Starting phenix.real_space_refine on Sat Jan 20 12:17:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmq_40230/01_2024/8gmq_40230_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmq_40230/01_2024/8gmq_40230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmq_40230/01_2024/8gmq_40230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmq_40230/01_2024/8gmq_40230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmq_40230/01_2024/8gmq_40230_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gmq_40230/01_2024/8gmq_40230_trim_updated.pdb" } resolution = 3.36 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= -0.018 sd= 0.372 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 144 5.16 5 C 9552 2.51 5 N 2408 2.21 5 O 2488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 38": "OD1" <-> "OD2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 223": "OD1" <-> "OD2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 223": "OD1" <-> "OD2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 223": "OD1" <-> "OD2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 223": "OD1" <-> "OD2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "F PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 223": "OD1" <-> "OD2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 223": "OD1" <-> "OD2" Residue "G PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 38": "OD1" <-> "OD2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 80": "OE1" <-> "OE2" Residue "H PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 14600 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "E" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "F" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "G" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "H" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.99, per 1000 atoms: 0.55 Number of scatterers: 14600 At special positions: 0 Unit cell: (127.544, 127.544, 101.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 8 15.00 O 2488 8.00 N 2408 7.00 C 9552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " 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: 5.83 Conformation dependent library (CDL) restraints added in 2.9 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 0 sheets defined 64.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 removed outlier: 4.051A pdb=" N TYR A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 69 removed outlier: 3.666A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.712A pdb=" N PHE A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 94 through 116 removed outlier: 3.746A pdb=" N GLN A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 122 through 125 No H-bonds generated for 'chain 'A' and resid 122 through 125' Processing helix chain 'A' and resid 134 through 137 No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 149 through 156 removed outlier: 4.901A pdb=" N ARG A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 202 removed outlier: 3.509A pdb=" N VAL A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 248 removed outlier: 3.742A pdb=" N LYS A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS A 244 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 36 removed outlier: 4.051A pdb=" N TYR B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 69 removed outlier: 3.666A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.711A pdb=" N PHE B 68 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 81 Processing helix chain 'B' and resid 94 through 116 removed outlier: 3.746A pdb=" N GLN B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 122 through 125 No H-bonds generated for 'chain 'B' and resid 122 through 125' Processing helix chain 'B' and resid 134 through 137 No H-bonds generated for 'chain 'B' and resid 134 through 137' Processing helix chain 'B' and resid 149 through 156 removed outlier: 4.901A pdb=" N ARG B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 202 removed outlier: 3.510A pdb=" N VAL B 175 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 202 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 248 removed outlier: 3.741A pdb=" N LYS B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE B 248 " --> pdb=" O CYS B 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 removed outlier: 4.051A pdb=" N TYR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 69 removed outlier: 3.666A pdb=" N LEU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.712A pdb=" N PHE C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 94 through 116 removed outlier: 3.746A pdb=" N GLN C 104 " --> pdb=" O CYS C 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 134 through 137 No H-bonds generated for 'chain 'C' and resid 134 through 137' Processing helix chain 'C' and resid 149 through 156 removed outlier: 4.901A pdb=" N ARG C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 202 removed outlier: 3.509A pdb=" N VAL C 175 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 248 removed outlier: 3.742A pdb=" N LYS C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 226 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE C 248 " --> pdb=" O CYS C 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 36 removed outlier: 4.050A pdb=" N TYR D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 69 removed outlier: 3.666A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.712A pdb=" N PHE D 68 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 81 Processing helix chain 'D' and resid 94 through 116 removed outlier: 3.747A pdb=" N GLN D 104 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 122 through 125 No H-bonds generated for 'chain 'D' and resid 122 through 125' Processing helix chain 'D' and resid 134 through 137 No H-bonds generated for 'chain 'D' and resid 134 through 137' Processing helix chain 'D' and resid 149 