Starting phenix.real_space_refine on Fri Mar 15 04:34:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/03_2024/3j63_5830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/03_2024/3j63_5830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/03_2024/3j63_5830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/03_2024/3j63_5830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/03_2024/3j63_5830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/03_2024/3j63_5830.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6675 2.51 5 N 1830 2.21 5 O 2025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 3": "NH1" <-> "NH2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3": "NH1" <-> "NH2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "D ARG 3": "NH1" <-> "NH2" Residue "D PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "H ARG 3": "NH1" <-> "NH2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "I ARG 3": "NH1" <-> "NH2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 80": "OE1" <-> "OE2" Residue "J ARG 3": "NH1" <-> "NH2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 3": "NH1" <-> "NH2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 3": "NH1" <-> "NH2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "N ARG 3": "NH1" <-> "NH2" Residue "N PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 80": "OE1" <-> "OE2" Residue "O ARG 3": "NH1" <-> "NH2" Residue "O PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10590 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "C" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "E" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "G" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "H" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "J" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "L" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "M" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "O" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 706 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Residues with excluded nonbonded symmetry interactions: 1365 residue: pdb=" N MET A 1 " occ=0.44 ... (6 atoms not shown) pdb=" CE MET A 1 " occ=0.44 residue: pdb=" N GLY A 2 " occ=0.41 ... (2 atoms not shown) pdb=" O GLY A 2 " occ=0.41 residue: pdb=" N ARG A 3 " occ=0.57 ... (9 atoms not shown) pdb=" NH2 ARG A 3 " occ=0.57 residue: pdb=" N ALA A 4 " occ=0.58 ... (3 atoms not shown) pdb=" CB ALA A 4 " occ=0.58 residue: pdb=" N ARG A 5 " occ=0.78 ... (9 atoms not shown) pdb=" NH2 ARG A 5 " occ=0.78 residue: pdb=" N ASP A 6 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP A 6 " occ=0.60 residue: pdb=" N ALA A 7 " occ=0.49 ... (3 atoms not shown) pdb=" CB ALA A 7 " occ=0.49 residue: pdb=" N ILE A 8 " occ=0.71 ... (6 atoms not shown) pdb=" CD1 ILE A 8 " occ=0.71 residue: pdb=" N LEU A 9 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 9 " occ=0.80 residue: pdb=" N ASP A 10 " occ=0.58 ... (6 atoms not shown) pdb=" OD2 ASP A 10 " occ=0.58 residue: pdb=" N ALA A 11 " occ=0.51 ... (3 atoms not shown) pdb=" CB ALA A 11 " occ=0.51 residue: pdb=" N LEU A 12 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU A 12 " occ=0.80 ... (remaining 1353 not shown) Time building chain proxies: 5.71, per 1000 atoms: 0.54 Number of scatterers: 10590 At special positions: 0 Unit cell: (93.96, 96.12, 99.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2025 8.00 N 1830 7.00 C 6675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 removed outlier: 3.828A pdb=" N ALA A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 30 removed outlier: 3.843A pdb=" N LYS A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 47 removed outlier: 3.667A pdb=" N LEU A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 61 through 76 removed outlier: 3.764A pdb=" N GLU A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 4.231A pdb=" N GLY A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 10 removed outlier: 3.702A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 30 removed outlier: 3.890A pdb=" N LYS B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 47 removed outlier: 3.589A pdb=" N LEU B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 60 Processing helix chain 'B' and resid 61 through 76 removed outlier: 3.712A pdb=" N GLU B 67 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 removed outlier: 4.268A pdb=" N GLY B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 10 removed outlier: 3.547A pdb=" N ALA C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 removed outlier: 3.881A pdb=" N LYS C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 47 removed outlier: 3.565A pdb=" N LEU C 44 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 60 Processing helix chain 'C' and resid 61 through 76 removed outlier: 3.689A pdb=" N GLU C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 91 removed outlier: 4.203A pdb=" N GLY C 83 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 88 " --> pdb=" O GLN C 84 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 9 Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.839A pdb=" N LYS D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 25 " --> pdb=" O LYS D 21 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 47 removed outlier: 3.692A pdb=" N LEU D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 removed outlier: 3.890A pdb=" N LEU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 76 removed outlier: 3.782A pdb=" N GLU D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 removed outlier: 3.611A pdb=" N GLN D 86 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 88 " --> pdb=" O GLN D 84 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 removed outlier: 4.106A pdb=" N ASP E 6 " --> pdb=" O GLY E 2 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.902A pdb=" N LYS E 21 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU E 25 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU E 28 " --> pdb=" O LYS E 24 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 47 removed outlier: 3.635A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 60 removed outlier: 4.019A pdb=" N LEU E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 76 removed outlier: 3.663A pdb=" N GLU E 67 " --> pdb=" O THR E 63 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 72 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 91 removed outlier: 4.218A pdb=" N GLY E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA E 88 " --> pdb=" O GLN E 84 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.727A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE F 8 " --> pdb=" O ALA F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 30 removed outlier: 3.519A pdb=" N LEU F 20 " --> pdb=" O THR F 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 47 removed outlier: 3.615A pdb=" N LEU F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 60 removed outlier: 4.056A pdb=" N LEU F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 76 removed outlier: 3.856A pdb=" N GLU F 67 " --> pdb=" O THR F 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 91 removed outlier: 4.249A pdb=" N GLY F 83 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA F 88 " --> pdb=" O GLN F 84 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 4 Processing helix chain 'G' and resid 5 through 10 Processing helix chain 'G' and resid 16 through 30 removed outlier: 3.885A pdb=" N LYS G 21 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 47 removed outlier: 3.672A pdb=" N LEU G 44 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 60 Processing helix chain 'G' and resid 61 through 76 removed outlier: 3.802A pdb=" N GLU G 67 " --> pdb=" O THR G 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 removed outlier: 3.539A pdb=" N GLN G 84 " --> pdb=" O GLU G 80 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA G 88 " --> pdb=" O GLN G 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 10 removed outlier: 3.705A pdb=" N ALA H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 30 removed outlier: 3.943A pdb=" N LYS H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 28 " --> pdb=" O LYS H 24 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 47 removed outlier: 3.568A pdb=" N LEU H 44 " --> pdb=" O PRO H 40 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 60 removed outlier: 3.836A pdb=" N LEU H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 76 removed outlier: 3.808A pdb=" N GLU H 67 " --> pdb=" O THR H 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 91 removed outlier: 3.636A pdb=" N GLN H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA H 88 " --> pdb=" O GLN H 84 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 10 removed outlier: 3.666A pdb=" N ALA I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE I 8 " --> pdb=" O ALA I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 30 removed outlier: 3.885A pdb=" N LYS I 21 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU I 28 " --> pdb=" O LYS I 24 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 47 removed outlier: 3.697A pdb=" N LEU I 44 " --> pdb=" O PRO I 40 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 60 removed outlier: 4.049A pdb=" N LEU I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 76 removed outlier: 3.806A pdb=" N GLU I 67 " --> pdb=" O THR I 63 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 91 removed outlier: 4.366A pdb=" N GLY I 83 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN I 84 " --> pdb=" O GLU I 80 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 86 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA I 88 " --> pdb=" O GLN I 84 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 10 removed outlier: 3.527A pdb=" N ALA J 7 " --> pdb=" O ARG J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 30 removed outlier: 3.951A pdb=" N LYS J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU J 28 " --> pdb=" O LYS J 24 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.671A pdb=" N LEU J 44 " --> pdb=" O PRO J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 60 removed outlier: 3.819A pdb=" N LEU J 56 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 3.763A pdb=" N GLU J 67 " --> pdb=" O THR J 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 91 removed outlier: 4.227A pdb=" N GLY J 83 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN J 84 " --> pdb=" O GLU J 80 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN J 86 " --> pdb=" O ALA J 82 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA J 88 " --> pdb=" O GLN J 84 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLN J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.959A pdb=" N ALA K 7 " --> pdb=" O ARG K 3 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE K 8 " --> pdb=" O ALA K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 30 removed outlier: 3.803A pdb=" N LYS K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU K 25 " --> pdb=" O LYS K 21 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU K 28 " --> pdb=" O LYS K 24 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 47 removed outlier: 3.633A pdb=" N LEU K 44 " --> pdb=" O PRO K 40 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 