Starting phenix.real_space_refine on Mon Jul 22 19:28:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/07_2024/7xq9_33391.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/07_2024/7xq9_33391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/07_2024/7xq9_33391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/07_2024/7xq9_33391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/07_2024/7xq9_33391.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq9_33391/07_2024/7xq9_33391.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.175 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 96 5.16 5 C 13080 2.51 5 N 3120 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A ASP 12": "OD1" <-> "OD2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "G ASP 3": "OD1" <-> "OD2" Residue "G ASP 12": "OD1" <-> "OD2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G ASP 67": "OD1" <-> "OD2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ASP 238": "OD1" <-> "OD2" Residue "B ASP 3": "OD1" <-> "OD2" Residue "B ASP 12": "OD1" <-> "OD2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B ARG 101": "NH1" <-> "NH2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C ASP 12": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "D ASP 3": "OD1" <-> "OD2" Residue "D ASP 12": "OD1" <-> "OD2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 103": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ASP 238": "OD1" <-> "OD2" Residue "E ASP 3": "OD1" <-> "OD2" Residue "E ASP 12": "OD1" <-> "OD2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ASP 238": "OD1" <-> "OD2" Residue "F ASP 3": "OD1" <-> "OD2" Residue "F ASP 12": "OD1" <-> "OD2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F ASP 238": "OD1" <-> "OD2" Residue "H ASP 3": "OD1" <-> "OD2" Residue "H ASP 12": "OD1" <-> "OD2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H ARG 101": "NH1" <-> "NH2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H ARG 148": "NH1" <-> "NH2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H ASP 238": "OD1" <-> "OD2" Residue "I ASP 3": "OD1" <-> "OD2" Residue "I ASP 12": "OD1" <-> "OD2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 42": "OE1" <-> "OE2" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I ASP 67": "OD1" <-> "OD2" Residue "I ARG 101": "NH1" <-> "NH2" Residue "I GLU 103": "OE1" <-> "OE2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "I ASP 238": "OD1" <-> "OD2" Residue "J ASP 3": "OD1" <-> "OD2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "J PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 48": "OE1" <-> "OE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J ASP 67": "OD1" <-> "OD2" Residue "J ARG 101": "NH1" <-> "NH2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J GLU 166": "OE1" <-> "OE2" Residue "J ASP 238": "OD1" <-> "OD2" Residue "K ASP 3": "OD1" <-> "OD2" Residue "K ASP 12": "OD1" <-> "OD2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K ASP 67": "OD1" <-> "OD2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K ASP 238": "OD1" <-> "OD2" Residue "L ASP 3": "OD1" <-> "OD2" Residue "L ASP 12": "OD1" <-> "OD2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L ARG 148": "NH1" <-> "NH2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "L ASP 238": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19632 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "G" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "F" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "H" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "I" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "J" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "K" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "L" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1636 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Time building chain proxies: 9.83, per 1000 atoms: 0.50 Number of scatterers: 19632 At special positions: 0 Unit cell: (106.392, 108.68, 181.896, 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 96 16.00 O 3336 8.00 N 3120 7.00 C 13080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.03 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: 7.95 Conformation dependent library (CDL) restraints added in 3.5 seconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.1% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.702A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 40 through 45' Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 110 Proline residue: A 88 - end of helix removed outlier: 3.584A pdb=" N LYS A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 236 removed outlier: 3.603A pdb=" N LYS A 206 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS G 23 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 40 through 45' Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 110 Proline residue: G 88 - end of helix removed outlier: 3.584A pdb=" N LYS G 102 " --> pdb=" O TYR G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 177 removed outlier: 3.658A pdb=" N TYR G 155 " --> pdb=" O LEU G 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER G 163 " --> pdb=" O ILE G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS G 206 " --> pdb=" O ARG G 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL G 236 " --> pdb=" O PHE G 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 Processing helix chain 'B' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 45' Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 110 Proline residue: B 88 - end of helix removed outlier: 3.584A pdb=" N LYS B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 40 through 45' Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 110 Proline residue: C 88 - end of helix removed outlier: 3.584A pdb=" N LYS C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER C 163 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS C 206 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS D 23 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 40 through 45' Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 110 Proline residue: D 88 - end of helix removed outlier: 3.584A pdb=" N LYS D 102 " --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER D 163 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 15 Processing helix chain 'E' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS E 23 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 40 through 45' Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 110 Proline residue: E 88 - end of helix removed outlier: 3.584A pdb=" N LYS E 102 " --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR E 155 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER E 163 " --> pdb=" O ILE E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS E 206 " --> pdb=" O ARG E 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 15 Processing helix chain 'F' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS F 23 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.702A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 110 Proline residue: F 88 - end of helix removed outlier: 3.583A pdb=" N LYS F 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR F 155 " --> pdb=" O LEU F 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER F 163 " --> pdb=" O ILE F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS F 206 " --> pdb=" O ARG F 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL F 236 " --> pdb=" O PHE F 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 19 through 40 removed outlier: 3.502A pdb=" N LYS H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.700A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 45' Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.685A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 110 Proline residue: H 88 - end of helix removed outlier: 3.584A pdb=" N LYS H 102 " --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR H 155 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 236 removed outlier: 3.603A pdb=" N LYS H 206 " --> pdb=" O ARG H 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL H 236 " --> pdb=" O PHE H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 15 Processing helix chain 'I' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS I 23 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 45' Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 110 Proline residue: I 88 - end of helix removed outlier: 3.584A pdb=" N LYS I 102 " --> pdb=" O TYR I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR I 155 " --> pdb=" O LEU I 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER I 163 " --> pdb=" O ILE I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS I 206 " --> pdb=" O ARG I 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL I 236 " --> pdb=" O PHE I 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 15 Processing helix chain 'J' and resid 19 through 40 removed outlier: 3.502A pdb=" N LYS J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 40 through 45' Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 110 Proline residue: J 88 - end of helix removed outlier: 3.584A pdb=" N LYS J 102 " --> pdb=" O TYR J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR J 155 " --> pdb=" O LEU J 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER J 163 " --> pdb=" O ILE J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 236 removed outlier: 3.603A pdb=" N LYS J 206 " --> pdb=" O ARG J 202 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL J 236 " --> pdb=" O PHE J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 15 Processing helix chain 'K' and resid 19 through 40 removed outlier: 3.503A pdb=" N LYS K 23 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 40 through 45' Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 110 Proline residue: K 88 - end of helix removed outlier: 3.584A pdb=" N LYS K 102 " --> pdb=" O TYR K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER K 163 " --> pdb=" O ILE K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS K 206 " --> pdb=" O ARG K 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL K 236 " --> pdb=" O PHE K 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 15 Processing helix chain 'L' and resid 19 through 40 removed outlier: 3.502A pdb=" N LYS L 23 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.701A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TRP L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 40 through 45' Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.684A pdb=" N VAL L 64 " --> pdb=" O GLY L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 110 Proline residue: L 88 - end of helix removed outlier: 3.584A pdb=" N LYS L 102 " --> pdb=" O TYR L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 177 removed outlier: 3.659A pdb=" N TYR L 155 " --> pdb=" O LEU L 151 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER L 163 " --> pdb=" O ILE L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 236 removed outlier: 3.602A pdb=" N LYS L 206 " --> pdb=" O ARG L 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.712A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.713A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 4068 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: 5.51 Time building geometry restraints manager: 8.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5796 1.34 - 1.46: 4036 1.46 - 1.57: 10196 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 20148 Sorted by residual: bond pdb=" N HIS F 194 " pdb=" CA HIS F 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.73e+00 bond pdb=" N HIS I 194 " pdb=" CA HIS I 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.67e+00 bond pdb=" N HIS B 194 " pdb=" CA HIS B 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.65e+00 bond pdb=" N HIS J 194 " pdb=" CA HIS J 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.64e+00 bond pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.16e-02 7.43e+03 4.63e+00 ... (remaining 20143 not shown) Histogram of bond angle deviations from ideal: 100.95 - 107.56: 588 107.56 - 114.17: 11371 114.17 - 120.77: 9313 120.77 - 127.38: 5788 127.38 - 133.99: 228 Bond angle restraints: 27288 Sorted by residual: angle pdb=" C PRO C 193 " pdb=" N HIS C 194 " pdb=" CA HIS C 194 " ideal model delta sigma weight residual 120.79 127.73 -6.94 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C PRO K 193 " pdb=" N HIS K 194 " pdb=" CA HIS K 194 " ideal model delta sigma weight residual 120.79 127.73 -6.94 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C PRO H 193 " pdb=" N HIS H 194 " pdb=" CA HIS H 194 " ideal model delta sigma weight residual 120.79 127.72 -6.93 1.39e+00 5.18e-01 2.49e+01 angle pdb=" C PRO D 193 " pdb=" N HIS D 194 " pdb=" CA HIS D 194 " ideal model delta sigma weight residual 120.79 127.72 -6.93 1.39e+00 5.18e-01 2.48e+01 angle pdb=" C PRO A 193 " pdb=" N HIS A 194 " pdb=" CA HIS A 194 " ideal model delta sigma weight residual 120.79 127.71 -6.92 1.39e+00 5.18e-01 2.48e+01 ... (remaining 27283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.95: 9458 11.95 - 23.89: 1534 23.89 - 35.84: 552 35.84 - 47.78: 192 47.78 - 59.73: 72 Dihedral angle restraints: 11808 sinusoidal: 4752 harmonic: 7056 Sorted by residual: dihedral pdb=" CB CYS B 61 " pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual 93.00 119.46 -26.46 1 1.00e+01 1.00e-02 1.01e+01 dihedral pdb=" CB CYS I 61 " pdb=" SG CYS I 61 " pdb=" SG CYS I 192 " pdb=" CB CYS I 192 " ideal model delta sinusoidal sigma weight residual 93.00 119.45 -26.45 1 1.00e+01 1.00e-02 1.01e+01 dihedral pdb=" CB CYS F 61 " pdb=" SG CYS F 61 " pdb=" SG CYS F 192 " pdb=" CB CYS F 192 " ideal model delta sinusoidal sigma weight residual 93.00 119.44 -26.44 1 1.00e+01 1.00e-02 1.00e+01 ... (remaining 11805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3012 0.113 - 0.226: 60 0.226 - 0.340: 12 0.340 - 0.453: 0 0.453 - 0.566: 12 Chirality restraints: 3096 Sorted by residual: chirality pdb=" CB ILE D 34 " pdb=" CA ILE D 34 " pdb=" CG1 ILE D 34 " pdb=" CG2 ILE D 34 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CB ILE L 34 " pdb=" CA ILE L 34 " pdb=" CG1 ILE L 34 " pdb=" CG2 ILE L 34 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 7.98e+00 ... (remaining 3093 not shown) Planarity restraints: 3300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP I 12 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CG ASP I 12 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP I 12 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP I 12 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 12 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" CG ASP K 12 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP K 12 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP K 12 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 12 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" CG ASP B 12 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP B 12 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 12 " -0.010 2.00e-02 2.50e+03 ... (remaining 3297 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4595 2.78 - 3.31: 16566 3.31 - 3.84: 31244 3.84 - 4.37: 31952 4.37 - 4.90: 59471 Nonbonded interactions: 143828 Sorted by model distance: nonbonded pdb=" O ILE K 72 " pdb=" OH TYR K 177 " model vdw 2.253 2.440 nonbonded pdb=" O ILE G 72 " pdb=" OH TYR G 177 " model vdw 2.253 2.440 nonbonded pdb=" O ILE B 72 " pdb=" OH TYR B 177 " model vdw 2.253 2.440 nonbonded pdb=" O ILE D 72 " pdb=" OH TYR D 177 " model vdw 2.253 2.440 nonbonded pdb=" O ILE C 72 " pdb=" OH TYR C 177 " model vdw 2.253 2.440 ... (remaining 143823 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 49.630 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 0.034 20148 Z= 0.320 Angle : 0.826 7.699 27288 Z= 0.480 Chirality : 0.057 0.566 3096 Planarity : 0.006 0.040 3300 Dihedral : 14.697 59.726 7140 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.89 % Allowed : 2.27 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: -2.05 (0.14), residues: 2364 helix: -0.92 (0.10), residues: 1668 sheet: 1.27 (0.48), residues: 132 loop : -2.97 (0.20), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 45 