through 156 removed outlier: 4.901A pdb=" N ARG D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 202 removed outlier: 3.510A pdb=" N VAL D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER D 202 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 248 removed outlier: 3.741A pdb=" N LYS D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 215 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS D 244 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE D 248 " --> pdb=" O CYS D 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 36 removed outlier: 4.051A pdb=" N TYR E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 69 removed outlier: 3.666A pdb=" N LEU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Proline residue: E 59 - end of helix removed outlier: 3.712A pdb=" N PHE E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 81 Processing helix chain 'E' and resid 94 through 116 removed outlier: 3.746A pdb=" N GLN E 104 " --> pdb=" O CYS E 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE E 108 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 122 through 125 No H-bonds generated for 'chain 'E' and resid 122 through 125' Processing helix chain 'E' and resid 134 through 137 No H-bonds generated for 'chain 'E' and resid 134 through 137' Processing helix chain 'E' and resid 149 through 156 removed outlier: 4.901A pdb=" N ARG E 156 " --> pdb=" O ARG E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 202 removed outlier: 3.509A pdb=" N VAL E 175 " --> pdb=" O ASN E 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN E 183 " --> pdb=" O ARG E 179 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER E 202 " --> pdb=" O PHE E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 248 removed outlier: 3.742A pdb=" N LYS E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER E 215 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS E 244 " --> pdb=" O PHE E 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE E 248 " --> pdb=" O CYS E 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 36 removed outlier: 4.051A pdb=" N TYR F 34 " --> pdb=" O SER F 30 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 69 removed outlier: 3.666A pdb=" N LEU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Proline residue: F 59 - end of helix removed outlier: 3.712A pdb=" N PHE F 68 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 81 Processing helix chain 'F' and resid 94 through 116 removed outlier: 3.747A pdb=" N GLN F 104 " --> pdb=" O CYS F 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE F 108 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 122 through 125 No H-bonds generated for 'chain 'F' and resid 122 through 125' Processing helix chain 'F' and resid 134 through 137 No H-bonds generated for 'chain 'F' and resid 134 through 137' Processing helix chain 'F' and resid 149 through 156 removed outlier: 4.900A pdb=" N ARG F 156 " --> pdb=" O ARG F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 202 removed outlier: 3.510A pdb=" N VAL F 175 " --> pdb=" O ASN F 171 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER F 202 " --> pdb=" O PHE F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 248 removed outlier: 3.741A pdb=" N LYS F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER F 215 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 226 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS F 244 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE F 248 " --> pdb=" O CYS F 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 36 removed outlier: 4.051A pdb=" N TYR G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 69 removed outlier: 3.666A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Proline residue: G 59 - end of helix removed outlier: 3.712A pdb=" N PHE G 68 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 94 through 116 removed outlier: 3.746A pdb=" N GLN G 104 " --> pdb=" O CYS G 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 122 through 125 No H-bonds generated for 'chain 'G' and resid 122 through 125' Processing helix chain 'G' and resid 134 through 137 No H-bonds generated for 'chain 'G' and resid 134 through 137' Processing helix chain 'G' and resid 149 through 156 removed outlier: 4.901A pdb=" N ARG G 156 " --> pdb=" O ARG G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 202 removed outlier: 3.509A pdb=" N VAL G 175 " --> pdb=" O ASN G 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN G 183 " --> pdb=" O ARG G 179 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER G 202 " --> pdb=" O PHE G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 248 removed outlier: 3.742A pdb=" N LYS G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER G 215 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG G 226 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS G 242 " --> pdb=" O LYS G 238 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL G 243 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS G 244 " --> pdb=" O PHE G 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN G 247 " --> pdb=" O VAL G 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE G 248 " --> pdb=" O CYS G 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 36 removed outlier: 4.050A pdb=" N TYR H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER H 35 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 36 " --> pdb=" O GLN H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 69 removed outlier: 3.666A pdb=" N LEU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Proline residue: H 59 - end of helix removed outlier: 3.712A pdb=" N PHE H 68 " --> pdb=" O PHE H 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL H 69 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 81 Processing helix chain 'H' and resid 94 through 116 removed outlier: 3.747A pdb=" N GLN