.8504 (ttmm) cc_final: 0.8002 (tttt) REVERT: J 59 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8066 (t0) REVERT: J 69 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8496 (tttm) REVERT: A 37 LYS cc_start: 0.8480 (ttmt) cc_final: 0.7207 (tttp) REVERT: B 69 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8334 (tptm) REVERT: C 72 ASP cc_start: 0.8726 (m-30) cc_final: 0.8434 (m-30) REVERT: D 53 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7551 (mm-30) REVERT: D 69 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.7958 (tptm) REVERT: E 59 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7722 (t0) outliers start: 63 outliers final: 43 residues processed: 291 average time/residue: 0.9034 time to fit residues: 289.0058 Evaluate side-chains 295 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 237 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 57 TYR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 50 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 15 LYS Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN L 61 GLN M 61 GLN N 61 GLN F 61 GLN F 78 ASN G 77 GLN H 61 GLN J 61 GLN J 77 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN E 77 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 11178 Z= 0.154 Angle : 0.405 3.606 15210 Z= 0.217 Chirality : 0.033 0.101 1728 Planarity : 0.003 0.021 1998 Dihedral : 3.365 14.879 1512 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.30 % Allowed : 13.59 % Favored : 81.11 % 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: 4.45 (0.22), residues: 1368 helix: 3.46 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.49 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 5 PHE 0.005 0.001 PHE K 68 TYR 0.011 0.001 TYR D 57 ARG 0.006 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 244 time to evaluate : 1.332 Fit side-chains REVERT: Q 32 ASP cc_start: 0.7777 (m-30) cc_final: 0.7418 (m-30) REVERT: K 53 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7837 (mm-30) REVERT: K 59 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8153 (m-40) REVERT: K 69 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.7840 (tptm) REVERT: L 24 GLN cc_start: 0.7913 (mp10) cc_final: 0.7154 (tp-100) REVERT: L 33 LYS cc_start: 0.8567 (mttt) cc_final: 0.8314 (mttm) REVERT: M 50 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8751 (mptt) REVERT: M 69 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.7849 (tptm) REVERT: N 32 ASP cc_start: 0.7665 (m-30) cc_final: 0.7076 (m-30) REVERT: N 59 ASN cc_start: 0.8406 (t0) cc_final: 0.8115 (t0) REVERT: N 69 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7733 (tptm) REVERT: O 32 ASP cc_start: 0.7472 (m-30) cc_final: 0.7206 (m-30) REVERT: O 69 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.7357 (tttt) REVERT: F 10 ASP cc_start: 0.8862 (m-30) cc_final: 0.8626 (m-30) REVERT: F 53 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7575 (mm-30) REVERT: F 69 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.7950 (tttm) REVERT: G 72 ASP cc_start: 0.8689 (m-30) cc_final: 0.8418 (m-30) REVERT: H 57 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.7263 (t80) REVERT: H 59 ASN cc_start: 0.8487 (m-40) cc_final: 0.8254 (t0) REVERT: H 69 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.7913 (tttm) REVERT: I 53 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7856 (mm-30) REVERT: I 59 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7833 (t0) REVERT: J 15 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8077 (tttt) REVERT: J 59 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8075 (t0) REVERT: J 69 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8493 (tttm) REVERT: A 29 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7439 (mt-10) REVERT: A 32 ASP cc_start: 0.7470 (m-30) cc_final: 0.6989 (m-30) REVERT: A 37 LYS cc_start: 0.8490 (ttmt) cc_final: 0.7216 (tttp) REVERT: B 69 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8328 (tptm) REVERT: C 72 ASP cc_start: 0.8730 (m-30) cc_final: 0.8442 (m-30) REVERT: D 53 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7547 (mm-30) REVERT: D 69 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.7958 (tptm) REVERT: E 32 ASP cc_start: 0.7831 (m-30) cc_final: 0.7526 (m-30) REVERT: E 59 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7727 (t0) outliers start: 62 outliers final: 44 residues processed: 291 average time/residue: 0.9029 time to fit residues: 288.5614 Evaluate side-chains 301 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 241 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 50 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 GLN L 61 GLN L 77 GLN M 61 GLN N 61 GLN O 61 GLN F 61 GLN G 77 GLN J 61 GLN J 77 GLN A 61 GLN B 61 GLN C 61 GLN D 61 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 11178 Z= 0.135 Angle : 0.390 3.455 15210 Z= 0.209 Chirality : 0.032 0.099 1728 Planarity : 0.003 0.026 1998 Dihedral : 3.270 14.031 1512 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.13 % Allowed : 14.02 % Favored : 80.85 % 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: 4.67 (0.22), residues: 1368 helix: 3.60 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.50 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 5 PHE 0.005 0.001 PHE O 68 TYR 0.009 0.001 TYR D 57 ARG 0.007 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 246 time to evaluate : 1.270 Fit side-chains REVERT: Q 32 ASP cc_start: 0.7772 (m-30) cc_final: 0.7439 (m-30) REVERT: K 53 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7686 (mm-30) REVERT: K 59 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8144 (m-40) REVERT: K 69 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.7834 (tptm) REVERT: L 24 GLN cc_start: 0.7902 (mp10) cc_final: 0.7170 (tp-100) REVERT: L 33 LYS cc_start: 0.8551 (mttt) cc_final: 0.8297 (mttm) REVERT: M 50 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8755 (mptt) REVERT: M 69 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.7830 (tptm) REVERT: N 32 ASP cc_start: 0.7628 (m-30) cc_final: 0.7116 (m-30) REVERT: N 59 ASN cc_start: 0.8393 (t0) cc_final: 0.8105 (t0) REVERT: N 69 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.7126 (tptm) REVERT: O 32 ASP cc_start: 0.7474 (m-30) cc_final: 0.7211 (m-30) REVERT: O 69 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8162 (tptm) REVERT: F 10 ASP cc_start: 0.8845 (m-30) cc_final: 0.8618 (m-30) REVERT: F 53 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7569 (mm-30) REVERT: F 69 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.7913 (tttm) REVERT: G 72 ASP cc_start: 0.8686 (m-30) cc_final: 0.8448 (m-30) REVERT: H 69 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.7901 (tttm) REVERT: I 59 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7866 (t0) REVERT: J 15 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8174 (tttt) REVERT: J 59 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8076 (t0) REVERT: J 69 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8480 (tttm) REVERT: A 32 ASP cc_start: 0.7468 (m-30) cc_final: 0.6932 (m-30) REVERT: A 37 LYS cc_start: 0.8502 (ttmt) cc_final: 0.7025 (tptt) REVERT: B 69 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8313 (tptm) REVERT: C 15 LYS cc_start: 0.8681 (ttmm) cc_final: 0.8457 (mtmt) REVERT: C 72 ASP cc_start: 0.8723 (m-30) cc_final: 0.8405 (m-30) REVERT: D 53 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7537 (mm-30) REVERT: D 69 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.7974 (tptm) REVERT: E 59 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7733 (t0) outliers start: 60 outliers final: 43 residues processed: 290 average time/residue: 0.9018 time to fit residues: 287.5961 Evaluate side-chains 293 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 236 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 50 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 57 TYR Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 61 GLN L 61 GLN M 61 GLN O 61 GLN F 61 GLN G 77 GLN H 78 ASN J 77 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11178 Z= 0.145 Angle : 0.400 3.829 15210 Z= 0.214 Chirality : 0.033 0.103 1728 Planarity : 0.003 0.027 1998 Dihedral : 3.258 13.763 1512 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.38 % Allowed : 13.93 % Favored : 80.68 % 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: 4.71 (0.22), residues: 1368 helix: 3.64 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.54 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 