HIS 0.001 0.001 HIS I 194 PHE 0.021 0.002 PHE H 212 TYR 0.011 0.001 TYR G 66 ARG 0.002 0.000 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 524 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9041 (tttt) cc_final: 0.8539 (ttmm) REVERT: A 17 TYR cc_start: 0.8697 (m-80) cc_final: 0.8321 (m-10) REVERT: A 101 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7903 (mtp-110) REVERT: A 189 ARG cc_start: 0.8230 (ttt180) cc_final: 0.7900 (ttm170) REVERT: A 230 TYR cc_start: 0.7924 (t80) cc_final: 0.7563 (t80) REVERT: G 13 LYS cc_start: 0.8982 (tttt) cc_final: 0.8551 (ttmm) REVERT: G 17 TYR cc_start: 0.8780 (m-80) cc_final: 0.8483 (m-80) REVERT: G 47 ASP cc_start: 0.8968 (p0) cc_final: 0.8767 (p0) REVERT: G 109 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.6020 (tptt) REVERT: B 13 LYS cc_start: 0.8854 (tttt) cc_final: 0.8564 (ttmm) REVERT: B 47 ASP cc_start: 0.8936 (p0) cc_final: 0.8638 (p0) REVERT: B 101 ARG cc_start: 0.8105 (mtp85) cc_final: 0.7736 (mtp-110) REVERT: B 230 TYR cc_start: 0.8049 (t80) cc_final: 0.7848 (t80) REVERT: C 13 LYS cc_start: 0.8993 (tttt) cc_final: 0.8486 (ttmm) REVERT: C 42 GLU cc_start: 0.8007 (tt0) cc_final: 0.7457 (tm-30) REVERT: C 47 ASP cc_start: 0.8860 (p0) cc_final: 0.8560 (p0) REVERT: C 53 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7495 (mtt180) REVERT: C 67 ASP cc_start: 0.8776 (t0) cc_final: 0.8541 (t0) REVERT: C 100 MET cc_start: 0.8481 (mtp) cc_final: 0.8123 (mtp) REVERT: C 189 ARG cc_start: 0.7702 (ttt180) cc_final: 0.7446 (ttt180) REVERT: D 53 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7645 (mmt90) REVERT: D 62 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6964 (tt0) REVERT: D 227 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8270 (mm-30) REVERT: E 13 LYS cc_start: 0.8864 (tttt) cc_final: 0.8526 (ttmm) REVERT: E 42 GLU cc_start: 0.7911 (tt0) cc_final: 0.7510 (tm-30) REVERT: E 47 ASP cc_start: 0.8942 (p0) cc_final: 0.8641 (p0) REVERT: E 189 ARG cc_start: 0.8444 (ttt180) cc_final: 0.8093 (ttm-80) REVERT: F 13 LYS cc_start: 0.8930 (tttt) cc_final: 0.8533 (ttmm) REVERT: F 17 TYR cc_start: 0.8737 (m-80) cc_final: 0.8421 (m-80) REVERT: F 53 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7579 (mtt180) REVERT: F 189 ARG cc_start: 0.8456 (ttt180) cc_final: 0.7975 (ttt180) REVERT: H 35 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8645 (tt) REVERT: H 227 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8269 (mm-30) REVERT: H 230 TYR cc_start: 0.7833 (t80) cc_final: 0.7603 (t80) REVERT: I 13 LYS cc_start: 0.8793 (tttt) cc_final: 0.8377 (ttmm) REVERT: I 39 THR cc_start: 0.9215 (m) cc_final: 0.8808 (p) REVERT: I 53 ARG cc_start: 0.7907 (mtt180) cc_final: 0.7665 (mtt180) REVERT: I 62 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7341 (mt-10) REVERT: J 13 LYS cc_start: 0.8907 (tttt) cc_final: 0.8498 (ttmm) REVERT: J 189 ARG cc_start: 0.8505 (ttt180) cc_final: 0.8248 (ttm170) REVERT: K 13 LYS cc_start: 0.8935 (tttt) cc_final: 0.8535 (ttmm) REVERT: K 42 GLU cc_start: 0.7870 (tt0) cc_final: 0.7309 (tm-30) REVERT: K 47 ASP cc_start: 0.8978 (p0) cc_final: 0.8709 (p0) REVERT: K 185 TYR cc_start: 0.8408 (t80) cc_final: 0.8103 (t80) REVERT: K 189 ARG cc_start: 0.8563 (ttt180) cc_final: 0.8280 (ttm170) REVERT: K 213 MET cc_start: 0.8981 (mmm) cc_final: 0.8776 (mmt) REVERT: L 13 LYS cc_start: 0.8861 (tttt) cc_final: 0.8463 (ttmm) REVERT: L 17 TYR cc_start: 0.8688 (m-80) cc_final: 0.8466 (m-80) REVERT: L 47 ASP cc_start: 0.8971 (p0) cc_final: 0.8718 (p0) REVERT: L 53 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7477 (mtt180) REVERT: L 189 ARG cc_start: 0.8476 (ttt180) cc_final: 0.8033 (ttm-80) outliers start: 84 outliers final: 34 residues processed: 582 average time/residue: 0.3713 time to fit residues: 320.4290 Evaluate side-chains 470 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 434 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 87 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9990 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 194 HIS D 15 GLN H 194 HIS I 15 GLN K 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20148 Z= 0.174 Angle : 0.481 5.646 27288 Z= 0.260 Chirality : 0.033 0.121 3096 Planarity : 0.004 0.033 3300 Dihedral : 6.657 56.934 2654 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.78 % Allowed : 10.56 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.33 (0.17), residues: 2364 helix: 1.88 (0.12), residues: 1668 sheet: 2.08 (0.49), residues: 132 loop : -2.66 (0.21), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 45 HIS 0.003 0.001 HIS B 194 PHE 0.012 0.001 PHE F 229 TYR 0.013 0.001 TYR E 230 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 457 time to evaluate : 2.273 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 13 LYS cc_start: 0.9015 (tttt) cc_final: 0.8583 (ttmm) REVERT: A 17 TYR cc_start: 0.8700 (m-80) cc_final: 0.8345 (m-10) REVERT: A 100 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8029 (mtm) REVERT: A 230 TYR cc_start: 0.7770 (t80) cc_final: 0.7498 (t80) REVERT: G 13 LYS cc_start: 0.8929 (tttt) cc_final: 0.8595 (ttmm) REVERT: G 17 TYR cc_start: 0.8773 (m-80) cc_final: 0.8493 (m-80) REVERT: G 47 ASP cc_start: 0.8962 (p0) cc_final: 0.8695 (p0) REVERT: G 55 ASN cc_start: 0.8879 (t0) cc_final: 0.8570 (t0) REVERT: G 101 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7599 (mtp-110) REVERT: B 13 LYS cc_start: 0.8887 (tttt) cc_final: 0.8589 (ttmm) REVERT: B 47 ASP cc_start: 0.8900 (p0) cc_final: 0.8600 (p0) REVERT: B 189 ARG cc_start: 0.7680 (ttm170) cc_final: 0.7474 (ttm170) REVERT: C 13 LYS cc_start: 0.8949 (tttt) cc_final: 0.8564 (ttmm) REVERT: C 42 GLU cc_start: 0.8034 (tt0) cc_final: 0.7489 (tm-30) REVERT: C 47 ASP cc_start: 0.8863 (p0) cc_final: 0.8568 (p0) REVERT: C 67 ASP cc_start: 0.8762 (t0) cc_final: 0.8525 (t0) REVERT: C 189 ARG cc_start: 0.7331 (ttt180) cc_final: 0.7059 (ttt180) REVERT: D 13 LYS cc_start: 0.9006 (tttt) cc_final: 0.8685 (ttmm) REVERT: D 227 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8271 (mm-30) REVERT: E 13 LYS cc_start: 0.8880 (tttt) cc_final: 0.8646 (ttmm) REVERT: E 42 GLU cc_start: 0.7993 (tt0) cc_final: 0.7584 (tm-30) REVERT: E 47 ASP cc_start: 0.8908 (p0) cc_final: 0.8582 (p0) REVERT: E 189 ARG cc_start: 0.8023 (ttt180) cc_final: 0.7690 (ttm170) REVERT: F 13 LYS cc_start: 0.8898 (tttt) cc_final: 0.8582 (ttmm) REVERT: F 17 TYR cc_start: 0.8765 (m-80) cc_final: 0.8457 (m-80) REVERT: F 55 ASN cc_start: 0.8873 (t0) cc_final: 0.8550 (t0) REVERT: H 17 TYR cc_start: 0.8710 (m-80) cc_final: 0.8367 (m-10) REVERT: H 227 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8295 (mm-30) REVERT: H 230 TYR cc_start: 0.7769 (t80) cc_final: 0.7521 (t80) REVERT: I 13 LYS cc_start: 0.8785 (tttt) cc_final: 0.8476 (ttmm) REVERT: J 13 LYS cc_start: 0.8901 (tttt) cc_final: 0.8563 (ttmm) REVERT: J 17 TYR cc_start: 0.8690 (m-80) cc_final: 0.8422 (m-80) REVERT: J 35 LEU cc_start: 0.8786 (tp) cc_final: 0.8581 (tt) REVERT: J 55 ASN cc_start: 0.8854 (t0) cc_final: 0.8460 (t0) REVERT: J 227 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8100 (mm-30) REVERT: K 13 LYS cc_start: 0.8993 (tttt) cc_final: 0.8656 (ttmm) REVERT: K 17 TYR cc_start: 0.8643 (m-80) cc_final: 0.8436 (m-80) REVERT: K 42 GLU cc_start: 0.7984 (tt0) cc_final: 0.7413 (tm-30) REVERT: K 47 ASP cc_start: 0.9002 (p0) cc_final: 0.8761 (p0) REVERT: K 100 MET cc_start: 0.8502 (mtp) cc_final: 0.8226 (mtm) REVERT: L 13 LYS cc_start: 0.8923 (tttt) cc_final: 0.8672 (ttmm) REVERT: L 17 TYR cc_start: 0.8661 (m-80) cc_final: 0.8417 (m-80) REVERT: L 47 ASP cc_start: 0.8954 (p0) cc_final: 0.8726 (p0) REVERT: L 101 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7797 (mtp-110) REVERT: L 189 ARG cc_start: 0.7897 (ttt180) cc_final: 0.7621 (ttm170) outliers start: 60 outliers final: 20 residues processed: 483 average time/residue: 0.3290 time to fit residues: 234.4524 Evaluate side-chains 459 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 438 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 7 LEU Chi-restraints excluded: chain L residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 181 optimal weight: 10.0000 chunk 148 