H 104 " --> pdb=" O CYS H 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 122 through 125 No H-bonds generated for 'chain 'H' and resid 122 through 125' Processing helix chain 'H' and resid 134 through 137 No H-bonds generated for 'chain 'H' and resid 134 through 137' Processing helix chain 'H' and resid 149 through 156 removed outlier: 4.901A pdb=" N ARG H 156 " --> pdb=" O ARG H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 202 removed outlier: 3.510A pdb=" N VAL H 175 " --> pdb=" O ASN H 171 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN H 183 " --> pdb=" O ARG H 179 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER H 202 " --> pdb=" O PHE H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 248 removed outlier: 3.742A pdb=" N LYS H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 215 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS H 220 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG H 226 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER H 239 " --> pdb=" O GLU H 235 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS H 244 " --> pdb=" O PHE H 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN H 247 " --> pdb=" O VAL H 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE H 248 " --> pdb=" O CYS H 244 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1920 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: 3.76 Time building geometry restraints manager: 6.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2200 1.31 - 1.44: 4032 1.44 - 1.56: 8488 1.56 - 1.69: 16 1.69 - 1.81: 192 Bond restraints: 14928 Sorted by residual: bond pdb=" C21 POV A 401 " pdb=" O21 POV A 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 POV C 401 " pdb=" O21 POV C 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 POV E 401 " pdb=" O21 POV E 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 POV F 401 " pdb=" O21 POV F 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 POV G 401 " pdb=" O21 POV G 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 14923 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.64: 440 106.64 - 113.49: 8383 113.49 - 120.34: 5920 120.34 - 127.19: 5346 127.19 - 134.03: 167 Bond angle restraints: 20256 Sorted by residual: angle pdb=" N ARG D 204 " pdb=" CA ARG D 204 " pdb=" C ARG D 204 " ideal model delta sigma weight residual 109.81 121.43 -11.62 2.21e+00 2.05e-01 2.77e+01 angle pdb=" N ARG G 204 " pdb=" CA ARG G 204 " pdb=" C ARG G 204 " ideal model delta sigma weight residual 109.81 121.42 -11.61 2.21e+00 2.05e-01 2.76e+01 angle pdb=" N ARG E 204 " pdb=" CA ARG E 204 " pdb=" C ARG E 204 " ideal model delta sigma weight residual 109.81 121.40 -11.59 2.21e+00 2.05e-01 2.75e+01 angle pdb=" N ARG A 204 " pdb=" CA ARG A 204 " pdb=" C ARG A 204 " ideal model delta sigma weight residual 109.81 121.40 -11.59 2.21e+00 2.05e-01 2.75e+01 angle pdb=" N ARG C 204 " pdb=" CA ARG C 204 " pdb=" C ARG C 204 " ideal model delta sigma weight residual 109.81 121.40 -11.59 2.21e+00 2.05e-01 2.75e+01 ... (remaining 20251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 8366 24.42 - 48.83: 458 48.83 - 73.25: 96 73.25 - 97.66: 32 97.66 - 122.08: 8 Dihedral angle restraints: 8960 sinusoidal: 3464 harmonic: 5496 Sorted by residual: dihedral pdb=" CA ARG B 204 " pdb=" C ARG B 204 " pdb=" N PRO B 205 " pdb=" CA PRO B 205 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ARG H 204 " pdb=" C ARG H 204 " pdb=" N PRO H 205 " pdb=" CA PRO H 205 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ARG A 204 " pdb=" C ARG A 204 " pdb=" N PRO A 205 " pdb=" CA PRO A 205 " ideal model delta harmonic sigma weight residual -180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 8957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1758 0.042 - 0.084: 498 0.084 - 0.126: 64 0.126 - 0.168: 0 0.168 - 0.210: 8 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA ARG F 204 " pdb=" N ARG F 204 " pdb=" C ARG F 204 " pdb=" CB ARG F 204 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ARG D 204 " pdb=" N ARG D 204 " pdb=" C ARG D 204 " pdb=" CB ARG D 204 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG G 204 " pdb=" N ARG G 204 " pdb=" C ARG G 204 " pdb=" CB ARG G 204 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2325 not shown) Planarity restraints: 2504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO A 60 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO E 60 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 60 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.030 5.00e-02 4.00e+02 ... (remaining 2501 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1434 2.73 - 3.27: 16080 3.27 - 3.81: 20777 3.81 - 4.36: 24129 4.36 - 4.90: 40914 Nonbonded interactions: 103334 Sorted by model distance: nonbonded pdb=" O GLY D 121 " pdb=" N THR D 125 " model vdw 2.187 2.520 nonbonded pdb=" O GLY H 121 " pdb=" N THR H 125 " model vdw 2.188 2.520 nonbonded pdb=" O GLY B 121 " pdb=" N THR B 125 " model vdw 2.188 2.520 nonbonded pdb=" O GLY E 121 " pdb=" N THR E 125 " model vdw 2.188 2.520 nonbonded pdb=" O GLY A 121 " pdb=" N THR A 125 " model vdw 2.188 2.520 ... (remaining 103329 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.740 Check model and map are aligned: 0.200 Set scattering table: 0.110 Process input model: 39.720 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 14928 Z= 0.502 Angle : 0.964 11.725 20256 Z= 0.454 Chirality : 0.039 0.210 2328 Planarity : 0.005 0.054 2504 Dihedral : 16.898 122.076 5368 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.15), residues: 1856 helix: -3.49 (0.09), residues: 1152 sheet: None (None), residues: 0 loop : -2.89 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 113 HIS 0.003 0.001 HIS D 143 PHE 0.010 0.002 PHE D 207 TYR 0.012 0.002 TYR D 221 ARG 0.002 0.000 ARG H 201 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 1.613 Fit