60 removed outlier: 3.883A pdb=" N LEU K 56 " --> pdb=" O LEU K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 76 removed outlier: 3.787A pdb=" N GLU K 67 " --> pdb=" O THR K 63 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL K 72 " --> pdb=" O LEU K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 91 removed outlier: 4.148A pdb=" N GLY K 83 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN K 84 " --> pdb=" O GLU K 80 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 86 " --> pdb=" O ALA K 82 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 removed outlier: 3.853A pdb=" N ALA L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE L 8 " --> pdb=" O ALA L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 30 removed outlier: 3.901A pdb=" N LYS L 21 " --> pdb=" O ALA L 17 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU L 25 " --> pdb=" O LYS L 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU L 28 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 47 removed outlier: 3.604A pdb=" N LEU L 44 " --> pdb=" O PRO L 40 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 60 removed outlier: 3.844A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 76 removed outlier: 3.646A pdb=" N GLU L 67 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL L 72 " --> pdb=" O LEU L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 91 removed outlier: 4.254A pdb=" N GLY L 83 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN L 86 " --> pdb=" O ALA L 82 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA L 88 " --> pdb=" O GLN L 84 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN L 91 " --> pdb=" O ALA L 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 10 removed outlier: 3.849A pdb=" N ALA M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE M 8 " --> pdb=" O ALA M 4 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU M 9 " --> pdb=" O ARG M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 30 removed outlier: 4.008A pdb=" N LYS M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU M 28 " --> pdb=" O LYS M 24 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER M 29 " --> pdb=" O LEU M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 45 removed outlier: 3.511A pdb=" N LEU M 44 " --> pdb=" O PRO M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 60 Processing helix chain 'M' and resid 61 through 76 removed outlier: 3.755A pdb=" N GLU M 67 " --> pdb=" O THR M 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL M 72 " --> pdb=" O LEU M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 91 removed outlier: 3.514A pdb=" N GLN M 84 " --> pdb=" O GLU M 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN M 86 " --> pdb=" O ALA M 82 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA M 88 " --> pdb=" O GLN M 84 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 10 removed outlier: 4.074A pdb=" N ASP N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.940A pdb=" N LYS N 21 " --> pdb=" O ALA N 17 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU N 25 " --> pdb=" O LYS N 21 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU N 28 " --> pdb=" O LYS N 24 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER N 29 " --> pdb=" O LEU N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 47 removed outlier: 3.635A pdb=" N LEU N 44 " --> pdb=" O PRO N 40 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER N 46 " --> pdb=" O GLY N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 60 Processing helix chain 'N' and resid 61 through 76 removed outlier: 3.630A pdb=" N GLU N 67 " --> pdb=" O THR N 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL N 72 " --> pdb=" O LEU N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 4.295A pdb=" N GLY N 83 " --> pdb=" O GLN N 79 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN N 84 " --> pdb=" O GLU N 80 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN N 86 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA N 88 " --> pdb=" O GLN N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 10 removed outlier: 3.701A pdb=" N ALA O 7 " --> pdb=" O ARG O 3 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 30 removed outlier: 4.002A pdb=" N LYS O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU O 25 " --> pdb=" O LYS O 21 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU O 28 " --> pdb=" O LYS O 24 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER O 29 " --> pdb=" O LEU O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 47 removed outlier: 3.783A pdb=" N LEU O 44 " --> pdb=" O PRO O 40 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER O 46 " --> pdb=" O GLY O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 60 removed outlier: 4.018A pdb=" N LEU O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 76 removed outlier: 3.819A pdb=" N GLU O 67 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL O 72 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 91 removed outlier: 3.630A pdb=" N GLN O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA O 88 " --> pdb=" O GLN O 84 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1404 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: 2.59 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3570 1.34 - 1.46: 1003 1.46 - 1.57: 6002 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 10695 Sorted by residual: bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 ... (remaining 10690 not shown) Histogram of bond angle deviations from ideal: 99.60 - 105.96: 180 105.96 - 112.33: 5199 112.33 - 118.69: 3359 