optimal weight: 0.0670 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 216 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN I 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20148 Z= 0.148 Angle : 0.436 5.347 27288 Z= 0.233 Chirality : 0.033 0.127 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.680 54.942 2596 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.57 % Allowed : 13.98 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.35 (0.17), residues: 2364 helix: 2.68 (0.12), residues: 1668 sheet: 2.18 (0.48), residues: 132 loop : -2.33 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 45 HIS 0.001 0.000 HIS H 194 PHE 0.011 0.001 PHE J 169 TYR 0.020 0.001 TYR B 230 ARG 0.003 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 479 time to evaluate : 2.170 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: symmetry clash REVERT: A 13 LYS cc_start: 0.9027 (tttt) cc_final: 0.8615 (ttmm) REVERT: A 17 TYR cc_start: 0.8748 (m-80) cc_final: 0.8300 (m-10) REVERT: A 42 GLU cc_start: 0.7942 (tt0) cc_final: 0.7292 (tm-30) REVERT: A 67 ASP cc_start: 0.8497 (t0) cc_final: 0.8131 (t0) REVERT: A 100 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.8058 (mtm) REVERT: A 230 TYR cc_start: 0.7685 (t80) cc_final: 0.7418 (t80) REVERT: G 13 LYS cc_start: 0.8947 (tttt) cc_final: 0.8594 (ttmm) REVERT: G 17 TYR cc_start: 0.8785 (m-80) cc_final: 0.8493 (m-80) REVERT: G 42 GLU cc_start: 0.8103 (tt0) cc_final: 0.7376 (tm-30) REVERT: G 47 ASP cc_start: 0.8966 (p0) cc_final: 0.8670 (p0) REVERT: G 55 ASN cc_start: 0.8846 (t0) cc_final: 0.8547 (t0) REVERT: B 13 LYS cc_start: 0.8874 (tttt) cc_final: 0.8561 (ttmm) REVERT: B 47 ASP cc_start: 0.8880 (p0) cc_final: 0.8594 (p0) REVERT: B 67 ASP cc_start: 0.8713 (t0) cc_final: 0.8460 (t0) REVERT: B 104 GLU cc_start: 0.8937 (tt0) cc_final: 0.8726 (tp30) REVERT: C 13 LYS cc_start: 0.8958 (tttt) cc_final: 0.8614 (ttmm) REVERT: C 35 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8315 (tp) REVERT: C 42 GLU cc_start: 0.8042 (tt0) cc_final: 0.7518 (tm-30) REVERT: C 47 ASP cc_start: 0.8914 (p0) cc_final: 0.8595 (p0) REVERT: C 55 ASN cc_start: 0.8890 (t0) cc_final: 0.8679 (t0) REVERT: C 67 ASP cc_start: 0.8740 (t0) cc_final: 0.8514 (t0) REVERT: C 189 ARG cc_start: 0.7601 (ttt180) cc_final: 0.7220 (ttt180) REVERT: D 13 LYS cc_start: 0.8979 (tttt) cc_final: 0.8637 (ttmm) REVERT: D 17 TYR cc_start: 0.8692 (m-80) cc_final: 0.8488 (m-80) REVERT: D 67 ASP cc_start: 0.8415 (t0) cc_final: 0.7957 (t0) REVERT: D 106 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6459 (mp) REVERT: D 227 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8267 (mm-30) REVERT: E 13 LYS cc_start: 0.8959 (tttt) cc_final: 0.8574 (ttmm) REVERT: E 42 GLU cc_start: 0.7992 (tt0) cc_final: 0.7643 (tm-30) REVERT: E 47 ASP cc_start: 0.8888 (p0) cc_final: 0.8544 (p0) REVERT: E 67 ASP cc_start: 0.8604 (t0) cc_final: 0.8393 (t0) REVERT: E 101 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7823 (mtp-110) REVERT: F 13 LYS cc_start: 0.8899 (tttt) cc_final: 0.8583 (ttmm) REVERT: F 17 TYR cc_start: 0.8762 (m-80) cc_final: 0.8401 (m-80) REVERT: F 42 GLU cc_start: 0.8100 (tt0) cc_final: 0.7487 (tm-30) REVERT: F 47 ASP cc_start: 0.8655 (p0) cc_final: 0.8452 (p0) REVERT: F 55 ASN cc_start: 0.8857 (t0) cc_final: 0.8526 (t0) REVERT: H 13 LYS cc_start: 0.8985 (tttt) cc_final: 0.8634 (ttmm) REVERT: H 17 TYR cc_start: 0.8740 (m-80) cc_final: 0.8440 (m-10) REVERT: H 42 GLU cc_start: 0.7908 (tt0) cc_final: 0.7362 (tm-30) REVERT: H 67 ASP cc_start: 0.8506 (t0) cc_final: 0.8275 (t0) REVERT: H 230 TYR cc_start: 0.7650 (t80) cc_final: 0.7389 (t80) REVERT: I 13 LYS cc_start: 0.8884 (tttt) cc_final: 0.8579 (ttmm) REVERT: I 62 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7357 (mt-10) REVERT: I 67 ASP cc_start: 0.8594 (t0) cc_final: 0.8352 (t0) REVERT: J 13 LYS cc_start: 0.8890 (tttt) cc_final: 0.8592 (ttmm) REVERT: J 17 TYR cc_start: 0.8725 (m-80) cc_final: 0.8354 (m-80) REVERT: J 42 GLU cc_start: 0.8014 (tt0) cc_final: 0.7475 (tm-30) REVERT: J 55 ASN cc_start: 0.8820 (t0) cc_final: 0.8471 (t0) REVERT: J 227 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8012 (mm-30) REVERT: K 13 LYS cc_start: 0.8984 (tttt) cc_final: 0.8636 (ttmm) REVERT: K 42 GLU cc_start: 0.8014 (tt0) cc_final: 0.7377 (tm-30) REVERT: K 47 ASP cc_start: 0.8986 (p0) cc_final: 0.8732 (p0) REVERT: K 100 MET cc_start: 0.8414 (mtp) cc_final: 0.8153 (mtm) REVERT: K 212 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7757 (t80) REVERT: L 13 LYS cc_start: 0.8938 (tttt) cc_final: 0.8602 (ttmm) REVERT: L 17 TYR cc_start: 0.8646 (m-80) cc_final: 0.8415 (m-80) REVERT: L 42 GLU cc_start: 0.7975 (tt0) cc_final: 0.7430 (tm-30) REVERT: L 47 ASP cc_start: 0.8920 (p0) cc_final: 0.8594 (p0) REVERT: L 67 ASP cc_start: 0.8609 (t0) cc_final: 0.8375 (t0) REVERT: L 101 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7797 (mtp-110) REVERT: L 189 ARG cc_start: 0.7998 (ttt180) cc_final: 0.7525 (ttm170) outliers start: 34 outliers final: 9 residues processed: 491 average time/residue: 0.3202 time to fit residues: 233.0404 Evaluate side-chains 456 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 443 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 212 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.1980 chunk 164 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 146 optimal weight: 0.8980 chunk 219 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 114 optimal weight: 0.0470 chunk 207 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20148 Z= 0.129 Angle : 0.418 5.518 27288 Z= 0.225 Chirality : 0.033 0.132 3096 Planarity : 0.003 0.030 3300 Dihedral : 3.191 13.479 2592 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.06 % Allowed : 16.16 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.69 (0.17), residues: 2364 helix: 2.94 (0.12), residues: 1668 sheet: 2.16 (0.46), residues: 132 loop : -2.23 (0.22), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 45 HIS 0.001 0.000 HIS I 95 PHE 0.013 0.001 PHE L 169 TYR 0.007 0.001 TYR G 66 ARG 0.003 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 475 time to evaluate : 2.143 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: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9062 (tttt) cc_final: 0.8672 (ttmm) REVERT: A 17 TYR cc_start: 0.8707 (m-80) cc_final: 0.8400 (m-10) REVERT: A 42 GLU cc_start: 0.7833 (tt0) cc_final: 0.7254 (tm-30) REVERT: A 67 ASP cc_start: 0.8462 (t0) cc_final: 0.8081 (t0) REVERT: A 100 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8044 (mtm) REVERT: G 13 LYS cc_start: 0.8944 (tttt) cc_final: 0.8581 (ttmm) REVERT: G 17 TYR cc_start: 0.8748 (m-80) cc_final: 0.8548 (m-80) REVERT: G 42 GLU cc_start: 0.8085 (tt0) cc_final: 0.7380 (tm-30) REVERT: G 47 ASP cc_start: 0.8975 (p0) cc_final: 0.8693 (p0) REVERT: G 55 ASN cc_start: 0.8784 (t0) cc_final: 0.8444 (t0) REVERT: B 13 LYS cc_start: 0.8881 (tttt) cc_final: 0.8584 (ttmm) REVERT: B 42 GLU cc_start: 0.8006 (tt0) cc_final: 0.7492 (tm-30) REVERT: B 47 ASP cc_start: 0.8876 (p0) cc_final: 0.8561 (p0) REVERT: B 230 TYR cc_start: 0.7981 (t80) cc_final: 0.7643 (t80) REVERT: C 13 LYS cc_start: 0.8947 (tttt) cc_final: 0.8649 (ttmm) REVERT: C 42 GLU cc_start: 0.8016 (tt0) cc_final: 0.7516 (tm-30) REVERT: C 47 ASP cc_start: 0.8910 (p0) cc_final: 0.8576 (p0) REVERT: C 55 ASN cc_start: 0.8841 (t0) cc_final: 0.8622 (t0) REVERT: C 67 ASP cc_start: 0.8696 (t0) cc_final: 0.8496 (t0) REVERT: C 189 ARG cc_start: 0.7453 (ttt180) cc_final: 0.7025 (ttt180) REVERT: D 13 LYS cc_start: 0.8973 (tttt) cc_final: 0.8621 (ttmm) REVERT: D 42 GLU cc_start: 0.7866 (tt0) cc_final: 0.7441 (tm-30) REVERT: D 67 ASP cc_start: 0.8407 (t0) cc_final: 0.8081 (t0) REVERT: D 106 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6388 (mp) REVERT: D 227 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8279 (mm-30) REVERT: E 13 LYS cc_start: 0.8958 (tttt) cc_final: 0.8601 (ttmm) REVERT: E 42 GLU cc_start: 0.7904 (tt0) cc_final: 0.7613 (tm-30) REVERT: E 47 ASP cc_start: 0.8892 (p0) cc_final: 0.8537 (p0) REVERT: E 101 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7728 (mtp-110) REVERT: F 13 LYS