Starting phenix.real_space_refine on Sat Dec 9 09:15:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/12_2023/3j63_5830.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/12_2023/3j63_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_5830/12_2023/3j63_5830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/12_2023/3j63_5830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/12_2023/3j63_5830.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j63_5830/12_2023/3j63_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 6.00, per 1000 atoms: 0.57 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: 4.70 Conformation dependent library (CDL) restraints added in 2.1 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: 1.09 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: 2.56 Time building geometry restraints manager: 5.02 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.970 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 31.240 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.100 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- 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 : 1.408 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 outliers start: 80 outliers final: 36 residues processed: 556 average time/residue: 0.2431 time to fit residues: 183.3847 Evaluate side-chains 391 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 355 time to evaluate : 1.236 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.0997 time to fit residues: 8.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 chunk 56 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 0.4980 chunk 64 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN B 14 ASN C 14 ASN E 14 ASN E 91 GLN F 14 ASN G 14 ASN G 71 ASN H 14 ASN J 14 ASN K 14 ASN L 14 ASN N 14 ASN O 14 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.4788 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= 0.227 Angle : 0.867 9.541 14385 Z= 0.424 Chirality : 0.040 0.180 1680 Planarity : 0.006 0.066 1860 Dihedral : 5.893 56.624 1500 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.11 % Allowed : 27.40 % Favored : 67.49 % 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: -2.53 (0.21), residues: 1335 helix: -2.12 (0.14), residues: 840 sheet: None (None), residues: 0 loop : -0.43 (0.31), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS O 90 PHE 0.027 0.002 PHE B 59 TYR 0.019 0.002 TYR G 64 ARG 0.003 0.000 ARG E 41 *********************** 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 504 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 448 time to evaluate : 1.284 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 outliers start: 56 outliers final: 25 residues processed: 480 average time/residue: 0.2676 time to fit residues: 171.2633 Evaluate side-chains 397 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 372 time to evaluate : 1.257 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1029 time to fit residues: 6.5222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 98 optimal weight: 0.3980 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 91 GLN G 91 GLN H 91 GLN K 91 GLN L 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10695 Z= 0.225 Angle : 0.802 7.742 14385 Z= 0.385 Chirality : 0.040 0.212 1680 Planarity : 0.005 0.060 1860 Dihedral : 5.517 51.661 1500 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 8.31 % Allowed : 29.77 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.22), residues: 1335 helix: -1.33 (0.16), residues: 840 sheet: None (None), residues: 0 loop : 0.28 (0.31), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 90 PHE 0.015 0.002 PHE B 59 TYR 0.016 0.002 TYR H 64 ARG 0.004 0.000 ARG B 5 *********************** 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 501 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 410 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 56 residues processed: 455 average time/residue: 0.2598 time to fit residues: 156.6040 Evaluate side-chains 427 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 371 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.1173 time to fit residues: 12.6893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 63 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 GLN E 86 GLN E 91 GLN I 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.6616 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= 0.195 Angle : 0.767 10.134 14385 Z= 0.359 Chirality : 0.038 0.160 1680 Planarity : 0.004 0.040 1860 Dihedral : 5.239 50.301 1500 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.66 % Allowed : 31.96 % Favored : 62.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.23), residues: 1335 helix: -1.01 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 0.83 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 90 PHE 0.011 0.001 PHE B 59 TYR 0.014 0.001 TYR H 64 ARG 0.006 0.000 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 480 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 418 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 34 residues processed: 456 average time/residue: 0.2575 time to fit residues: 157.7029 Evaluate side-chains 405 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 371 time to evaluate : 1.380 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1307 time to fit residues: 9.0031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 20.0000 chunk 111 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 0 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 117 optimal weight: 40.0000 chunk 32 optimal weight: 10.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN B 91 GLN N 86 GLN N 91 GLN O 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.7116 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= 0.190 Angle : 0.756 9.710 14385 Z= 0.351 Chirality : 0.038 0.187 1680 Planarity : 0.004 0.048 1860 Dihedral : 5.172 47.226 1500 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 5.48 % Allowed : 34.16 % Favored : 60.