Starting phenix.real_space_refine on Sat Feb 17 02:51:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lto_0976/02_2024/6lto_0976.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lto_0976/02_2024/6lto_0976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lto_0976/02_2024/6lto_0976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lto_0976/02_2024/6lto_0976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lto_0976/02_2024/6lto_0976.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lto_0976/02_2024/6lto_0976.pdb" } resolution = 3.1 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 11494 2.51 5 N 2674 2.21 5 O 3017 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 29": "NH1" <-> "NH2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A ASP 35": "OD1" <-> "OD2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A GLU 144": "OE1" <-> "OE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ASP 261": "OD1" <-> "OD2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C ASP 35": "OD1" <-> "OD2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C ASP 261": "OD1" <-> "OD2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "E GLU 31": "OE1" <-> "OE2" Residue "E ASP 35": "OD1" <-> "OD2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ASP 35": "OD1" <-> "OD2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F GLU 144": "OE1" <-> "OE2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G GLU 31": "OE1" <-> "OE2" Residue "G ASP 35": "OD1" <-> "OD2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "G ASP 261": "OD1" <-> "OD2" Residue "G PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 352": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17255 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2465 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2465 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2465 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2465 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2465 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2465 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2465 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 9.22, per 1000 atoms: 0.53 Number of scatterers: 17255 At special positions: 0 Unit cell: (111.961, 111.961, 120.657, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 3017 8.00 N 2674 7.00 C 11494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " 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: 6.37 Conformation dependent library (CDL) restraints added in 2.8 seconds 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4200 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 66.6% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 32 through 60 removed outlier: 3.732A pdb=" N LYS A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.554A pdb=" N ALA A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 120 removed outlier: 3.961A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 131 through 157 removed outlier: 3.843A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A 152 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE A 154 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.888A pdb=" N LYS A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 209 through 238 removed outlier: 4.462A pdb=" N SER A 238 " --> pdb=" O TYR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 294 removed outlier: 3.502A pdb=" N PHE A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.824A pdb=" N GLU A 310 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.596A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 339 removed outlier: 4.198A pdb=" N ILE A 339 " --> pdb=" O GLU A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 339' Processing helix chain 'A' and resid 342 through 350 removed outlier: 3.800A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 60 removed outlier: 3.732A pdb=" N LYS B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.554A pdb=" N ALA B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 99 through 120 removed outlier: 3.961A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 108 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 131 through 157 removed outlier: 3.843A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 154 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.888A pdb=" N LYS B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 209 through 238 removed outlier: 4.462A pdb=" N SER B 238 " --> pdb=" O TYR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 294 removed outlier: 3.503A pdb=" N PHE B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.823A pdb=" N GLU B 310 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.596A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 339 removed outlier: 4.198A pdb=" N ILE B 339 " --> pdb=" O GLU B 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 336 through 339' Processing helix chain 'B' and resid 342 through 350 removed outlier: 3.800A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 60 removed outlier: 3.732A pdb=" N LYS C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.553A pdb=" N ALA C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 120 removed outlier: 3.961A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 108 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'C' and resid 131 through 157 removed outlier: 3.844A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C 152 " --> pdb=" O LYS C 148 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE C 154 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.888A