cc_start: 0.8886 (tttt) cc_final: 0.8580 (ttmm) REVERT: F 17 TYR cc_start: 0.8702 (m-80) cc_final: 0.8482 (m-80) REVERT: F 42 GLU cc_start: 0.8016 (tt0) cc_final: 0.7452 (tm-30) REVERT: F 47 ASP cc_start: 0.8670 (p0) cc_final: 0.8401 (p0) REVERT: F 55 ASN cc_start: 0.8813 (t0) cc_final: 0.8472 (t0) REVERT: H 13 LYS cc_start: 0.8984 (tttt) cc_final: 0.8630 (ttmm) REVERT: H 17 TYR cc_start: 0.8758 (m-80) cc_final: 0.8555 (m-80) REVERT: H 42 GLU cc_start: 0.7895 (tt0) cc_final: 0.7379 (tm-30) REVERT: H 67 ASP cc_start: 0.8473 (t0) cc_final: 0.8113 (t0) REVERT: H 230 TYR cc_start: 0.7568 (t80) cc_final: 0.7341 (t80) REVERT: I 13 LYS cc_start: 0.8897 (tttt) cc_final: 0.8513 (ttmm) REVERT: I 67 ASP cc_start: 0.8567 (t0) cc_final: 0.8260 (t0) REVERT: I 101 ARG cc_start: 0.7892 (mtp85) cc_final: 0.7597 (mtp-110) REVERT: J 13 LYS cc_start: 0.8887 (tttt) cc_final: 0.8601 (ttmm) REVERT: J 42 GLU cc_start: 0.8066 (tt0) cc_final: 0.7490 (tm-30) REVERT: J 55 ASN cc_start: 0.8716 (t0) cc_final: 0.8354 (t0) REVERT: J 227 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8044 (mm-30) REVERT: K 13 LYS cc_start: 0.8974 (tttt) cc_final: 0.8644 (ttmm) REVERT: K 42 GLU cc_start: 0.8066 (tt0) cc_final: 0.7381 (tm-30) REVERT: K 47 ASP cc_start: 0.8992 (p0) cc_final: 0.8731 (p0) REVERT: K 227 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8324 (mm-30) REVERT: L 13 LYS cc_start: 0.8944 (tttt) cc_final: 0.8602 (ttmm) REVERT: L 42 GLU cc_start: 0.7925 (tt0) cc_final: 0.7561 (tm-30) REVERT: L 47 ASP cc_start: 0.8912 (p0) cc_final: 0.8648 (p0) REVERT: L 67 ASP cc_start: 0.8561 (t0) cc_final: 0.8352 (t0) REVERT: L 101 ARG cc_start: 0.7958 (mtp85) cc_final: 0.7649 (mtp-110) REVERT: L 189 ARG cc_start: 0.7840 (ttt180) cc_final: 0.7465 (ttm170) outliers start: 23 outliers final: 16 residues processed: 481 average time/residue: 0.3320 time to fit residues: 234.8751 Evaluate side-chains 475 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 457 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 81 GLN C 81 GLN E 81 GLN F 81 GLN J 81 GLN L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20148 Z= 0.244 Angle : 0.485 5.421 27288 Z= 0.261 Chirality : 0.035 0.134 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.246 12.234 2592 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.22 % Allowed : 15.09 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.81 (0.17), residues: 2364 helix: 2.93 (0.12), residues: 1680 sheet: 2.37 (0.47), residues: 132 loop : -1.99 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 25 HIS 0.002 0.000 HIS H 194 PHE 0.013 0.001 PHE A 32 TYR 0.023 0.001 TYR I 230 ARG 0.002 0.000 ARG I 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 437 time to evaluate : 2.188 Fit side-chains REVERT: A 17 TYR cc_start: 0.8735 (m-80) cc_final: 0.8440 (m-10) REVERT: A 42 GLU cc_start: 0.7952 (tt0) cc_final: 0.7293 (tm-30) REVERT: A 67 ASP cc_start: 0.8514 (t0) cc_final: 0.8200 (t0) REVERT: G 13 LYS cc_start: 0.8957 (tttt) cc_final: 0.8656 (ttmm) REVERT: G 17 TYR cc_start: 0.8780 (m-80) cc_final: 0.8555 (m-80) REVERT: G 42 GLU cc_start: 0.8079 (tt0) cc_final: 0.7395 (tm-30) REVERT: G 47 ASP cc_start: 0.8988 (p0) cc_final: 0.8697 (p0) REVERT: B 13 LYS cc_start: 0.8852 (tttt) cc_final: 0.8546 (ttmm) REVERT: B 42 GLU cc_start: 0.8041 (tt0) cc_final: 0.7431 (tm-30) REVERT: B 47 ASP cc_start: 0.8917 (p0) cc_final: 0.8571 (p0) REVERT: B 62 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7279 (mt-10) REVERT: C 13 LYS cc_start: 0.8934 (tttt) cc_final: 0.8615 (ttmm) REVERT: C 35 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8485 (tp) REVERT: C 42 GLU cc_start: 0.8132 (tt0) cc_final: 0.7623 (tm-30) REVERT: C 47 ASP cc_start: 0.8947 (p0) cc_final: 0.8632 (p0) REVERT: C 189 ARG cc_start: 0.7920 (ttt180) cc_final: 0.7696 (ttt180) REVERT: D 13 LYS cc_start: 0.8964 (tttt) cc_final: 0.8603 (ttmm) REVERT: D 35 LEU cc_start: 0.8841 (tp) cc_final: 0.8601 (tt) REVERT: D 42 GLU cc_start: 0.7955 (tt0) cc_final: 0.7355 (tm-30) REVERT: D 55 ASN cc_start: 0.8859 (t0) cc_final: 0.8648 (t0) REVERT: D 67 ASP cc_start: 0.8447 (t0) cc_final: 0.8073 (t0) REVERT: D 106 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6018 (mp) REVERT: D 227 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8238 (mm-30) REVERT: E 13 LYS cc_start: 0.8922 (tttt) cc_final: 0.8552 (ttmm) REVERT: E 39 THR cc_start: 0.8929 (m) cc_final: 0.8712 (m) REVERT: E 42 GLU cc_start: 0.8010 (tt0) cc_final: 0.7634 (tm-30) REVERT: E 47 ASP cc_start: 0.8915 (p0) cc_final: 0.8567 (p0) REVERT: E 67 ASP cc_start: 0.8665 (t0) cc_final: 0.8443 (t0) REVERT: E 101 ARG cc_start: 0.7997 (mtp85) cc_final: 0.7726 (mtp-110) REVERT: F 13 LYS cc_start: 0.8895 (tttt) cc_final: 0.8578 (ttmm) REVERT: F 17 TYR cc_start: 0.8735 (m-80) cc_final: 0.8518 (m-80) REVERT: F 42 GLU cc_start: 0.8092 (tt0) cc_final: 0.7484 (tm-30) REVERT: F 47 ASP cc_start: 0.8739 (p0) cc_final: 0.8441 (p0) REVERT: H 13 LYS cc_start: 0.8999 (tttt) cc_final: 0.8624 (ttmm) REVERT: H 17 TYR cc_start: 0.8737 (m-80) cc_final: 0.8527 (m-80) REVERT: H 42 GLU cc_start: 0.7933 (tt0) cc_final: 0.7358 (tm-30) REVERT: H 67 ASP cc_start: 0.8543 (t0) cc_final: 0.8245 (t0) REVERT: H 106 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5866 (mp) REVERT: H 227 GLU cc_start: 0.8502 (tp30) cc_final: 0.8288 (mm-30) REVERT: I 13 LYS cc_start: 0.8899 (tttt) cc_final: 0.8565 (ttmm) REVERT: I 17 TYR cc_start: 0.8682 (m-80) cc_final: 0.8465 (m-80) REVERT: I 62 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7425 (mt-10) REVERT: I 67 ASP cc_start: 0.8642 (t0) cc_final: 0.8383 (t0) REVERT: I 101 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7561 (mtp-110) REVERT: J 13 LYS cc_start: 0.8884 (tttt) cc_final: 0.8581 (ttmm) REVERT: J 42 GLU cc_start: 0.8121 (tt0) cc_final: 0.7508 (tm-30) REVERT: J 47 ASP cc_start: 0.8567 (p0) cc_final: 0.8102 (p0) REVERT: J 55 ASN cc_start: 0.8961 (t0) cc_final: 0.8562 (t0) REVERT: J 67 ASP cc_start: 0.8629 (t0) cc_final: 0.8335 (t0) REVERT: J 227 GLU cc_start: 0.8639 (mm-30) cc_final: 0.7958 (mm-30) REVERT: K 13 LYS cc_start: 0.8993 (tttt) cc_final: 0.8669 (ttmm) REVERT: K 42 GLU cc_start: 0.8083 (tt0) cc_final: 0.7283 (tm-30) REVERT: K 47 ASP cc_start: 0.9012 (p0) cc_final: 0.8781 (p0) REVERT: K 67 ASP cc_start: 0.8465 (t0) cc_final: 0.8109 (t0) REVERT: K 212 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7931 (t80) REVERT: L 13 LYS cc_start: 0.8886 (tttt) cc_final: 0.8512 (ttmm) REVERT: L 42 GLU cc_start: 0.7942 (tt0) cc_final: 0.7551 (tm-30) REVERT: L 47 ASP cc_start: 0.8916 (p0) cc_final: 0.8602 (p0) REVERT: L 67 ASP cc_start: 0.8690 (t0) cc_final: 0.8456 (t0) REVERT: L 101 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7717 (mtp-110) REVERT: L 103 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8166 (tm-30) REVERT: L 189 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7630 (ttm170) outliers start: 48 outliers final: 30 residues processed: 462 average time/residue: 0.3337 time to fit residues: 226.6023 Evaluate side-chains 467 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 433 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 43 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 107 ASN Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.7980 chunk 208 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 76 optimal weight: 0.0980 chunk 121 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 55 ASN F 81 GLN H 55 ASN K 55 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20148 Z= 0.133 Angle : 0.422 5.383 27288 Z= 0.225 Chirality : 0.033 0.148 3096 Planarity : 0.003 0.030 3300 Dihedral : 3.114 13.416 2592 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.11 % Allowed : 17.08 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.17), residues: 2364 helix: 3.13 (0.12), residues: 1680 sheet: 2.30 (0.46), residues: 132 loop : -1.95 (0.23), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 45 HIS 0.001 0.000 HIS H 194 PHE 0.010 0.001 PHE A 32 TYR 0.017 0.001 TYR H 230 ARG 0.002 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 466 time to evaluate : 2.197 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: A 17 TYR