118.69 - 125.05: 5599 125.05 - 131.41: 48 Bond angle restraints: 14385 Sorted by residual: angle pdb=" N SER G 29 " pdb=" CA SER G 29 " pdb=" C SER G 29 " ideal model delta sigma weight residual 111.28 119.35 -8.07 1.09e+00 8.42e-01 5.49e+01 angle pdb=" N VAL D 30 " pdb=" CA VAL D 30 " pdb=" C VAL D 30 " ideal model delta sigma weight residual 108.96 117.07 -8.11 1.10e+00 8.26e-01 5.44e+01 angle pdb=" N VAL B 30 " pdb=" CA VAL B 30 " pdb=" C VAL B 30 " ideal model delta sigma weight residual 108.96 116.99 -8.03 1.10e+00 8.26e-01 5.33e+01 angle pdb=" N VAL E 30 " pdb=" CA VAL E 30 " pdb=" C VAL E 30 " ideal model delta sigma weight residual 108.96 116.73 -7.77 1.10e+00 8.26e-01 4.99e+01 angle pdb=" N VAL M 30 " pdb=" CA VAL M 30 " pdb=" C VAL M 30 " ideal model delta sigma weight residual 108.96 116.41 -7.45 1.10e+00 8.26e-01 4.59e+01 ... (remaining 14380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 5853 17.23 - 34.46: 487 34.46 - 51.69: 136 51.69 - 68.92: 140 68.92 - 86.15: 14 Dihedral angle restraints: 6630 sinusoidal: 2715 harmonic: 3915 Sorted by residual: dihedral pdb=" CB GLU L 80 " pdb=" CG GLU L 80 " pdb=" CD GLU L 80 " pdb=" OE1 GLU L 80 " ideal model delta sinusoidal sigma weight residual 0.00 86.15 -86.15 1 3.00e+01 1.11e-03 9.95e+00 dihedral pdb=" N LEU D 61 " pdb=" CA LEU D 61 " pdb=" CB LEU D 61 " pdb=" CG LEU D 61 " ideal model delta sinusoidal sigma weight residual -180.00 -120.71 -59.29 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET O 1 " pdb=" CG MET O 1 " pdb=" SD MET O 1 " pdb=" CE MET O 1 " ideal model delta sinusoidal sigma weight residual -180.00 -120.73 -59.27 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 6627 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 729 0.045 - 0.090: 595 0.090 - 0.135: 264 0.135 - 0.179: 78 0.179 - 0.224: 14 Chirality restraints: 1680 Sorted by residual: chirality pdb=" CA SER C 29 " pdb=" N SER C 29 " pdb=" C SER C 29 " pdb=" CB SER C 29 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA SER L 29 " pdb=" N SER L 29 " pdb=" C SER L 29 " pdb=" CB SER L 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA SER G 29 " pdb=" N SER G 29 " pdb=" C SER G 29 " pdb=" CB SER G 29 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1677 not shown) Planarity restraints: 1860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 36 " 0.028 2.00e-02 2.50e+03 1.41e-02 3.98e+00 pdb=" CG TYR O 36 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR O 36 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR O 36 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR O 36 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR O 36 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR O 36 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR O 36 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL O 30 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO O 31 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO O 31 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO O 31 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 30 " 0.028 5.00e-02 4.00e+02 4.17e-02 2.79e+00 pdb=" N PRO M 31 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO M 31 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 31 " 0.023 5.00e-02 4.00e+02 ... (remaining 1857 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 979 2.73 - 3.27: 12830 3.27 - 3.81: 17234 3.81 - 4.36: 20542 4.36 - 4.90: 31132 Nonbonded interactions: 82717 Sorted by model distance: nonbonded pdb=" O VAL M 57 " pdb=" O TYR M 60 " model vdw 2.184 3.040 nonbonded pdb=" O LEU M 50 " pdb=" OG1 THR M 53 " model vdw 2.281 2.440 nonbonded pdb=" O LEU H 50 " pdb=" OG1 THR H 53 " model vdw 2.286 2.440 nonbonded pdb=" O LEU A 50 " pdb=" OG1 THR A 53 " model vdw 2.290 2.440 nonbonded pdb=" O LEU J 50 " pdb=" OG1 THR J 53 " model vdw 2.293 2.440 ... (remaining 82712 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' } 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=0.30 max=0.99 mean=0.64 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.050 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: 0.000 Extract box with map and model: 0.860 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.340 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 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 : 0.005 0.033 10695 Z= 0.295 Angle : 1.252 9.305 14385 Z= 0.876 Chirality : 0.072 0.224 1680 Planarity : 0.004 0.042 1860 Dihedral : 17.395 86.154 4110 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 54.83 Ramachandran Plot: Outliers : 3.07 % Allowed : 10.26 % Favored : 86.67 % Rotamer: Outliers : 7.31 % Allowed : 15.25 % Favored : 77.44 % 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: -4.14 (0.19), residues: 1335 helix: -4.38 (0.12), residues: 510 sheet: None (None), residues: 0 loop : -1.64 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 90 PHE 0.008 0.002 PHE B 23 TYR 0.028 0.004 TYR O 36 ARG 0.006 0.001 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 519 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5777 (mtm) cc_final: 0.5392 (ttt) REVERT: A 85 LEU cc_start: 0.6904 (tp) cc_final: 0.6538 (tp) REVERT: B 1 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4407 (ttt) REVERT: B 12 LEU cc_start: 0.6904 (mm) cc_final: 0.6435 (mm) REVERT: B 50 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6925 (mt) REVERT: C 1 MET cc_start: 0.5610 (mtm) cc_final: 0.4611 (ttp) REVERT: C 51 ASP cc_start: 0.6024 (m-30) cc_final: 0.5677 (m-30) REVERT: D 1 MET cc_start: 0.5761 (mtm) cc_final: 0.4999 (ttt) REVERT: D 50 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7522 (mt) REVERT: F 1 MET