pdb=" N LYS C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 238 removed outlier: 4.461A pdb=" N SER C 238 " --> pdb=" O TYR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 294 removed outlier: 3.502A pdb=" N PHE C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.823A pdb=" N GLU C 310 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.596A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 339 removed outlier: 4.197A pdb=" N ILE C 339 " --> pdb=" O GLU C 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 336 through 339' Processing helix chain 'C' and resid 342 through 350 removed outlier: 3.799A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 60 removed outlier: 3.732A pdb=" N LYS D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.554A pdb=" N ALA D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 99 through 120 removed outlier: 3.961A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE D 108 " --> pdb=" O TRP D 104 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 121 through 131 Processing helix chain 'D' and resid 131 through 157 removed outlier: 3.844A pdb=" N ILE D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS D 155 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.888A pdb=" N LYS D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 209 through 238 removed outlier: 4.462A pdb=" N SER D 238 " --> pdb=" O TYR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 294 removed outlier: 3.503A pdb=" N PHE D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 306 through 312 removed outlier: 3.823A pdb=" N GLU D 310 " --> pdb=" O LYS D 307 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.596A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 339 removed outlier: 4.198A pdb=" N ILE D 339 " --> pdb=" O GLU D 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 336 through 339' Processing helix chain 'D' and resid 342 through 350 removed outlier: 3.799A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 60 removed outlier: 3.732A pdb=" N LYS E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 87 removed outlier: 3.554A pdb=" N ALA E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 120 removed outlier: 3.961A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE E 108 " --> pdb=" O TRP E 104 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 131 through 157 removed outlier: 3.844A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG E 152 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E 153 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE E 154 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS E 155 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 156 " --> pdb=" O ARG E 152 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 203 removed outlier: 3.888A pdb=" N LYS E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 206 No H-bonds generated for 'chain 'E' and resid 204 through 206' Processing helix chain 'E' and resid 209 through 238 removed outlier: 4.462A pdb=" N SER E 238 " --> pdb=" O TYR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 294 removed outlier: 3.502A pdb=" N PHE E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.823A pdb=" N GLU E 310 " --> pdb=" O LYS E 307 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 335 removed outlier: 3.595A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU E 333 " --> pdb=" O SER E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 339 removed outlier: 4.198A pdb=" N ILE E 339 " --> pdb=" O GLU E 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 336 through 339' Processing helix chain 'E' and resid 342 through 350 removed outlier: 3.800A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 60 removed outlier: 3.732A pdb=" N LYS F 36 " --> pdb=" O LEU F 32 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 87 removed outlier: 3.553A pdb=" N ALA F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 120 removed outlier: 3.961A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE F 108 " --> pdb=" O TRP F 104 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 121 through 131 Processing helix chain 'F' and resid 131 through 157 removed outlier: 3.844A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA F 153 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE F 154 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS F 155 " --> pdb=" O ASN F 151 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 156 " --> pdb=" O ARG F 152 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 203 removed outlier: 3.888A pdb=" N LYS F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 209 through 238 removed outlier: 4.461A pdb=" N SER F 238 " --> pdb=" O TYR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 294 removed outlier: 3.502A pdb=" N PHE F 273 " --> pdb=" O ALA F 269 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 306 through 312 removed outlier: 3.823A pdb=" N GLU F 310 " --> pdb=" O LYS F 307 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 335 removed outlier: 3.596A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 339 removed outlier: 4.198A pdb=" N ILE F 339 " --> pdb=" O GLU F 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 336 through 339' Processing helix chain 'F' and resid 342 through 350 removed outlier: 3.800A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 60 removed outlier: 3.732A pdb=" N LYS G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 87 removed outlier: 3.554A pdb=" N ALA G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 