5 PHE 0.005 0.001 PHE K 68 TYR 0.010 0.001 TYR D 57 ARG 0.007 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 238 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: Q 32 ASP cc_start: 0.7776 (m-30) cc_final: 0.7440 (m-30) REVERT: K 53 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7705 (mm-30) REVERT: K 59 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8136 (m-40) REVERT: K 69 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.7833 (tptm) REVERT: L 24 GLN cc_start: 0.7887 (mp10) cc_final: 0.7204 (tp-100) REVERT: L 33 LYS cc_start: 0.8552 (mttt) cc_final: 0.8300 (mttm) REVERT: M 69 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.7832 (tptm) REVERT: N 32 ASP cc_start: 0.7639 (m-30) cc_final: 0.7128 (m-30) REVERT: N 59 ASN cc_start: 0.8402 (t0) cc_final: 0.8111 (t0) REVERT: N 69 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.7127 (tptm) REVERT: O 32 ASP cc_start: 0.7473 (m-30) cc_final: 0.7233 (m-30) REVERT: O 69 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.7336 (tttt) REVERT: F 10 ASP cc_start: 0.8843 (m-30) cc_final: 0.8622 (m-30) REVERT: F 53 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7612 (mm-30) REVERT: F 69 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.7970 (tttm) REVERT: G 69 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.7979 (tttm) REVERT: G 72 ASP cc_start: 0.8684 (m-30) cc_final: 0.8443 (m-30) REVERT: H 57 TYR cc_start: 0.9075 (OUTLIER) cc_final: 0.7251 (t80) REVERT: H 59 ASN cc_start: 0.8487 (m110) cc_final: 0.8237 (t0) REVERT: H 69 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.7908 (tttm) REVERT: I 59 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7838 (t0) REVERT: J 15 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8176 (tttt) REVERT: J 59 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8075 (t0) REVERT: J 69 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8150 (tptm) REVERT: A 37 LYS cc_start: 0.8520 (ttmt) cc_final: 0.7236 (tttp) REVERT: B 69 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8325 (tptm) REVERT: C 72 ASP cc_start: 0.8712 (m-30) cc_final: 0.8424 (m-30) REVERT: D 53 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7539 (mm-30) REVERT: D 69 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.7976 (tptm) REVERT: E 32 ASP cc_start: 0.7809 (m-30) cc_final: 0.7474 (m-30) REVERT: E 59 ASN cc_start: 0.8102 (OUTLIER) cc_final: 0.7727 (t0) outliers start: 63 outliers final: 45 residues processed: 286 average time/residue: 0.9727 time to fit residues: 306.8429 Evaluate side-chains 295 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 235 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 57 TYR Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 59 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN Q 61 GLN L 61 GLN M 61 GLN N 61 GLN F 61 GLN H 61 GLN J 77 GLN B 61 GLN C 61 GLN D 61 GLN D 77 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.003 0.019 11178 Z= 0.163 Angle : 0.411 4.001 15210 Z= 0.220 Chirality : 0.033 0.113 1728 Planarity : 0.003 0.026 1998 Dihedral : 3.275 13.520 1512 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.47 % Allowed : 13.76 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.73 (0.22), residues: 1368 helix: 3.65 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.50 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 5 PHE 0.006 0.001 PHE K 68 TYR 0.011 0.001 TYR D 57 ARG 0.007 0.000 ARG H 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 241 time to evaluate : 1.245 Fit side-chains revert: symmetry clash REVERT: Q 32 ASP cc_start: 0.7778 (m-30) cc_final: 0.7439 (m-30) REVERT: K 53 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7729 (mm-30) REVERT: K 59 ASN cc_start: 0.8451 (OUTLIER) cc_final: 0.8152 (m-40) REVERT: K 69 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.7824 (tptm) REVERT: L 24 GLN cc_start: 0.7813 (mp10) cc_final: 0.7156 (tp-100) REVERT: L 33 LYS cc_start: 0.8568 (mttt) cc_final: 0.8319 (mttm) REVERT: M 69 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.7888 (tptm) REVERT: N 32 ASP cc_start: 0.7633 (m-30) cc_final: 0.7130 (m-30) REVERT: N 59 ASN cc_start: 0.8412 (t0) cc_final: 0.8121 (t0) REVERT: N 69 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.7158 (tptm) REVERT: O 32 ASP cc_start: 0.7473 (m-30) cc_final: 0.7196 (m-30) REVERT: O 69 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8184 (tptm) REVERT: F 10 ASP cc_start: 0.8855 (m-30) cc_final: 0.8626 (m-30) REVERT: F 53 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7613 (mm-30) REVERT: F 69 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.7986 (tttm) REVERT: G 69 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8001 (tttm) REVERT: G 72 ASP cc_start: 0.8685 (m-30) cc_final: 0.8410 (m-30) REVERT: H 57 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.7260 (t80) REVERT: H 59 ASN cc_start: 0.8494 (m110) cc_final: 0.8247 (t0) REVERT: H 69 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.7911 (tttm) REVERT: I 59 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7803 (t0) REVERT: J 15 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8090 (tttt) REVERT: J 59 ASN cc_start: 0.8406 (OUTLIER) cc_final: 0.8088 (t0) REVERT: J 69 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8478 (tttm) REVERT: A 37 LYS cc_start: 0.8551 (ttmt) cc_final: 0.7264 (tttp) REVERT: B 69 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8328 (tptm) REVERT: C 15 LYS cc_start: 0.8756 (ttmm) cc_final: 0.8455 (mtmt) REVERT: C 72 ASP cc_start: 0.8727 (m-30) cc_final: 0.8428 (m-30) REVERT: D 32 ASP cc_start: 0.7827 (m-30) cc_final: 0.7224 (m-30) REVERT: D 53 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7542 (mm-30) REVERT: D 69 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.7967 (tptm) REVERT: E 22 ASN cc_start: 0.7930 (p0) cc_final: 0.7514 (p0) REVERT: E 32 ASP cc_start: 0.7770 (m-30) cc_final: 0.7442 (m-30) REVERT: E 59 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7736 (t0) REVERT: E 69 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8260 (tttm) outliers start: 64 outliers final: 43 residues processed: 287 average time/residue: 0.9140 time to fit residues: 287.8497 Evaluate side-chains 299 residues out of total 1170 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 240 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 62 SER Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 57 TYR Chi-restraints excluded: chain R residue 25 THR Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 57 TYR Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 59 ASN Chi-restraints excluded: chain K residue 69 LYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 33 LYS Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 LYS Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 62 SER Chi-restraints excluded: chain N residue 69 LYS Chi-restraints excluded: chain O residue 6 SER Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 57 TYR Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 69 LYS Chi-restraints excluded: chain F residue 6 SER Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 59 ASN Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 69 LYS Chi-restraints excluded: chain H residue 6 SER Chi-restraints excluded: chain H residue 57 TYR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 69 LYS Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 59 ASN Chi-restraints excluded: chain E residue 69 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.0770 chunk 92 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 61 GLN L 61 GLN N 61 GLN O 61 GLN G 61 GLN H 61 GLN J 77 GLN A 61 GLN C 61 GLN D 61 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096857 restraints weight = 15525.372| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.73 r_work: 0.3014 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 11178 Z= 0.112 Angle : 0.376 3.506 15210 Z= 0.202 Chirality : 0.031 0.100 1728 Planarity : 0.003 0.028 1998 Dihedral : 3.112 12.049 1512 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.02 % Allowed : 15.30 % Favored : 80.68 % 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: 5.02 (0.22), residues: 1368 helix: 3.85 (0.13), residues: 1224 sheet: None (None), residues: 0 loop : -2.53 (0.52), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 5 PHE 0.005 0.001 PHE A 16 TYR 0.007 0.001 TYR D 57 ARG 0.006 0.000 ARG H 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4636.74 seconds wall clock time: 82 minutes 50.26 seconds (4970.26 seconds total)