cc_start: 0.5443 (mtm) cc_final: 0.4991 (ttt) REVERT: F 50 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6691 (mt) REVERT: I 1 MET cc_start: 0.6093 (mtm) cc_final: 0.4462 (ttt) REVERT: J 1 MET cc_start: 0.6505 (mtm) cc_final: 0.4544 (ttt) REVERT: J 51 ASP cc_start: 0.5744 (m-30) cc_final: 0.5136 (m-30) REVERT: K 1 MET cc_start: 0.5903 (mtt) cc_final: 0.5185 (ttm) REVERT: K 34 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: K 51 ASP cc_start: 0.5821 (m-30) cc_final: 0.5243 (m-30) REVERT: K 85 LEU cc_start: 0.6151 (tp) cc_final: 0.5909 (tp) REVERT: M 50 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.6889 (mt) REVERT: N 12 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6157 (mm) REVERT: N 50 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7408 (mt) REVERT: N 51 ASP cc_start: 0.5731 (m-30) cc_final: 0.5207 (m-30) REVERT: N 85 LEU cc_start: 0.6346 (tp) cc_final: 0.6046 (tp) REVERT: O 1 MET cc_start: 0.6501 (mtt) cc_final: 0.5412 (ttt) REVERT: O 34 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6360 (pm20) REVERT: O 47 MET cc_start: 0.7473 (mmt) cc_final: 0.7237 (mmt) REVERT: O 51 ASP cc_start: 0.5588 (m-30) cc_final: 0.4977 (m-30) outliers start: 80 outliers final: 36 residues processed: 556 average time/residue: 0.2294 time to fit residues: 173.4532 Evaluate side-chains 407 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 362 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 34 GLU Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 72 VAL Chi-restraints excluded: chain G residue 34 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 6 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain K residue 8 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 34 GLU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain O residue 34 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 20.0000 chunk 102 optimal weight: 0.0060 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 overall best weight: 3.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 91 GLN B 14 ASN C 14 ASN D 91 GLN E 14 ASN E 91 GLN F 14 ASN G 14 ASN G 71 ASN I 91 GLN J 14 ASN K 14 ASN L 14 ASN N 14 ASN O 14 ASN O 90 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10695 Z= 0.221 Angle : 0.857 9.558 14385 Z= 0.419 Chirality : 0.040 0.181 1680 Planarity : 0.006 0.077 1860 Dihedral : 8.780 58.924 1595 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.76 % Allowed : 27.31 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.21), residues: 1335 helix: -2.15 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -0.45 (0.31), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS O 90 PHE 0.030 0.002 PHE B 59 TYR 0.019 0.002 TYR G 64 ARG 0.004 0.001 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 442 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5240 (OUTLIER) cc_final: 0.4581 (ttt) REVERT: B 6 ASP cc_start: 0.6239 (t0) cc_final: 0.5930 (t0) REVERT: C 1 MET cc_start: 0.5462 (mtm) cc_final: 0.4476 (ttp) REVERT: C 53 THR cc_start: 0.6763 (p) cc_final: 0.6530 (p) REVERT: D 1 MET cc_start: 0.6096 (mtm) cc_final: 0.4737 (ttt) REVERT: E 58 SER cc_start: 0.6523 (p) cc_final: 0.6268 (t) REVERT: F 1 MET cc_start: 0.5471 (mtm) cc_final: 0.4693 (ttt) REVERT: G 59 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5777 (t80) REVERT: G 89 THR cc_start: 0.6679 (p) cc_final: 0.6341 (p) REVERT: H 1 MET cc_start: 0.3184 (ttt) cc_final: 0.2813 (ttt) REVERT: I 1 MET cc_start: 0.6060 (mtt) cc_final: 0.4113 (ttt) REVERT: J 1 MET cc_start: 0.6156 (mtm) cc_final: 0.3938 (ttt) REVERT: J 76 MET cc_start: 0.2342 (ttt) cc_final: 0.2127 (ttp) REVERT: K 1 MET cc_start: 0.6151 (mtt) cc_final: 0.4809 (ttm) REVERT: L 89 THR cc_start: 0.6363 (p) cc_final: 0.6148 (p) REVERT: O 1 MET cc_start: 0.6591 (mtt) cc_final: 0.5408 (ttt) REVERT: O 51 ASP cc_start: 0.5179 (m-30) cc_final: 0.4855 (m-30) outliers start: 74 outliers final: 36 residues processed: 482 average time/residue: 0.2496 time to fit residues: 160.5546 Evaluate side-chains 396 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 358 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain K residue 5 ARG Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain O residue 12 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 109 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN G 91 GLN H 91 GLN J 91 GLN K 91 GLN L 91 GLN O 91 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10695 Z= 0.246 Angle : 0.818 7.735 14385 Z= 0.391 Chirality : 0.040 0.191 1680 Planarity : 0.005 0.055 1860 Dihedral : 6.973 58.948 1519 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 11.32 % Allowed : 29.22 % Favored : 59.45 % 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: -1.53 (0.22), residues: 1335 helix: -1.49 (0.16), residues: 825 sheet: None (None), residues: 0 loop : 0.22 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.012 0.002 PHE B 59 TYR 0.014 0.002 TYR H 64 ARG 0.005 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 397 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5051 (OUTLIER) cc_final: 0.4562 (ttt) REVERT: C 1 MET cc_start: 0.5224 (mtm) cc_final: 0.4970 (mtp) REVERT: D 1 MET cc_start: 0.6190 (mtm) cc_final: 0.4821 (ttt) REVERT: F 1 MET cc_start: 0.5229 (mtm) cc_final: 0.4913 (ttt) REVERT: G 59 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.6190 (t80) REVERT: G 89 THR cc_start: 0.6616 (p) cc_final: 0.6253 (p) REVERT: I 1 MET cc_start: 0.5536 (mtt) cc_final: 0.4480 (ttt) REVERT: I 39 ILE cc_start: 0.8414 (mp) cc_final: 0.7959 (mm) REVERT: I 89 THR cc_start: 0.5929 (p) cc_final: 0.5598 (p) REVERT: J 1 MET cc_start: 0.6219 (mtm) cc_final: 0.4410 (ttt) REVERT: K 1 MET cc_start: 0.6381 (mtt) cc_final: 0.4843 (ttm) REVERT: M 39 ILE cc_start: 0.8281 (mp) cc_final: 0.7941 (mm) REVERT: N 85 LEU cc_start: 0.5725 (tp) cc_final: 0.5425 (tp) REVERT: O 1 MET cc_start: 0.6652 (mtt) cc_final: 0.5336 (ttt) outliers start: 124 outliers final: 89 residues processed: 464 average time/residue: 0.2437 time to fit residues: 150.8108 Evaluate side-chains 463 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 372 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 24 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 5 ARG Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 63 optimal weight: 30.0000 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 130 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10695 Z= 0.276 Angle : 0.812 8.549 14385 Z= 0.388 Chirality : 0.038 0.176 1680 Planarity : 0.005 0.054 1860 Dihedral : 7.021 57.467 1519 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 12.79 % Allowed : 30.05 % Favored : 57.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1335 helix: -1.30 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 0.98 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 90 PHE 0.014 0.002 PHE I 59 TYR 0.018 0.002 TYR F 64 ARG 0.006 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 394 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.6701 (mm) cc_final: 0.6397 (tp) REVERT: D 1 MET cc_start: 0.6199 (mtm) cc_final: 0.4731 (ttt) REVERT: D 81 MET cc_start: 0.6042 (ppp) cc_final: 0.5612 (ppp) REVERT: F 1 MET cc_start: 0.5297 (mtm) cc_final: 0.4783 (ttt) REVERT: G 89 THR cc_start: 0.6504 (p) cc_final: 0.6247 (p) REVERT: I 1 MET cc_start: 0.5749 (mtt) cc_final: 0.4891 (ttt) REVERT: J 1 MET cc_start: 0.6131 (mtm) cc_final: 0.4431 (ttt) REVERT: L 39 ILE cc_start: 0.8696 (mp) cc_final: 0.8481 (mm) REVERT: L 81 MET cc_start: 0.5514 (ppp) cc_final: 0.4678 (ppp) REVERT: M 39 ILE cc_start: 0.8475 (mp) cc_final: 0.8203 (mm) REVERT: N 85 LEU cc_start: 0.5765 (tp) cc_final: 0.5472 (tp) REVERT: O 1 MET cc_start: 0.6452 (mtt) cc_final: 0.5243 (ttt) outliers start: 140 outliers final: 106 residues processed: 472 average time/residue: 0.2469 time to fit residues: 156.4364 Evaluate side-chains 471 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 365 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 59 PHE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 48 ASP Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 30.0000 chunk 74 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 90 optimal weight: 30.0000 chunk 0 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 117 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN M 91 GLN N 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.6927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10695 Z= 0.209 Angle : 0.758 8.680 14385 Z= 0.354 Chirality : 0.038 0.185 1680 Planarity : 0.004 0.041 1860 Dihedral : 6.700 56.558 1516 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 11.60 % Allowed : 33.06 % Favored : 55.34 % 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: -0.83 (0.23), residues: 1335 helix: -1.06 (0.16), residues: 825 sheet: None (None), residues: 0 loop : 0.77 (0.32), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.009 0.002 PHE I 59 TYR 0.025 0.002 TYR J 64 ARG 0.004 0.000 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 397 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.6563 (mm) cc_final: 0.6362 (tp) REVERT: D 1 MET cc_start: 0.5983 (mtm) cc_final: 0.4795 (ttt) REVERT: D 81 MET cc_start: 0.5852 (ppp) cc_final: 0.5371 (ppp) REVERT: F 1 MET cc_start: 0.5243 (mtm) cc_final: 0.4733 (ttt) REVERT: G 89 THR cc_start: 0.6501 (p) cc_final: 0.6213 (p) REVERT: I 1 MET cc_start: 0.5896 (mtt) cc_final: 0.4974 (ttt) REVERT: J 1 MET cc_start: 0.6070 (mtm) cc_final: 0.4679 (ttt) REVERT: L 81 MET cc_start: 0.5361 (ppp) cc_final: 0.4942 (ppp) REVERT: M 39 ILE cc_start: 0.8452 (mp) cc_final: 0.8184 (mm) REVERT: N 85 LEU cc_start: 0.5671 (tp) cc_final: 0.5281 (tp) REVERT: O 1 MET cc_start: 0.6611 (mtt) cc_final: 0.5261 (ttt) outliers start: 127 outliers final: 90 residues processed: 464 average time/residue: 0.2425 time to fit residues: 151.5865 Evaluate side-chains 453 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 363 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 32 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 26 LYS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 PHE Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 50.0000 chunk 25 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 60 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN D 14 ASN E 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10695 Z= 0.278 Angle : 0.830 8.614 14385 Z= 0.391 Chirality : 0.040 0.183 1680 Planarity : 0.005 0.050 1860 Dihedral : 6.887 56.741 1516 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 12.79 % Allowed : 33.33 % Favored : 53.88 % 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: -0.73 (0.23), residues: 1335 helix: -1.08 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.34 (0.34), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 90 PHE 0.015 0.002 PHE E 59 TYR 0.030 0.002 TYR J 64 ARG 0.004 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 386 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.5391 (ppp) cc_final: 0.5176 (ppp) REVERT: D 1 MET cc_start: 0.6147 (mtm) cc_final: 0.5415 (ttt) REVERT: D 81 MET cc_start: 0.6051 (ppp) cc_final: 0.5568 (ppp) REVERT: F 1 MET cc_start: 0.5243 (mtm) cc_final: 0.4957 (ttt) REVERT: G 89 THR cc_start: 0.6604 (p) cc_final: 0.6177 (p) REVERT: H 22 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6943 (mtmm) REVERT: I 1 MET cc_start: 0.5835 (mtt) cc_final: 0.5360 (ttt) REVERT: J 1 MET cc_start: 0.6077 (mtm) cc_final: 0.4808 (ttt) REVERT: J 59 PHE cc_start: 0.5784 (OUTLIER) cc_final: 0.5577 (t80) REVERT: L 39 ILE cc_start: 0.8529 (mp) cc_final: 0.8189 (mm) REVERT: L 81 MET cc_start: 0.5443 (ppp) cc_final: 0.4855 (ppp) REVERT: M 36 TYR cc_start: 0.6831 (m-80) cc_final: 0.6562 (m-80) REVERT: M 39 ILE cc_start: 0.8467 (mp) cc_final: 0.8234 (mm) REVERT: O 1 MET cc_start: 0.6727 (mtt) cc_final: 0.5238 (ttt) outliers start: 140 outliers final: 105 residues processed: 474 average time/residue: 0.2412 time to fit residues: 153.8156 Evaluate side-chains 473 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 366 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 10 ASP Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 PHE Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 34 GLU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 81 optimal weight: 30.0000 chunk 79 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.7590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10695 Z= 0.200 Angle : 0.800 8.398 14385 Z= 0.372 Chirality : 0.041 0.237 1680 Planarity : 0.005 0.071 1860 Dihedral : 6.764 56.162 1516 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 10.41 % Allowed : 37.63 % Favored : 51.96 % 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: -0.49 (0.24), residues: 1335 helix: -0.91 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.48 (0.35), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 90 PHE 0.009 0.001 PHE I 59 TYR 0.015 0.001 TYR J 64 ARG 0.004 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 403 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6015 (mtm) cc_final: 0.5397 (ttt) REVERT: D 81 MET cc_start: 0.5855 (ppp) cc_final: 0.5274 (ppp) REVERT: F 5 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.6377 (ptm160) REVERT: G 26 LYS cc_start: 0.7926 (ttpt) cc_final: 0.7660 (ttpt) REVERT: G 89 THR cc_start: 0.6004 (p) cc_final: 0.5661 (p) REVERT: H 6 ASP cc_start: 0.6634 (t0) cc_final: 0.6425 (t0) REVERT: H 22 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6875 (mtmm) REVERT: I 1 MET cc_start: 0.5751 (mtt) cc_final: 0.4937 (ttt) REVERT: I 39 ILE cc_start: 0.8437 (mp) cc_final: 0.8056 (mm) REVERT: J 1 MET cc_start: 0.5928 (mtm) cc_final: 0.4652 (ttt) REVERT: J 81 MET cc_start: 0.5089 (ppp) cc_final: 0.4718 (ppp) REVERT: L 81 MET cc_start: 0.5065 (ppp) cc_final: 0.4830 (ppp) REVERT: M 39 ILE cc_start: 0.8421 (mp) cc_final: 0.8203 (mm) REVERT: M 81 MET cc_start: 0.5676 (ppp) cc_final: 0.5092 (ppp) REVERT: O 1 MET cc_start: 0.6589 (mtt) cc_final: 0.5308 (ttt) outliers start: 114 outliers final: 85 residues processed: 466 average time/residue: 0.2428 time to fit residues: 153.0658 Evaluate side-chains 455 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 368 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 5 ARG Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 39 optimal weight: 0.0270 chunk 25 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 12 optimal weight: 0.6980 chunk 102 optimal weight: 0.0270 chunk 118 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 overall best weight: 2.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 86 GLN N 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.7917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10695 Z= 0.195 Angle : 0.819 10.510 14385 Z= 0.375 Chirality : 0.041 0.224 1680 Planarity : 0.005 0.044 1860 Dihedral : 6.548 57.709 1514 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 9.68 % Allowed : 37.81 % Favored : 52.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1335 helix: -0.92 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.43 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 90 PHE 0.013 0.001 PHE L 59 TYR 0.015 0.001 TYR L 64 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 396 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1 MET cc_start: 0.6251 (mtm) cc_final: 0.5380 (ttt) REVERT: D 81 MET cc_start: 0.5763 (ppp) cc_final: 0.5277 (ppp) REVERT: F 5 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.6272 (ptm160) REVERT: G 26 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7699 (ttpt) REVERT: G 89 THR cc_start: 0.6021 (p) cc_final: 0.5816 (p) REVERT: H 22 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6858 (mtmm) REVERT: I 1 MET cc_start: 0.5704 (mtt) cc_final: 0.5010 (ttt) REVERT: I 39 ILE cc_start: 0.8375 (mp) cc_final: 0.7989 (mm) REVERT: J 1 MET cc_start: 0.5956 (mtm) cc_final: 0.4582 (ttt) REVERT: K 3 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.5138 (tmt170) REVERT: K 6 ASP cc_start: 0.6748 (t0) cc_final: 0.6305 (t0) REVERT: M 39 ILE cc_start: 0.8379 (mp) cc_final: 0.8154 (mm) REVERT: M 81 MET cc_start: 0.5612 (ppp) cc_final: 0.4970 (ppp) REVERT: N 81 MET cc_start: 0.5778 (ppp) cc_final: 0.5181 (ppp) REVERT: O 39 ILE cc_start: 0.7911 (mp) cc_final: 0.7537 (mm) outliers start: 106 outliers final: 89 residues processed: 455 average time/residue: 0.2335 time to fit residues: 144.9305 Evaluate side-chains 466 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 374 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 59 PHE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 PHE Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 79 optimal weight: 0.0470 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 HIS H 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.8117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10695 Z= 0.211 Angle : 0.849 11.723 14385 Z= 0.385 Chirality : 0.040 0.218 1680 Planarity : 0.005 0.042 1860 Dihedral : 6.329 57.515 1512 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 9.50 % Allowed : 37.35 % Favored : 53.