side-chains REVERT: A 96 ARG cc_start: 0.8836 (mtp180) cc_final: 0.8629 (ttp-110) REVERT: A 216 ARG cc_start: 0.9391 (tpp80) cc_final: 0.8793 (tpt-90) REVERT: A 231 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 235 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 244 CYS cc_start: 0.8697 (t) cc_final: 0.8353 (t) REVERT: B 46 ARG cc_start: 0.8636 (mtp180) cc_final: 0.8422 (mtp85) REVERT: B 96 ARG cc_start: 0.8832 (mtp180) cc_final: 0.8602 (ttm110) REVERT: B 216 ARG cc_start: 0.9386 (tpp80) cc_final: 0.9040 (ttt90) REVERT: B 231 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 235 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8288 (tm-30) REVERT: C 96 ARG cc_start: 0.8836 (mtp180) cc_final: 0.8627 (ttp-110) REVERT: C 216 ARG cc_start: 0.9393 (tpp80) cc_final: 0.8813 (tpt-90) REVERT: C 231 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 235 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 244 CYS cc_start: 0.8709 (t) cc_final: 0.8367 (t) REVERT: D 46 ARG cc_start: 0.8639 (mtp180) cc_final: 0.8416 (mtp85) REVERT: D 96 ARG cc_start: 0.8835 (mtp180) cc_final: 0.8598 (ttm110) REVERT: D 216 ARG cc_start: 0.9401 (tpp80) cc_final: 0.9059 (ttt90) REVERT: D 231 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 235 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8297 (tm-30) REVERT: E 96 ARG cc_start: 0.8833 (mtp180) cc_final: 0.8590 (ttm-80) REVERT: E 216 ARG cc_start: 0.9391 (tpp80) cc_final: 0.8811 (tpt-90) REVERT: E 231 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8158 (tm-30) REVERT: E 235 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8236 (tm-30) REVERT: E 244 CYS cc_start: 0.8705 (t) cc_final: 0.8357 (t) REVERT: F 96 ARG cc_start: 0.8837 (mtp180) cc_final: 0.8627 (ttm110) REVERT: F 105 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7745 (ttm-80) REVERT: F 216 ARG cc_start: 0.9412 (tpp80) cc_final: 0.9059 (ttt90) REVERT: F 231 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8166 (tm-30) REVERT: F 235 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8306 (tm-30) REVERT: G 96 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8587 (ttm-80) REVERT: G 216 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8807 (tpt-90) REVERT: G 231 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8171 (tm-30) REVERT: G 235 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8233 (tm-30) REVERT: G 244 CYS cc_start: 0.8710 (t) cc_final: 0.8368 (t) REVERT: H 96 ARG cc_start: 0.8826 (mtp180) cc_final: 0.8599 (ttm110) REVERT: H 216 ARG cc_start: 0.9390 (tpp80) cc_final: 0.9041 (ttt90) REVERT: H 230 ASP cc_start: 0.8457 (m-30) cc_final: 0.8179 (m-30) REVERT: H 231 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8176 (tm-30) REVERT: H 235 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8296 (tm-30) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2830 time to fit residues: 151.2986 Evaluate side-chains 307 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 307 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 139 optimal weight: 0.0050 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.0040 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN C 73 ASN E 73 ASN G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14928 Z= 0.202 Angle : 0.676 10.241 20256 Z= 0.347 Chirality : 0.042 0.230 2328 Planarity : 0.005 0.053 2504 Dihedral : 13.050 115.928 2360 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 1.93 % Allowed : 13.47 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.18), residues: 1856 helix: -1.04 (0.14), residues: 1128 sheet: None (None), residues: 0 loop : -2.97 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 218 HIS 0.004 0.001 HIS E 236 PHE 0.010 0.001 PHE F 240 TYR 0.009 0.001 TYR D 221 ARG 0.007 0.001 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 350 time to evaluate : 1.589 Fit side-chains REVERT: A 80 GLU cc_start: 0.8716 (tp30) cc_final: 0.8159 (tp30) REVERT: A 231 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 235 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7989 (tm-30) REVERT: A 246 GLN cc_start: 0.8430 (mm110) cc_final: 0.7289 (tm-30) REVERT: B 196 LEU cc_start: 0.8951 (tp) cc_final: 0.8598 (tt) REVERT: B 244 CYS cc_start: 0.8581 (t) cc_final: 0.8084 (t) REVERT: B 246 GLN cc_start: 0.8461 (mm110) cc_final: 0.7372 (tm-30) REVERT: C 80 GLU cc_start: 0.8723 (tp30) cc_final: 0.8160 (tp30) REVERT: C 231 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8123 (tm-30) REVERT: C 235 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7992 (tm-30) REVERT: C 246 GLN cc_start: 0.8416 (mm110) cc_final: 0.7279 (tm-30) REVERT: D 196 LEU cc_start: 0.8945 (tp) cc_final: 0.8596 (tt) REVERT: D 244 CYS cc_start: 0.8568 (t) cc_final: 0.8067 (t) REVERT: D 246 GLN cc_start: 0.8454 (mm110) cc_final: 0.7358 (tm-30) REVERT: E 80 GLU cc_start: 0.8731 (tp30) cc_final: 0.8163 (tp30) REVERT: E 231 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8126 (tm-30) REVERT: E 235 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7993 (tm-30) REVERT: E 246 GLN cc_start: 0.8417 (mm110) cc_final: 0.7282 (tm-30) REVERT: F 196 LEU cc_start: 0.8867 (tp) cc_final: 0.8550 (tt) REVERT: F 244 CYS cc_start: 0.8525 (t) cc_final: 0.8023 (t) REVERT: F 246 GLN cc_start: 0.8469 (mm110) cc_final: 0.7448 (tm-30) REVERT: G 80 GLU cc_start: 0.8723 (tp30) cc_final: 0.8160 (tp30) REVERT: G 231 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8098 (tm-30) REVERT: G 235 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7988 (tm-30) REVERT: G 246 GLN cc_start: 0.8433 (mm110) cc_final: 0.7300 (tm-30) REVERT: H 196 LEU cc_start: 0.8935 (tp) cc_final: 0.8584 (tt) REVERT: H 244 CYS cc_start: 0.8583 (t) cc_final: 0.8078 (t) REVERT: H 246 GLN cc_start: 0.8443 (mm110) cc_final: 0.7372 (tm-30) outliers start: 28 outliers final: 17 residues processed: 350 average time/residue: 0.2100 time to fit residues: 115.1430 Evaluate side-chains 324 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 307 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.3980 chunk 139 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 chunk 134 optimal weight: 3.