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1335 helix: -0.80 (0.16), residues: 810 sheet: None (None), residues: 0 loop : 0.90 (0.31), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 90 PHE 0.011 0.001 PHE G 59 TYR 0.018 0.002 TYR D 64 ARG 0.005 0.000 ARG J 33 *********************** 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 485 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 425 time to evaluate : 1.167 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 outliers start: 60 outliers final: 30 residues processed: 446 average time/residue: 0.2587 time to fit residues: 155.6690 Evaluate side-chains 404 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 374 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.0952 time to fit residues: 7.0139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 4.9990 chunk 117 optimal weight: 40.0000 chunk 25 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 108 optimal weight: 40.0000 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.7438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10695 Z= 0.245 Angle : 0.806 10.168 14385 Z= 0.374 Chirality : 0.039 0.190 1680 Planarity : 0.004 0.041 1860 Dihedral : 5.345 44.609 1500 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.39 % Allowed : 34.98 % Favored : 59.63 % 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: -0.69 (0.23), residues: 1335 helix: -0.99 (0.16), residues: 885 sheet: None (None), residues: 0 loop : 1.22 (0.34), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.018 0.002 PHE O 59 TYR 0.021 0.002 TYR J 64 ARG 0.003 0.000 ARG E 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 465 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 406 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 30 residues processed: 434 average time/residue: 0.2507 time to fit residues: 146.6185 Evaluate side-chains 404 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 374 time to evaluate : 1.252 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1110 time to fit residues: 7.5232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 81 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 14 ASN M 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.7734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10695 Z= 0.236 Angle : 0.842 14.636 14385 Z= 0.385 Chirality : 0.040 0.211 1680 Planarity : 0.004 0.056 1860 Dihedral : 5.328 42.717 1500 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.20 % Allowed : 37.99 % Favored : 57.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1335 helix: -0.86 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.06 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.017 0.002 PHE K 59 TYR 0.020 0.002 TYR D 64 ARG 0.004 0.001 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 449 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 403 time to evaluate : 1.263 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 outliers start: 46 outliers final: 27 residues processed: 423 average time/residue: 0.2594 time to fit residues: 147.8825 Evaluate side-chains 405 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 378 time to evaluate : 1.302 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1611 time to fit residues: 8.5543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 20.0000 chunk 88 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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: 0.6691 moved from start: 0.8083 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= 0.218 Angle : 0.844 11.832 14385 Z= 0.379 Chirality : 0.041 0.263 1680 Planarity : 0.004 0.039 1860 Dihedral : 5.259 42.204 1500 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.01 % Allowed : 38.54 % Favored : 58.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.23), residues: 1335 helix: -0.78 (0.16), residues: 855 sheet: None (None), residues: 0 loop : 1.11 (0.33), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 90 PHE 0.019 0.002 PHE G 59 TYR 0.018 0.001 TYR D 64 ARG 0.008 0.000 ARG B 74 *********************** 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 444 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 411 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 426 average time/residue: 0.2501 time to fit residues: 143.4792 Evaluate side-chains 406 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 387 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0990 time to fit residues: 5.1835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 114 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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: 0.6761 moved from start: 0.8170 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= 0.249 Angle : 0.881 11.687 14385 Z= 0.403 Chirality : 0.042 0.174 1680 Planarity : 0.004 0.043 1860 Dihedral : 5.277 37.919 1500 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.65 % Allowed : 39.45 % Favored : 57.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.23), residues: 1335 helix: -0.76 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.03 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS N 90 PHE 0.023 0.002 PHE G 59 TYR 0.022 0.002 TYR D 64 ARG 0.006 0.001 ARG B 74 *********************** 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 424 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 395 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 404 average time/residue: 0.2517 time to fit residues: 138.1227 Evaluate side-chains 397 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 378 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1006 time to fit residues: 5.2643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 91 GLN N 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.8417 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= 0.241 Angle : 0.901 11.401 14385 Z= 0.411 Chirality : 0.044 0.317 1680 Planarity : 0.004 0.042 1860 Dihedral : 5.266 36.121 1500 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.28 % Allowed : 40.82 % Favored : 57.90 % 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: -0.45 (0.23), residues: 1335 helix: -0.73 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.04 (0.34), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 90 PHE 0.020 0.002 PHE G 59 TYR 0.018 0.002 TYR D 64 ARG 0.008 0.001 ARG B 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 417 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 403 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 407 average time/residue: 0.2708 time to fit residues: 147.7698 Evaluate side-chains 388 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 377 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1152 time to fit residues: 4.1938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.119322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.112451 restraints weight = 34048.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.114559 restraints weight = 17039.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.115929 restraints weight = 9805.685| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 0.99 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3404 r_free = 0.3404 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3404 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.8675 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= 0.229 Angle : 0.910 11.488 14385 Z= 0.410 Chirality : 0.042 0.224 1680 Planarity : 0.004 0.043 1860 Dihedral : 5.252 36.676 1500 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.82 % Allowed : 42.28 % Favored : 56.89 % 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: -0.41 (0.23), residues: 1335 helix: -0.77 (0.16), residues: 870 sheet: None (None), residues: 0 loop : 1.24 (0.33), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 90 PHE 0.018 0.002 PHE C 59 TYR 0.016 0.001 TYR D 64 ARG 0.008 0.000 ARG B 74 =============================================================================== Job complete usr+sys time: 2847.36 seconds wall clock time: 52 minutes 3.75 seconds (3123.75 seconds total)