cc_start: 0.8712 (m-80) cc_final: 0.8454 (m-10) REVERT: A 42 GLU cc_start: 0.7883 (tt0) cc_final: 0.7241 (tm-30) REVERT: A 67 ASP cc_start: 0.8460 (t0) cc_final: 0.8122 (t0) REVERT: A 103 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8271 (tm-30) REVERT: G 13 LYS cc_start: 0.8992 (tttt) cc_final: 0.8687 (ttmm) REVERT: G 42 GLU cc_start: 0.8066 (tt0) cc_final: 0.7454 (tm-30) REVERT: G 47 ASP cc_start: 0.8974 (p0) cc_final: 0.8676 (p0) REVERT: G 55 ASN cc_start: 0.8791 (t0) cc_final: 0.8462 (t0) REVERT: B 13 LYS cc_start: 0.8882 (tttt) cc_final: 0.8553 (ttmm) REVERT: B 42 GLU cc_start: 0.7937 (tt0) cc_final: 0.7416 (tm-30) REVERT: B 47 ASP cc_start: 0.8903 (p0) cc_final: 0.8668 (p0) REVERT: C 13 LYS cc_start: 0.8929 (tttt) cc_final: 0.8618 (ttmm) REVERT: C 42 GLU cc_start: 0.8078 (tt0) cc_final: 0.7611 (tm-30) REVERT: C 47 ASP cc_start: 0.8906 (p0) cc_final: 0.8575 (p0) REVERT: C 55 ASN cc_start: 0.8834 (t0) cc_final: 0.8551 (t0) REVERT: D 13 LYS cc_start: 0.8954 (tttt) cc_final: 0.8601 (ttmm) REVERT: D 42 GLU cc_start: 0.7965 (tt0) cc_final: 0.7442 (tm-30) REVERT: D 67 ASP cc_start: 0.8380 (t0) cc_final: 0.7980 (t0) REVERT: D 106 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6223 (mp) REVERT: D 227 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8303 (mm-30) REVERT: E 13 LYS cc_start: 0.8928 (tttt) cc_final: 0.8539 (ttmm) REVERT: E 39 THR cc_start: 0.8795 (m) cc_final: 0.8565 (m) REVERT: E 42 GLU cc_start: 0.7900 (tt0) cc_final: 0.7589 (tm-30) REVERT: E 47 ASP cc_start: 0.8900 (p0) cc_final: 0.8622 (p0) REVERT: E 67 ASP cc_start: 0.8613 (t0) cc_final: 0.8228 (t0) REVERT: E 101 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7699 (mtp-110) REVERT: E 189 ARG cc_start: 0.7912 (ttt180) cc_final: 0.7581 (ttt180) REVERT: F 13 LYS cc_start: 0.8907 (tttt) cc_final: 0.8630 (ttmm) REVERT: F 42 GLU cc_start: 0.7988 (tt0) cc_final: 0.7443 (tm-30) REVERT: F 47 ASP cc_start: 0.8693 (p0) cc_final: 0.8369 (p0) REVERT: F 55 ASN cc_start: 0.8764 (t0) cc_final: 0.8439 (t0) REVERT: H 13 LYS cc_start: 0.8998 (tttt) cc_final: 0.8644 (ttmm) REVERT: H 42 GLU cc_start: 0.7936 (tt0) cc_final: 0.7284 (tm-30) REVERT: H 67 ASP cc_start: 0.8498 (t0) cc_final: 0.8194 (t0) REVERT: H 106 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5919 (mp) REVERT: I 13 LYS cc_start: 0.8918 (tttt) cc_final: 0.8583 (ttmm) REVERT: I 17 TYR cc_start: 0.8654 (m-80) cc_final: 0.8450 (m-80) REVERT: I 42 GLU cc_start: 0.8046 (tt0) cc_final: 0.7481 (tm-30) REVERT: I 67 ASP cc_start: 0.8531 (t0) cc_final: 0.8237 (t0) REVERT: I 101 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7576 (mtp-110) REVERT: J 13 LYS cc_start: 0.8877 (tttt) cc_final: 0.8594 (ttmm) REVERT: J 42 GLU cc_start: 0.7986 (tt0) cc_final: 0.7457 (tm-30) REVERT: J 47 ASP cc_start: 0.8594 (p0) cc_final: 0.8328 (p0) REVERT: J 55 ASN cc_start: 0.8800 (t0) cc_final: 0.8443 (t0) REVERT: J 66 TYR cc_start: 0.8713 (t80) cc_final: 0.8497 (t80) REVERT: K 13 LYS cc_start: 0.9000 (tttt) cc_final: 0.8698 (ttmm) REVERT: K 42 GLU cc_start: 0.7893 (tt0) cc_final: 0.7130 (tm-30) REVERT: K 47 ASP cc_start: 0.9047 (p0) cc_final: 0.8826 (p0) REVERT: K 67 ASP cc_start: 0.8442 (t0) cc_final: 0.8060 (t0) REVERT: K 212 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7790 (t80) REVERT: L 13 LYS cc_start: 0.8888 (tttt) cc_final: 0.8545 (ttmm) REVERT: L 42 GLU cc_start: 0.7913 (tt0) cc_final: 0.7566 (tm-30) REVERT: L 47 ASP cc_start: 0.8910 (p0) cc_final: 0.8627 (p0) REVERT: L 67 ASP cc_start: 0.8649 (t0) cc_final: 0.8449 (t0) REVERT: L 101 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7733 (mtp-110) REVERT: L 189 ARG cc_start: 0.7832 (ttt180) cc_final: 0.7321 (ttm170) outliers start: 24 outliers final: 18 residues processed: 472 average time/residue: 0.3365 time to fit residues: 233.1603 Evaluate side-chains 476 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 455 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 132 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN H 55 ASN K 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20148 Z= 0.220 Angle : 0.467 5.431 27288 Z= 0.250 Chirality : 0.034 0.147 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.118 12.425 2592 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.81 % Allowed : 16.94 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.17), residues: 2364 helix: 3.14 (0.12), residues: 1680 sheet: 2.37 (0.46), residues: 132 loop : -1.87 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 25 HIS 0.002 0.000 HIS H 194 PHE 0.013 0.001 PHE B 169 TYR 0.009 0.001 TYR G 66 ARG 0.002 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 447 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9047 (tttt) cc_final: 0.8634 (ttmm) REVERT: A 17 TYR cc_start: 0.8721 (m-80) cc_final: 0.8496 (m-80) REVERT: A 42 GLU cc_start: 0.7999 (tt0) cc_final: 0.7155 (tm-30) REVERT: A 67 ASP cc_start: 0.8565 (t0) cc_final: 0.8265 (t0) REVERT: G 13 LYS cc_start: 0.8984 (tttt) cc_final: 0.8681 (ttmm) REVERT: G 42 GLU cc_start: 0.8071 (tt0) cc_final: 0.7448 (tm-30) REVERT: G 47 ASP cc_start: 0.8984 (p0) cc_final: 0.8678 (p0) REVERT: B 13 LYS cc_start: 0.8876 (tttt) cc_final: 0.8542 (ttmm) REVERT: B 42 GLU cc_start: 0.7958 (tt0) cc_final: 0.7421 (tm-30) REVERT: B 47 ASP cc_start: 0.8925 (p0) cc_final: 0.8696 (p0) REVERT: C 13 LYS cc_start: 0.8929 (tttt) cc_final: 0.8625 (ttmm) REVERT: C 35 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8530 (tp) REVERT: C 42 GLU cc_start: 0.8116 (tt0) cc_final: 0.7607 (tm-30) REVERT: C 47 ASP cc_start: 0.8927 (p0) cc_final: 0.8606 (p0) REVERT: D 13 LYS cc_start: 0.8963 (tttt) cc_final: 0.8602 (ttmm) REVERT: D 35 LEU cc_start: 0.8823 (tp) cc_final: 0.8593 (tt) REVERT: D 42 GLU cc_start: 0.7843 (tt0) cc_final: 0.7249 (tm-30) REVERT: D 67 ASP cc_start: 0.8452 (t0) cc_final: 0.8087 (t0) REVERT: D 106 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5832 (mp) REVERT: D 227 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8223 (mm-30) REVERT: E 13 LYS cc_start: 0.8858 (tttt) cc_final: 0.8482 (ttmm) REVERT: E 39 THR cc_start: 0.8847 (m) cc_final: 0.8617 (m) REVERT: E 42 GLU cc_start: 0.7915 (tt0) cc_final: 0.7593 (tm-30) REVERT: E 47 ASP cc_start: 0.8910 (p0) cc_final: 0.8640 (p0) REVERT: E 67 ASP cc_start: 0.8683 (t0) cc_final: 0.8400 (t0) REVERT: E 101 ARG cc_start: 0.7978 (mtp85) cc_final: 0.7710 (mtp-110) REVERT: F 13 LYS cc_start: 0.8909 (tttt) cc_final: 0.8616 (ttmm) REVERT: F 42 GLU cc_start: 0.8008 (tt0) cc_final: 0.7473 (tm-30) REVERT: F 47 ASP cc_start: 0.8764 (p0) cc_final: 0.8433 (p0) REVERT: H 13 LYS cc_start: 0.9001 (tttt) cc_final: 0.8632 (ttmm) REVERT: H 42 GLU cc_start: 0.7935 (tt0) cc_final: 0.7253 (tm-30) REVERT: H 67 ASP cc_start: 0.8573 (t0) cc_final: 0.8238 (t0) REVERT: H 106 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5689 (mp) REVERT: I 13 LYS cc_start: 0.8875 (tttt) cc_final: 0.8529 (ttmm) REVERT: I 17 TYR cc_start: 0.8689 (m-80) cc_final: 0.8484 (m-80) REVERT: I 42 GLU cc_start: 0.8042 (tt0) cc_final: 0.7425 (tm-30) REVERT: I 67 ASP cc_start: 0.8599 (t0) cc_final: 0.8301 (t0) REVERT: I 101 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7544 (mtp-110) REVERT: J 13 LYS cc_start: 0.8901 (tttt) cc_final: 0.8619 (ttmm) REVERT: J 42 GLU cc_start: 0.7968 (tt0) cc_final: 0.7436 (tm-30) REVERT: J 47 ASP cc_start: 0.8649 (p0) cc_final: 0.8361 (p0) REVERT: J 55 ASN cc_start: 0.8944 (t0) cc_final: 0.8565 (t0) REVERT: J 67 ASP cc_start: 0.8605 (t0) cc_final: 0.8225 (t0) REVERT: K 13 LYS cc_start: 0.8984 (tttt) cc_final: 0.8671 (ttmm) REVERT: K 42 GLU cc_start: 0.7924 (tt0) cc_final: 0.7159 (tm-30) REVERT: K 47 ASP cc_start: 0.9049 (p0) cc_final: 0.8840 (p0) REVERT: K 67 ASP cc_start: 0.8464 (t0) cc_final: 0.8178 (t0) REVERT: K 212 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7869 (t80) REVERT: L 13 LYS cc_start: 0.8881 (tttt) cc_final: 0.8535 (ttmm) REVERT: L 42 GLU cc_start: 0.7931 (tt0) cc_final: 0.7562 (tm-30) REVERT: L 47 ASP cc_start: 0.8925 (p0) cc_final: 0.8659 (p0) REVERT: L 67 ASP cc_start: 0.8699 (t0) cc_final: 0.8472 (t0) REVERT: L 101 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7744 (mtp-110) REVERT: L 189 ARG