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 220 HIS B 220 HIS C 40 ASN C 220 HIS D 220 HIS E 40 ASN E 220 HIS F 220 HIS G 40 ASN G 220 HIS H 220 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14928 Z= 0.195 Angle : 0.614 9.859 20256 Z= 0.315 Chirality : 0.039 0.193 2328 Planarity : 0.005 0.054 2504 Dihedral : 11.481 117.393 2360 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 5.32 % Allowed : 16.09 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1856 helix: 0.32 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -2.79 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 218 HIS 0.001 0.000 HIS D 236 PHE 0.006 0.001 PHE F 207 TYR 0.012 0.001 TYR H 177 ARG 0.003 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 321 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 235 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8029 (tm-30) REVERT: A 246 GLN cc_start: 0.8229 (mm110) cc_final: 0.7193 (tm-30) REVERT: B 242 LYS cc_start: 0.8102 (tmtt) cc_final: 0.7882 (tmtt) REVERT: C 149 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8455 (mp0) REVERT: C 231 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8105 (tm-30) REVERT: C 235 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 246 GLN cc_start: 0.8213 (mm110) cc_final: 0.7181 (tm-30) REVERT: D 242 LYS cc_start: 0.8122 (tmtt) cc_final: 0.7905 (tmtt) REVERT: E 149 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: E 231 GLU cc_start: 0.8306 (tm-30) cc_final: 0.8095 (tm-30) REVERT: E 235 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8036 (tm-30) REVERT: E 246 GLN cc_start: 0.8236 (mm110) cc_final: 0.7178 (tm-30) REVERT: F 196 LEU cc_start: 0.8863 (tp) cc_final: 0.8450 (tt) REVERT: F 242 LYS cc_start: 0.8132 (tmtt) cc_final: 0.7906 (tmtt) REVERT: F 244 CYS cc_start: 0.8481 (t) cc_final: 0.8084 (t) REVERT: G 231 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8110 (tm-30) REVERT: G 235 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8036 (tm-30) REVERT: G 246 GLN cc_start: 0.8231 (mm110) cc_final: 0.7197 (tm-30) REVERT: H 242 LYS cc_start: 0.8106 (tmtt) cc_final: 0.7885 (tmtt) outliers start: 77 outliers final: 37 residues processed: 349 average time/residue: 0.2200 time to fit residues: 118.8125 Evaluate side-chains 340 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 301 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 167 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 40 ASN E 40 ASN G 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14928 Z= 0.260 Angle : 0.645 10.103 20256 Z= 0.327 Chirality : 0.040 0.182 2328 Planarity : 0.004 0.055 2504 Dihedral : 11.239 115.376 2360 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 4.35 % Allowed : 19.06 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1856 helix: 0.74 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -2.72 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 218 HIS 0.001 0.000 HIS E 143 PHE 0.007 0.001 PHE F 198 TYR 0.014 0.002 TYR D 177 ARG 0.003 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 302 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8678 (tpp) cc_final: 0.8427 (ttm) REVERT: A 149 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8508 (mp0) REVERT: A 231 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 235 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 246 GLN cc_start: 0.8290 (mm110) cc_final: 0.7299 (tm-30) REVERT: A 250 GLN cc_start: 0.8760 (pp30) cc_final: 0.8477 (pp30) REVERT: B 246 GLN cc_start: 0.8381 (mm110) cc_final: 0.7313 (tm-30) REVERT: B 250 GLN cc_start: 0.8736 (pp30) cc_final: 0.8499 (pp30) REVERT: C 107 MET cc_start: 0.8693 (tpp) cc_final: 0.8370 (ttm) REVERT: C 231 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8062 (tm-30) REVERT: C 235 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8100 (tm-30) REVERT: C 246 GLN cc_start: 0.8267 (mm110) cc_final: 0.7281 (tm-30) REVERT: C 250 GLN cc_start: 0.8758 (pp30) cc_final: 0.8474 (pp30) REVERT: D 246 GLN cc_start: 0.8373 (mm110) cc_final: 0.7313 (tm-30) REVERT: D 250 GLN cc_start: 0.8745 (pp30) cc_final: 0.8511 (pp30) REVERT: E 107 MET cc_start: 0.8695 (tpp) cc_final: 0.8370 (ttm) REVERT: E 231 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8070 (tm-30) REVERT: E 235 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8133 (tm-30) REVERT: E 246 GLN cc_start: 0.8272 (mm110) cc_final: 0.7279 (tm-30) REVERT: E 250 GLN cc_start: 0.8757 (pp30) cc_final: 0.8469 (pp30) REVERT: F 62 ILE cc_start: 0.8890 (mt) cc_final: 0.8663 (mt) REVERT: F 196 LEU cc_start: 0.8851 (tp) cc_final: 0.8358 (tt) REVERT: F 242 LYS cc_start: 0.8130 (tmtt) cc_final: 0.7857 (tmtt) REVERT: F 244 CYS cc_start: 0.8532 (t) cc_final: 0.8141 (t) REVERT: G 107 MET cc_start: 0.8686 (tpp) cc_final: 0.8363 (ttm) REVERT: G 149 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: G 231 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8069 (tm-30) REVERT: G 235 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8131 (tm-30) REVERT: G 246 GLN cc_start: 0.8282 (mm110) cc_final: 0.7296 (tm-30) REVERT: G 250 GLN cc_start: 0.8754 (pp30) cc_final: 0.8471 (pp30) REVERT: H 246 GLN cc_start: 0.8383 (mm110) cc_final: 0.7323 (tm-30) REVERT: H 250 GLN cc_start: 0.8741 (pp30) cc_final: 0.8505 (pp30) outliers start: 63 outliers final: 48 residues processed: 334 average time/residue: 0.2246 time to fit residues: 116.9609 Evaluate side-chains 341 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 291 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 151 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 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 40 