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1335 helix: -0.87 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.43 (0.35), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 90 PHE 0.012 0.002 PHE D 23 TYR 0.015 0.001 TYR J 64 ARG 0.009 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 382 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.3922 (ttt) cc_final: 0.3404 (ttm) REVERT: D 1 MET cc_start: 0.5909 (mtm) cc_final: 0.5115 (ttt) REVERT: D 81 MET cc_start: 0.5699 (ppp) cc_final: 0.5103 (ppp) REVERT: F 5 ARG cc_start: 0.6593 (OUTLIER) cc_final: 0.6208 (ptm160) REVERT: G 47 MET cc_start: 0.4875 (mmm) cc_final: 0.4549 (mmt) REVERT: H 22 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6778 (mtmm) REVERT: I 1 MET cc_start: 0.5678 (mtt) cc_final: 0.5073 (ttt) REVERT: I 39 ILE cc_start: 0.8384 (mp) cc_final: 0.8011 (mm) REVERT: J 1 MET cc_start: 0.5946 (mtm) cc_final: 0.4593 (ttt) REVERT: M 81 MET cc_start: 0.5689 (ppp) cc_final: 0.5033 (ppp) REVERT: N 81 MET cc_start: 0.5752 (ppp) cc_final: 0.5210 (ppp) outliers start: 104 outliers final: 93 residues processed: 443 average time/residue: 0.2421 time to fit residues: 145.0194 Evaluate side-chains 464 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 369 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 73 LEU Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 59 PHE Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 76 MET Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 54 ASP Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 chunk 85 optimal weight: 0.4980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.8396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10695 Z= 0.207 Angle : 0.877 10.601 14385 Z= 0.395 Chirality : 0.042 0.269 1680 Planarity : 0.004 0.040 1860 Dihedral : 6.308 56.057 1512 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 8.77 % Allowed : 38.08 % Favored : 53.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1335 helix: -0.87 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.34 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 90 PHE 0.010 0.002 PHE K 59 TYR 0.012 0.001 TYR L 64 ARG 0.004 0.000 ARG I 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2670 Ramachandran restraints generated. 1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 402 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7212 (m-30) cc_final: 0.6994 (m-30) REVERT: B 1 MET cc_start: 0.3738 (ttt) cc_final: 0.3251 (ttm) REVERT: D 1 MET cc_start: 0.5770 (mtm) cc_final: 0.5411 (ttt) REVERT: D 8 ILE cc_start: 0.5313 (mp) cc_final: 0.5082 (mp) REVERT: D 81 MET cc_start: 0.5640 (ppp) cc_final: 0.5102 (ppp) REVERT: F 5 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.6132 (ptm160) REVERT: H 22 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6809 (mtmm) REVERT: I 1 MET cc_start: 0.6009 (mtt) cc_final: 0.5202 (ttt) REVERT: J 1 MET cc_start: 0.5849 (mtm) cc_final: 0.4379 (ttt) REVERT: N 10 ASP cc_start: 0.6475 (t0) cc_final: 0.6234 (t0) REVERT: N 39 ILE cc_start: 0.8235 (mp) cc_final: 0.7977 (mm) REVERT: N 81 MET cc_start: 0.5546 (ppp) cc_final: 0.5021 (ppp) outliers start: 96 outliers final: 84 residues processed: 451 average time/residue: 0.2458 time to fit residues: 149.4481 Evaluate side-chains 459 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 373 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 59 PHE Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 59 PHE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 53 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 59 PHE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 59 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 20 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain K residue 3 ARG Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 56 LEU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 3 ARG Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 59 PHE Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 50 LEU Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 51 ASP Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 59 PHE Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 16 THR Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 59 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 98 optimal weight: 0.0060 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 110 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.119600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112838 restraints weight = 34492.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.114907 restraints weight = 17438.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.116252 restraints weight = 10086.818| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 0.99 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.8664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10695 Z= 0.222 Angle : 0.920 12.803 14385 Z= 0.410 Chirality : 0.043 0.380 1680 Planarity : 0.004 0.047 1860 Dihedral : 6.342 54.602 1512 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 8.58 % Allowed : 39.27 % Favored : 52.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1335 helix: -0.80 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.18 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 90 PHE 0.007 0.001 PHE K 59 TYR 0.021 0.001 TYR N 64 ARG 0.008 0.000 ARG E 38 =============================================================================== Job complete usr+sys time: 2783.95 seconds wall clock time: 50 minutes 45.85 seconds (3045.85 seconds total)