cc_start: 0.8048 (ttt180) cc_final: 0.7711 (ttt180) outliers start: 39 outliers final: 30 residues processed: 463 average time/residue: 0.3429 time to fit residues: 230.9822 Evaluate side-chains 477 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 443 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 107 ASN Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 147 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 55 ASN D 55 ASN E 224 ASN H 55 ASN K 55 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20148 Z= 0.150 Angle : 0.436 5.495 27288 Z= 0.234 Chirality : 0.033 0.154 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.090 12.062 2592 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.53 % Allowed : 17.45 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.17), residues: 2364 helix: 3.28 (0.12), residues: 1680 sheet: 2.34 (0.47), residues: 132 loop : -1.88 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 45 HIS 0.001 0.000 HIS H 194 PHE 0.011 0.001 PHE B 169 TYR 0.008 0.001 TYR L 17 ARG 0.002 0.000 ARG K 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 465 time to evaluate : 2.140 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 13 LYS cc_start: 0.9044 (tttt) cc_final: 0.8648 (ttmm) REVERT: A 17 TYR cc_start: 0.8714 (m-80) cc_final: 0.8501 (m-80) REVERT: A 42 GLU cc_start: 0.7937 (tt0) cc_final: 0.7078 (tm-30) REVERT: A 67 ASP cc_start: 0.8546 (t0) cc_final: 0.8238 (t0) REVERT: A 103 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8395 (tm-30) REVERT: G 13 LYS cc_start: 0.8955 (tttt) cc_final: 0.8659 (ttmm) REVERT: G 42 GLU cc_start: 0.8047 (tt0) cc_final: 0.7449 (tm-30) REVERT: G 47 ASP cc_start: 0.8971 (p0) cc_final: 0.8670 (p0) REVERT: G 55 ASN cc_start: 0.8825 (t0) cc_final: 0.8479 (t0) REVERT: B 13 LYS cc_start: 0.8873 (tttt) cc_final: 0.8536 (ttmm) REVERT: B 42 GLU cc_start: 0.7939 (tt0) cc_final: 0.7423 (tm-30) REVERT: B 47 ASP cc_start: 0.8914 (p0) cc_final: 0.8652 (p0) REVERT: C 13 LYS cc_start: 0.8933 (tttt) cc_final: 0.8627 (ttmm) REVERT: C 42 GLU cc_start: 0.8035 (tt0) cc_final: 0.7553 (tm-30) REVERT: C 47 ASP cc_start: 0.8934 (p0) cc_final: 0.8616 (p0) REVERT: C 55 ASN cc_start: 0.8860 (t0) cc_final: 0.8545 (t0) REVERT: D 13 LYS cc_start: 0.8988 (tttt) cc_final: 0.8654 (ttmm) REVERT: D 35 LEU cc_start: 0.8778 (tp) cc_final: 0.8562 (tt) REVERT: D 42 GLU cc_start: 0.7852 (tt0) cc_final: 0.7182 (tm-30) REVERT: D 67 ASP cc_start: 0.8413 (t0) cc_final: 0.8046 (t0) REVERT: D 106 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5860 (mp) REVERT: D 227 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8298 (mm-30) REVERT: E 13 LYS cc_start: 0.8849 (tttt) cc_final: 0.8472 (ttmm) REVERT: E 35 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8338 (tt) REVERT: E 39 THR cc_start: 0.8787 (m) cc_final: 0.8513 (m) REVERT: E 42 GLU cc_start: 0.7889 (tt0) cc_final: 0.7597 (tm-30) REVERT: E 47 ASP cc_start: 0.8916 (p0) cc_final: 0.8659 (p0) REVERT: E 67 ASP cc_start: 0.8626 (t0) cc_final: 0.8272 (t0) REVERT: E 101 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7745 (mtp-110) REVERT: E 103 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8384 (mm-30) REVERT: E 189 ARG cc_start: 0.7973 (ttt180) cc_final: 0.7649 (ttt180) REVERT: F 13 LYS cc_start: 0.8906 (tttt) cc_final: 0.8617 (ttmm) REVERT: F 42 GLU cc_start: 0.8022 (tt0) cc_final: 0.7482 (tm-30) REVERT: F 47 ASP cc_start: 0.8752 (p0) cc_final: 0.8410 (p0) REVERT: F 55 ASN cc_start: 0.8872 (t0) cc_final: 0.8502 (t0) REVERT: H 13 LYS cc_start: 0.9022 (tttt) cc_final: 0.8678 (ttmm) REVERT: H 42 GLU cc_start: 0.7936 (tt0) cc_final: 0.7182 (tm-30) REVERT: H 67 ASP cc_start: 0.8521 (t0) cc_final: 0.8173 (t0) REVERT: H 106 LEU cc_start: 0.5955 (OUTLIER) cc_final: 0.5673 (mp) REVERT: I 13 LYS cc_start: 0.8820 (tttt) cc_final: 0.8487 (ttmm) REVERT: I 42 GLU cc_start: 0.8023 (tt0) cc_final: 0.7424 (tm-30) REVERT: I 67 ASP cc_start: 0.8577 (t0) cc_final: 0.8251 (t0) REVERT: I 101 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7535 (mtp-110) REVERT: J 13 LYS cc_start: 0.8936 (tttt) cc_final: 0.8669 (ttmm) REVERT: J 42 GLU cc_start: 0.7977 (tt0) cc_final: 0.7442 (tm-30) REVERT: J 47 ASP cc_start: 0.8660 (p0) cc_final: 0.8360 (p0) REVERT: J 55 ASN cc_start: 0.8898 (t0) cc_final: 0.8527 (t0) REVERT: J 67 ASP cc_start: 0.8598 (t0) cc_final: 0.8230 (t0) REVERT: K 13 LYS cc_start: 0.8978 (tttt) cc_final: 0.8643 (ttmm) REVERT: K 42 GLU cc_start: 0.7904 (tt0) cc_final: 0.7148 (tm-30) REVERT: K 47 ASP cc_start: 0.9051 (p0) cc_final: 0.8805 (p0) REVERT: K 67 ASP cc_start: 0.8436 (t0) cc_final: 0.8129 (t0) REVERT: K 212 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7836 (t80) REVERT: L 13 LYS cc_start: 0.8872 (tttt) cc_final: 0.8523 (ttmm) REVERT: L 39 THR cc_start: 0.8856 (m) cc_final: 0.8610 (m) REVERT: L 42 GLU cc_start: 0.7889 (tt0) cc_final: 0.7560 (tm-30) REVERT: L 47 ASP cc_start: 0.8915 (p0) cc_final: 0.8667 (p0) REVERT: L 101 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7694 (mtp-110) REVERT: L 103 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8114 (tm-30) REVERT: L 189 ARG cc_start: 0.7913 (ttt180) cc_final: 0.7429 (ttm170) outliers start: 33 outliers final: 28 residues processed: 478 average time/residue: 0.3389 time to fit residues: 236.3911 Evaluate side-chains 491 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 459 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 55 ASN Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain K residue 55 ASN Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 194 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.7954 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20148 Z= 0.191 Angle : 0.455 5.411 27288 Z= 0.244 Chirality : 0.034 0.161 3096 Planarity : 0.003 0.028 3300 Dihedral : 3.075 11.808 2592 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.67 % Allowed : 17.69 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.17), residues: 2364 helix: 3.28 (0.12), residues: 1680 sheet: 2.37 (0.47), residues: 132 loop : -1.86 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 25 HIS 0.001 0.000 HIS H 194 PHE 0.012 0.001 PHE B 169 TYR 0.021 0.001 TYR F 230 ARG 0.002 0.000 ARG K 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 462 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9042 (tttt) cc_final: 0.8658 (ttmm) REVERT: A 42 GLU cc_start: 0.7988 (tt0) cc_final: 0.7099 (tm-30) REVERT: A 67 ASP cc_start: 0.8562 (t0) cc_final: 0.8250 (t0) REVERT: G 13 LYS cc_start: 0.8930 (tttt) cc_final: 0.8641 (ttmm) REVERT: G 42 GLU cc_start: 0.8058 (tt0) cc_final: 0.7457 (tm-30) REVERT: G 47 ASP cc_start: 0.8985 (p0) cc_final: 0.8690 (p0) REVERT: G 55 ASN cc_start: 0.8862 (t0) cc_final: 0.8504 (t0) REVERT: B 13 LYS cc_start: 0.8874 (tttt) cc_final: 0.8553 (ttmm) REVERT: B 42 GLU cc_start: 0.7947 (tt0) cc_final: 0.7427 (tm-30) REVERT: B 47 ASP cc_start: 0.8919 (p0) cc_final: 0.8664 (p0) REVERT: B 230 TYR cc_start: 0.7661 (t80) cc_final: 0.7387 (t80) REVERT: C 13 LYS cc_start: 0.8908 (tttt) cc_final: 0.8610 (ttmm) REVERT: C 35 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8515 (tp) REVERT: C 42 GLU cc_start: 0.8146 (tt0) cc_final: 0.7611 (tm-30) REVERT: C 47 ASP cc_start: 0.8941 (p0) cc_final: 0.8652 (p0) REVERT: C 55 ASN cc_start: 0.8886 (t0) cc_final: 0.8572 (t0) REVERT: D 13 LYS cc_start: 0.8992 (tttt) cc_final: 0.8654 (ttmm) REVERT: D 35 LEU cc_start: 0.8788 (tp) cc_final: 0.8557 (tt) REVERT: D 42 GLU cc_start: 0.8059 (tt0) cc_final: 0.7341 (tm-30) REVERT: D 67 ASP cc_start: 0.8439 (t0) cc_final: 0.8066 (t0) REVERT: D 106 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.5935 (mp) REVERT: D 227 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8206 (mm-30) REVERT: E 13 LYS cc_start: 0.8844 (tttt) cc_final: 0.8463 (ttmm) REVERT: E 35 LEU cc_start: 0.8662 (tp) cc_final: 0.8325 (tt) REVERT: E 39 THR cc_start: 0.8800 (m) cc_final: 0.8523 (m) REVERT: E 42 GLU cc_start: 0.7890 (tt0) cc_final: 0.7604 (tm-30) REVERT: E 47 ASP cc_start: 0.8925 (p0) cc_final: 0.8672 (p0) REVERT: E 67 ASP cc_start: 0.8643 (t0) cc_final: 0.8409 (t0) REVERT: E 101 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7730 (mtp-110) REVERT: E 103 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8344 (mm-30) REVERT: F 13 LYS cc_start: 0.8909 (tttt) cc_final: 0.8616 (ttmm) REVERT: F 42 GLU cc_start: 0.8034 (tt0) cc_final: 0.7485 (tm-30) REVERT: F 47 ASP cc_start: 0.8763 (p0) cc_final: 0.8395 (p0) REVERT: F 55 ASN cc_start: 0.8901 (t0) cc_final: 0.8530 (t0) REVERT: H 13 LYS cc_start: 0.9013 (tttt) cc_final: 0.8658 (ttmm) REVERT: H 42 GLU cc_start: 0.7953 (tt0) cc_final: 0.7180 (tm-30) REVERT: H 67 ASP cc_start: 0.8534 (t0) cc_final: 0.8200 (t0) REVERT: H 106 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5690 (mp) REVERT: I 13 LYS cc_start: 0.8803 (tttt) cc_final: 0.8479 (ttmm) REVERT: I 42 GLU cc_start: 0.8030 (tt0) cc_final: 0.7427 (tm-30) REVERT: I 67 ASP cc_start: 0.8596 (t0) cc_final: 0.8280 (t0) REVERT: I 101 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7526 (mtp-110) REVERT: J 13 LYS cc_start: 0.8918 (tttt) cc_final: 0.8647 (ttmm) REVERT: J 42 GLU cc_start: 0.7953 (tt0) cc_final: 0.7439 (tm-30) REVERT: J 47 ASP cc_start: 0.8711 (p0) cc_final: 0.8388 (p0) REVERT: J 55 ASN cc_start: 0.8933 (t0) cc_final: 0.8556 (t0) REVERT: J 67 ASP cc_start: 0.8616 (t0) cc_final: 0.8266 (t0) REVERT: K 13 LYS cc_start: 0.8961 (tttt) cc_final: 0.8618 (ttmm) REVERT: K 42 GLU cc_start: 0.7922 (tt0) cc_final: 0.7155 (tm-30) REVERT: K 47 ASP cc_start: 0.9056 (p0) cc_final: 0.8813 (p0) REVERT: K 67 ASP cc_start: 0.8478 (t0) cc_final: 0.8219 (t0) REVERT: L 13 LYS cc_start: 0.8873 (tttt) cc_final: 0.8541 (ttmm) REVERT: L 39 THR cc_start: 0.8862 (m) cc_final: 0.8616 (m) REVERT: L 42 GLU cc_start: 0.7896 (tt0) cc_final: 0.7563 (tm-30) REVERT: L 47 ASP cc_start: 0.8926 (p0) cc_final: 0.8683 (p0) REVERT: L 101 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7696 (mtp-110) REVERT: L 103 GLU cc_start: 0.8376 (tm-30) cc_final: 0.8145 (tm-30) REVERT: L 189 ARG cc_start: 0.7832 (ttt180) cc_final: 0.7496 (ttm170) outliers start: 36 outliers final: 30 residues processed: 478 average time/residue: 0.3349 time to fit residues: 233.9600 Evaluate side-chains 486 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 453 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 220 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN D 55 ASN L 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20148 Z= 0.179 Angle : 0.456 5.811 27288 Z= 0.244 Chirality : 0.034 0.157 3096 Planarity : 0.003 0.029 3300 Dihedral : 3.066 12.092 2592 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.67 % Allowed : 17.59 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.34 (0.17), residues: 2364 helix: 3.37 (0.12), residues: 1680 sheet: 2.35 (0.47), residues: 132 loop : -1.86 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 45 HIS 0.001 0.000 HIS H 194 PHE 0.011 0.001 PHE B 169 TYR 0.011 0.001 TYR C 66 ARG 0.003 0.000 ARG A 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 454 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 LYS cc_start: 0.9023 (tttt) cc_final: 0.8698 (ttmm) REVERT: A 42 GLU cc_start: 0.7988 (tt0) cc_final: 0.7098 (tm-30) REVERT: A 67 ASP cc_start: 0.8558 (t0) cc_final: 0.8248 (t0) REVERT: A 104 GLU cc_start: 0.9055 (tt0) cc_final: 0.8847 (tp30) REVERT: G 13 LYS cc_start: 0.8922 (tttt) cc_final: 0.8647 (ttmm) REVERT: G 42 GLU cc_start: 0.8089 (tt0) cc_final: 0.7460 (tm-30) REVERT: G 47 ASP cc_start: 0.8972 (p0) cc_final: 0.8667 (p0) REVERT: G 55 ASN cc_start: 0.8867 (t0) cc_final: 0.8505 (t0) REVERT: B 13 LYS cc_start: 0.8868 (tttt) cc_final: 0.8546 (ttmm) REVERT: B 42 GLU cc_start: 0.7937 (tt0) cc_final: 0.7426 (tm-30) REVERT: B 47 ASP cc_start: 0.8929 (p0) cc_final: 0.8675 (p0) REVERT: C 13 LYS cc_start: 0.8910 (tttt) cc_final: 0.8611 (ttmm) REVERT: C 35 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8522 (tp) REVERT: C 42 GLU cc_start: 0.8057 (tt0) cc_final: 0.7544 (tm-30) REVERT: C 47 ASP cc_start: 0.8968 (p0) cc_final: 0.8658 (p0) REVERT: C 55 ASN cc_start: 0.8886 (t0) cc_final: 0.8550 (t0) REVERT: D 13 LYS cc_start: 0.9003 (tttt) cc_final: 0.8661 (ttmm) REVERT: D 35 LEU cc_start: 0.8778 (tp) cc_final: 0.8558 (tt) REVERT: D 42 GLU cc_start: 0.7957 (tt0) cc_final: 0.7258 (tm-30) REVERT: D 67 ASP cc_start: 0.8436 (t0) cc_final: 0.8051 (t0) REVERT: D 106 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5879 (mp) REVERT: D 227 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8303 (mm-30) REVERT: E 13 LYS cc_start: 0.8843 (tttt) cc_final: 0.8488 (ttmm) REVERT: E 35 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8335 (tt) REVERT: E 39 THR cc_start: 0.8788 (m) cc_final: 0.8517 (m) REVERT: E 42 GLU cc_start: 0.7896 (tt0) cc_final: 0.7598 (tm-30) REVERT: E 47 ASP cc_start: 0.8929 (p0) cc_final: 0.8679 (p0) REVERT: E 67 ASP cc_start: 0.8642 (t0) cc_final: 0.8416 (t0) REVERT: E 101 ARG cc_start: 0.7973 (mtp85) cc_final: 0.7725 (mtp-110) REVERT: F 13 LYS cc_start: 0.8937 (tttt) cc_final: 0.8661 (ttmm) REVERT: F 42 GLU cc_start: 0.8012 (tt0) cc_final: 0.7486 (tm-30) REVERT: F 47 ASP cc_start: 0.8769 (p0) cc_final: 0.8402 (p0) REVERT: F 55 ASN cc_start: 0.8881 (t0) cc_final: 0.8515 (t0) REVERT: H 13 LYS cc_start: 0.9017 (tttt) cc_final: 0.8661 (ttmm) REVERT: H 42 GLU cc_start: 0.7999 (tt0) cc_final: 0.7183 (tm-30) REVERT: H 67 ASP cc_start: 0.8556 (t0) cc_final: 0.8228 (t0) REVERT: H 106 LEU cc_start: 0.5906 (OUTLIER) cc_final: 0.5598 (mp) REVERT: I 13 LYS cc_start: 0.8800 (tttt) cc_final: 0.8481 (ttmm) REVERT: I 42 GLU cc_start: 0.7959 (tt0) cc_final: 0.7413 (tm-30) REVERT: I 67 ASP cc_start: 0.8586 (t0) cc_final: 0.8274 (t0) REVERT: I 101 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7534 (mtp-110) REVERT: J 13 LYS cc_start: 0.8899 (tttt) cc_final: 0.8624 (ttmm) REVERT: J 42 GLU cc_start: 0.7987 (tt0) cc_final: 0.7444 (tm-30) REVERT: J 47 ASP cc_start: 0.8714 (p0) cc_final: 0.8382 (p0) REVERT: J 55 ASN cc_start: 0.8887 (t0) cc_final: 0.8517 (t0) REVERT: J 67 ASP cc_start: 0.8616 (t0) cc_final: 0.8268 (t0) REVERT: K 13 LYS cc_start: 0.8984 (tttt) cc_final: 0.8661 (ttmm) REVERT: K 42 GLU cc_start: 0.7922 (tt0) cc_final: 0.7142 (tm-30) REVERT: K 47 ASP cc_start: 0.9055 (p0) cc_final: 0.8838 (p0) REVERT: K 67 ASP cc_start: 0.8430 (t0) cc_final: 0.8175 (t0) REVERT: L 13 LYS cc_start: 0.8867 (tttt) cc_final: 0.8540 (ttmm) REVERT: L 39 THR cc_start: 0.8846 (m) cc_final: 0.8601 (m) REVERT: L 42 GLU cc_start: 0.7885 (tt0) cc_final: 0.7559 (tm-30) REVERT: L 47 ASP cc_start: 0.8924 (p0) cc_final: 0.8693 (p0) REVERT: L 101 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7703 (mtp-110) REVERT: L 103 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8132 (tm-30) REVERT: L 189 ARG cc_start: 0.7819 (ttt180) cc_final: 0.7490 (ttm170) outliers start: 36 outliers final: 31 residues processed: 471 average time/residue: 0.3391 time to fit residues: 232.3362 Evaluate side-chains 483 residues out of total 2160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 448 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 212 PHE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 43 SER Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 212 PHE Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 212 PHE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 212 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 195 optimal weight: 0.0070 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.099897 restraints weight = 28801.870| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.54 r_work: 0.3104 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20148 Z= 0.135 Angle : 0.440 7.380 27288 Z= 0.236 Chirality : 0.033 0.173 3096 Planarity : 0.003 0.029 3300 Dihedral : 2.994 12.155 2592 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.30 % Allowed : 18.10 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.17), residues: 2364 helix: 3.40 (0.12), residues: 1680 sheet: 2.31 (0.47), residues: 132 loop : -1.86 (0.24), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 45 HIS 0.001 0.000 HIS H 194 PHE 0.010 0.001 PHE A 32 TYR 0.022 0.001 TYR J 230 ARG 0.003 0.000 ARG D 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4703.49 seconds wall clock time: 84 minutes 8.97 seconds (5048.97 seconds total)