ASN C 40 ASN E 40 ASN G 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14928 Z= 0.257 Angle : 0.641 10.033 20256 Z= 0.325 Chirality : 0.040 0.187 2328 Planarity : 0.004 0.055 2504 Dihedral : 11.189 115.128 2360 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.01 % Allowed : 21.06 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1856 helix: 0.90 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -2.84 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 218 HIS 0.001 0.000 HIS G 143 PHE 0.006 0.001 PHE F 198 TYR 0.014 0.002 TYR D 177 ARG 0.002 0.000 ARG D 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 283 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8530 (mp0) REVERT: A 231 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8065 (tm-30) REVERT: A 235 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 246 GLN cc_start: 0.8281 (mm110) cc_final: 0.7293 (tm-30) REVERT: A 250 GLN cc_start: 0.8768 (pp30) cc_final: 0.8487 (pp30) REVERT: B 246 GLN cc_start: 0.8350 (mm110) cc_final: 0.7304 (tm-30) REVERT: B 250 GLN cc_start: 0.8714 (pp30) cc_final: 0.8494 (pp30) REVERT: C 80 GLU cc_start: 0.8740 (tp30) cc_final: 0.8102 (tp30) REVERT: C 90 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8059 (mmtt) REVERT: C 107 MET cc_start: 0.8671 (tpp) cc_final: 0.8414 (ttm) REVERT: C 149 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: C 231 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 235 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8090 (tm-30) REVERT: C 246 GLN cc_start: 0.8260 (mm110) cc_final: 0.7274 (tm-30) REVERT: C 250 GLN cc_start: 0.8768 (pp30) cc_final: 0.8484 (pp30) REVERT: D 246 GLN cc_start: 0.8350 (mm110) cc_final: 0.7313 (tm-30) REVERT: D 250 GLN cc_start: 0.8723 (pp30) cc_final: 0.8513 (pp30) REVERT: E 80 GLU cc_start: 0.8714 (tp30) cc_final: 0.8126 (tp30) REVERT: E 107 MET cc_start: 0.8671 (tpp) cc_final: 0.8414 (ttm) REVERT: E 149 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: E 231 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8065 (tm-30) REVERT: E 235 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8111 (tm-30) REVERT: E 246 GLN cc_start: 0.8317 (mm110) cc_final: 0.7309 (tm-30) REVERT: E 250 GLN cc_start: 0.8755 (pp30) cc_final: 0.8470 (pp30) REVERT: F 62 ILE cc_start: 0.8879 (mt) cc_final: 0.8644 (mt) REVERT: F 242 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7902 (tmtt) REVERT: F 244 CYS cc_start: 0.8490 (t) cc_final: 0.8149 (t) REVERT: G 80 GLU cc_start: 0.8720 (tp30) cc_final: 0.8125 (tp30) REVERT: G 107 MET cc_start: 0.8664 (tpp) cc_final: 0.8407 (ttm) REVERT: G 149 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8532 (mp0) REVERT: G 231 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8071 (tm-30) REVERT: G 235 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8097 (tm-30) REVERT: G 246 GLN cc_start: 0.8269 (mm110) cc_final: 0.7291 (tm-30) REVERT: G 250 GLN cc_start: 0.8763 (pp30) cc_final: 0.8482 (pp30) REVERT: H 246 GLN cc_start: 0.8356 (mm110) cc_final: 0.7313 (tm-30) REVERT: H 250 GLN cc_start: 0.8720 (pp30) cc_final: 0.8502 (pp30) outliers start: 58 outliers final: 40 residues processed: 314 average time/residue: 0.2090 time to fit residues: 103.0126 Evaluate side-chains 320 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.0030 chunk 160 optimal weight: 0.0040 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 178 optimal weight: 0.0570 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.3720 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14928 Z= 0.174 Angle : 0.595 9.681 20256 Z= 0.300 Chirality : 0.038 0.178 2328 Planarity : 0.004 0.055 2504 Dihedral : 10.873 110.079 2360 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.97 % Allowed : 22.86 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1856 helix: 1.37 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -2.75 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 218 HIS 0.001 0.000 HIS A 220 PHE 0.009 0.001 PHE A 189 TYR 0.009 0.001 TYR E 51 ARG 0.002 0.000 ARG H 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 317 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.8644 (ttm) cc_final: 0.8342 (ttm) REVERT: A 149 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: A 231 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 235 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 246 GLN cc_start: 0.8165 (mm110) cc_final: 0.7307 (tm-30) REVERT: A 250 GLN cc_start: 0.8776 (pp30) cc_final: 0.8519 (pp30) REVERT: B 107 MET cc_start: 0.8512 (ttm) cc_final: 0.8147 (ttp) REVERT: C 149 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8515 (mp0) REVERT: C 231 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8056 (tm-30) REVERT: C 235 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8063 (tm-30) REVERT: C 246 GLN cc_start: 0.8142 (mm110) cc_final: 0.7289 (tm-30) REVERT: C 250 GLN cc_start: 0.8773 (pp30) cc_final: 0.8515 (pp30) REVERT: D 107 MET cc_start: 0.8498 (ttm) cc_final: 0.8132 (ttp) REVERT: E 149 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8498 (mp0) REVERT: E 231 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8069 (tm-30) REVERT: E 235 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8067 (tm-30) REVERT: E 246 GLN cc_start: 0.8140 (mm110) cc_final: 0.7271 (tm-30) REVERT: E 250 GLN cc_start: 0.8774 (pp30) cc_final: 0.8504 (pp30) REVERT: F 105 ARG cc_start: 0.7569 (mtp85) cc_final: 0.7367 (tpp80) REVERT: F 196 LEU cc_start: 0.8863 (tp) cc_final: 0.8351 (tt) REVERT: G 149 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8527 (mp0) REVERT: G 231 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8075 (tm-30) REVERT: G 235 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8056 (tm-30) REVERT: G 246 GLN cc_start: 0.8164 (mm110) cc_final: 0.7339 (tm-30) REVERT: G 250 GLN cc_start: 0.8771 (pp30) cc_final: 0.8514 (pp30) REVERT: H 107 MET cc_start: 0.8512 (ttm) cc_final: 0.8144 (ttp) outliers start: 43 outliers final: 29 residues processed: 340 average time/residue: 0.2250 time to fit residues: 116.3296 Evaluate side-chains 322 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 289 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 0.0570 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 0.0770 chunk 149 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 40 ASN G 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14928 Z= 0.166 Angle : 0.592 9.568 20256 Z= 0.296 Chirality : 0.037 0.153 2328 Planarity : 0.004 0.055 2504 Dihedral : 10.744 108.468 2360 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.66 % Allowed : 23.41 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1856 helix: 1.64 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -2.72 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 218 HIS 0.001 0.000 HIS F 220 PHE 0.006 0.001 PHE G 189 TYR 0.008 0.001 TYR A 177 ARG 0.004 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 333 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.8286 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 246 GLN cc_start: 0.8058 (mm110) cc_final: 0.7267 (tm-30) REVERT: A 250 GLN cc_start: 0.8769 (pp30) cc_final: 0.8522 (pp30) REVERT: B 115 SER cc_start: 0.9414 (p) cc_final: 0.9172 (p) REVERT: C 80 GLU cc_start: 0.8785 (tp30) cc_final: 0.8159 (tp30) REVERT: C 90 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8070 (mmtt) REVERT: C 196 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8509 (tt) REVERT: C 235 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 246 GLN cc_start: 0.8058 (mm110) cc_final: 0.7264 (tm-30) REVERT: C 250 GLN cc_start: 0.8764 (pp30) cc_final: 0.8517 (pp30) REVERT: D 115 SER cc_start: 0.9412 (p) cc_final: 0.9175 (p) REVERT: E 80 GLU cc_start: 0.8639 (tp30) cc_final: 0.8172 (tp30) REVERT: E 196 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8507 (tt) REVERT: E 235 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8073 (tm-30) REVERT: E 246 GLN cc_start: 0.8063 (mm110) cc_final: 0.7251 (tm-30) REVERT: E 250 GLN cc_start: 0.8764 (pp30) cc_final: 0.8505 (pp30) REVERT: F 105 ARG cc_start: 0.7602 (mtp85) cc_final: 0.7376 (tpp80) REVERT: F 246 GLN cc_start: 0.7955 (mm110) cc_final: 0.7091 (tm-30) REVERT: G 80 GLU cc_start: 0.8649 (tp30) cc_final: 0.8175 (tp30) REVERT: G 196 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8499 (tt) REVERT: G 235 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8062 (tm-30) REVERT: G 246 GLN cc_start: 0.8132 (mm110) cc_final: 0.7321 (tm-30) REVERT: G 250 GLN cc_start: 0.8762 (pp30) cc_final: 0.8514 (pp30) REVERT: H 115 SER cc_start: 0.9410 (p) cc_final: 0.9175 (p) outliers start: 53 outliers final: 34 residues processed: 357 average time/residue: 0.2099 time to fit residues: 117.4698 Evaluate side-chains 356 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 319 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 40 ASN G 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14928 Z= 0.254 Angle : 0.639 9.933 20256 Z= 0.322 Chirality : 0.040 0.208 2328 Planarity : 0.004 0.054 2504 Dihedral : 10.604 111.107 2360 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.38 % Allowed : 23.62 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1856 helix: 1.51 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -2.63 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 218 HIS 0.001 0.000 HIS H 143 PHE 0.007 0.001 PHE G 189 TYR 0.015 0.002 TYR B 177 ARG 0.003 0.000 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 297 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ASP cc_start: 0.8915 (t70) cc_final: 0.8562 (t70) REVERT: A 235 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8097 (tm-30) REVERT: A 246 GLN cc_start: 0.8240 (mm110) cc_final: 0.7353 (tm-30) REVERT: A 250 GLN cc_start: 0.8774 (pp30) cc_final: 0.8495 (pp30) REVERT: C 80 GLU cc_start: 0.8760 (tp30) cc_final: 0.8145 (tp30) REVERT: C 196 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8554 (tt) REVERT: C 223 ASP cc_start: 0.8902 (t70) cc_final: 0.8559 (t70) REVERT: C 235 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 246 GLN cc_start: 0.8224 (mm110) cc_final: 0.7337 (tm-30) REVERT: C 250 GLN cc_start: 0.8769 (pp30) cc_final: 0.8490 (pp30) REVERT: E 80 GLU cc_start: 0.8646 (tp30) cc_final: 0.8119 (tp30) REVERT: E 196 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8543 (tt) REVERT: E 223 ASP cc_start: 0.8912 (t70) cc_final: 0.8565 (t70) REVERT: E 235 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8098 (tm-30) REVERT: E 246 GLN cc_start: 0.8232 (mm110) cc_final: 0.7330 (tm-30) REVERT: E 250 GLN cc_start: 0.8768 (pp30) cc_final: 0.8484 (pp30) REVERT: G 80 GLU cc_start: 0.8658 (tp30) cc_final: 0.8123 (tp30) REVERT: G 196 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8548 (tt) REVERT: G 223 ASP cc_start: 0.8924 (t70) cc_final: 0.8576 (t70) REVERT: G 235 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8071 (tm-30) REVERT: G 246 GLN cc_start: 0.8221 (mm110) cc_final: 0.7347 (tm-30) REVERT: G 250 GLN cc_start: 0.8766 (pp30) cc_final: 0.8486 (pp30) outliers start: 49 outliers final: 40 residues processed: 317 average time/residue: 0.2153 time to fit residues: 108.3187 Evaluate side-chains 330 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 287 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.1980 chunk 155 optimal weight: 0.1980 chunk 165 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.2980 chunk 129 optimal weight: 0.0270 chunk 50 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 40 ASN C 73 ASN E 73 ASN G 40 ASN G 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14928 Z= 0.173 Angle : 0.618 9.314 20256 Z= 0.312 Chirality : 0.038 0.205 2328 Planarity : 0.004 0.056 2504 Dihedral : 10.592 109.156 2360 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.18 % Allowed : 25.35 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1856 helix: 1.75 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -2.63 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 218 HIS 0.001 0.000 HIS F 220 PHE 0.006 0.001 PHE H 189 TYR 0.008 0.001 TYR C 177 ARG 0.004 0.000 ARG C 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 322 time to evaluate : 1.836 Fit side-chains revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8578 (mp0) cc_final: 0.8314 (mp0) REVERT: A 235 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8079 (tm-30) REVERT: A 246 GLN cc_start: 0.8099 (mm110) cc_final: 0.7309 (tm-30) REVERT: A 250 GLN cc_start: 0.8744 (pp30) cc_final: 0.8502 (pp30) REVERT: B 246 GLN cc_start: 0.7997 (mm110) cc_final: 0.7206 (tm-30) REVERT: C 80 GLU cc_start: 0.8795 (tp30) cc_final: 0.8085 (tp30) REVERT: C 90 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8010 (mmtt) REVERT: C 196 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8352 (tt) REVERT: C 235 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8084 (tm-30) REVERT: C 246 GLN cc_start: 0.8112 (mm110) cc_final: 0.7312 (tm-30) REVERT: C 250 GLN cc_start: 0.8741 (pp30) cc_final: 0.8494 (pp30) REVERT: E 80 GLU cc_start: 0.8641 (tp30) cc_final: 0.8105 (tp30) REVERT: E 149 GLU cc_start: 0.8592 (mp0) cc_final: 0.8331 (mp0) REVERT: E 196 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8352 (tt) REVERT: E 206 CYS cc_start: 0.6841 (t) cc_final: 0.6616 (t) REVERT: E 235 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8095 (tm-30) REVERT: E 246 GLN cc_start: 0.8088 (mm110) cc_final: 0.7282 (tm-30) REVERT: E 250 GLN cc_start: 0.8742 (pp30) cc_final: 0.8484 (pp30) REVERT: F 246 GLN cc_start: 0.8093 (mm110) cc_final: 0.7318 (tm-30) REVERT: G 80 GLU cc_start: 0.8650 (tp30) cc_final: 0.8107 (tp30) REVERT: G 149 GLU cc_start: 0.8581 (mp0) cc_final: 0.8318 (mp0) REVERT: G 196 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8406 (tt) REVERT: G 235 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8080 (tm-30) REVERT: G 246 GLN cc_start: 0.8130 (mm110) cc_final: 0.7333 (tm-30) REVERT: G 250 GLN cc_start: 0.8735 (pp30) cc_final: 0.8492 (pp30) REVERT: H 246 GLN cc_start: 0.8005 (mm110) cc_final: 0.7218 (tm-30) outliers start: 46 outliers final: 36 residues processed: 342 average time/residue: 0.1979 time to fit residues: 107.7829 Evaluate side-chains 353 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 314 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 0.0000 chunk 121 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN C 104 GLN E 104 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14928 Z= 0.224 Angle : 0.620 9.907 20256 Z= 0.312 Chirality : 0.039 0.185 2328 Planarity : 0.004 0.054 2504 Dihedral : 10.401 110.952 2360 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.90 % Allowed : 24.38 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1856 helix: 1.72 (0.16), residues: 1184 sheet: None (None), residues: 0 loop : -2.69 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 218 HIS 0.001 0.000 HIS C 143 PHE 0.007 0.001 PHE G 37 TYR 0.013 0.001 TYR H 177 ARG 0.003 0.000 ARG C 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 302 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLU cc_start: 0.8591 (mp0) cc_final: 0.8328 (mp0) REVERT: A 223 ASP cc_start: 0.8894 (t70) cc_final: 0.8554 (t70) REVERT: A 235 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8124 (tm-30) REVERT: A 246 GLN cc_start: 0.8173 (mm110) cc_final: 0.7288 (tm-30) REVERT: A 250 GLN cc_start: 0.8760 (pp30) cc_final: 0.8488 (pp30) REVERT: C 196 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8469 (tt) REVERT: C 223 ASP cc_start: 0.8882 (t70) cc_final: 0.8572 (t70) REVERT: C 235 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 246 GLN cc_start: 0.8139 (mm110) cc_final: 0.7278 (tm-30) REVERT: C 250 GLN cc_start: 0.8757 (pp30) cc_final: 0.8482 (pp30) REVERT: E 196 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8459 (tt) REVERT: E 223 ASP cc_start: 0.8887 (t70) cc_final: 0.8552 (t70) REVERT: E 235 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8134 (tm-30) REVERT: E 246 GLN cc_start: 0.8157 (mm110) cc_final: 0.7273 (tm-30) REVERT: E 250 GLN cc_start: 0.8756 (pp30) cc_final: 0.8477 (pp30) REVERT: G 196 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8463 (tt) REVERT: G 223 ASP cc_start: 0.8895 (t70) cc_final: 0.8567 (t70) REVERT: G 235 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8138 (tm-30) REVERT: G 246 GLN cc_start: 0.8161 (mm110) cc_final: 0.7303 (tm-30) REVERT: G 250 GLN cc_start: 0.8745 (pp30) cc_final: 0.8472 (pp30) outliers start: 42 outliers final: 35 residues processed: 319 average time/residue: 0.2068 time to fit residues: 104.0375 Evaluate side-chains 336 residues out of total 1592 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 298 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0870 chunk 44 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.118390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.091538 restraints weight = 29370.136| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 3.75 r_work: 0.3038 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14928 Z= 0.197 Angle : 0.610 9.662 20256 Z= 0.306 Chirality : 0.039 0.183 2328 Planarity : 0.004 0.054 2504 Dihedral : 9.975 108.869 2360 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.69 % Allowed : 24.52 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.22), residues: 1856 helix: 1.75 (0.16), residues: 1184 sheet: None (None), residues: 0 loop : -2.69 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 218 HIS 0.001 0.000 HIS A 143 PHE 0.006 0.001 PHE E 189 TYR 0.011 0.001 TYR H 177 ARG 0.003 0.000 ARG E 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3253.34 seconds wall clock time: 59 minutes 29.20 seconds (3569.20 seconds total)