120 removed outlier: 3.962A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'G' and resid 131 through 157 removed outlier: 3.843A pdb=" N ILE G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA G 153 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE G 154 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS G 155 " --> pdb=" O ASN G 151 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA G 156 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 157 " --> pdb=" O ALA G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 203 removed outlier: 3.889A pdb=" N LYS G 201 " --> pdb=" O GLU G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 209 through 238 removed outlier: 4.462A pdb=" N SER G 238 " --> pdb=" O TYR G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 294 removed outlier: 3.503A pdb=" N PHE G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 306 through 312 removed outlier: 3.823A pdb=" N GLU G 310 " --> pdb=" O LYS G 307 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.596A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU G 333 " --> pdb=" O SER G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 339 removed outlier: 4.198A pdb=" N ILE G 339 " --> pdb=" O GLU G 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 336 through 339' Processing helix chain 'G' and resid 342 through 350 removed outlier: 3.800A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 885 hydrogen bonds defined for protein. 2592 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: 4.34 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4991 1.34 - 1.46: 3005 1.46 - 1.57: 9595 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 17668 Sorted by residual: bond pdb=" C GLU B 22 " pdb=" N PRO B 23 " ideal model delta sigma weight residual 1.334 1.383 -0.050 2.34e-02 1.83e+03 4.49e+00 bond pdb=" C GLU F 22 " pdb=" N PRO F 23 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.47e+00 bond pdb=" C GLU C 22 " pdb=" N PRO C 23 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.47e+00 bond pdb=" C GLU G 22 " pdb=" N PRO G 23 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.46e+00 bond pdb=" C GLU D 22 " pdb=" N PRO D 23 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.44e+00 ... (remaining 17663 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.72: 469 106.72 - 113.53: 9771 113.53 - 120.35: 7328 120.35 - 127.16: 6256 127.16 - 133.97: 186 Bond angle restraints: 24010 Sorted by residual: angle pdb=" CA LEU A 237 " pdb=" CB LEU A 237 " pdb=" CG LEU A 237 " ideal model delta sigma weight residual 116.30 130.81 -14.51 3.50e+00 8.16e-02 1.72e+01 angle pdb=" CA LEU F 237 " pdb=" CB LEU F 237 " pdb=" CG LEU F 237 " ideal model delta sigma weight residual 116.30 130.80 -14.50 3.50e+00 8.16e-02 1.72e+01 angle pdb=" CA LEU B 237 " pdb=" CB LEU B 237 " pdb=" CG LEU B 237 " ideal model delta sigma weight residual 116.30 130.79 -14.49 3.50e+00 8.16e-02 1.71e+01 angle pdb=" CA LEU E 237 " pdb=" CB LEU E 237 " pdb=" CG LEU E 237 " ideal model delta sigma weight residual 116.30 130.79 -14.49 3.50e+00 8.16e-02 1.71e+01 angle pdb=" CA LEU G 237 " pdb=" CB LEU G 237 " pdb=" CG LEU G 237 " ideal model delta sigma weight residual 116.30 130.77 -14.47 3.50e+00 8.16e-02 1.71e+01 ... (remaining 24005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 9471 16.80 - 33.60: 924 33.60 - 50.41: 147 50.41 - 67.21: 28 67.21 - 84.01: 42 Dihedral angle restraints: 10612 sinusoidal: 4165 harmonic: 6447 Sorted by residual: dihedral pdb=" CA LEU A 237 " pdb=" C LEU A 237 " pdb=" N SER A 238 " pdb=" CA SER A 238 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA LEU D 237 " pdb=" C LEU D 237 " pdb=" N SER D 238 " pdb=" CA SER D 238 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LEU C 237 " pdb=" C LEU C 237 " pdb=" N SER C 238 " pdb=" CA SER C 238 " ideal model delta harmonic sigma weight residual 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 10609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1756 0.042 - 0.084: 780 0.084 - 0.126: 247 0.126 - 0.168: 52 0.168 - 0.211: 21 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CB VAL A 317 " pdb=" CA VAL A 317 " pdb=" CG1 VAL A 317 " pdb=" CG2 VAL A 317 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL C 317 " pdb=" CA VAL C 317 " pdb=" CG1 VAL C 317 " pdb=" CG2 VAL C 317 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB VAL F 317 " pdb=" CA VAL F 317 " pdb=" CG1 VAL F 317 " pdb=" CG2 VAL F 317 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2853 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 101 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.44e+00 pdb=" N PRO B 102 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 102 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 102 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 101 " -0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO A 102 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 101 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D 102 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 102 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 102 " -0.036 5.00e-02 4.00e+02 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 5414 2.83 - 3.35: 16176 3.35 - 3.87: 26278 3.87 - 4.38: 28971 4.38 - 4.90: 51825 Nonbonded interactions: 128664 Sorted by model distance: nonbonded pdb=" OE1 GLN A 56 " pdb=" OH TYR F 111 " model vdw 2.318 2.440 nonbonded pdb=" O SER E 238 " pdb=" OG SER E 238 " model vdw 2.322 2.440 nonbonded pdb=" OH TYR E 111 " pdb=" OE1 GLN G 56 " model vdw 2.322 2.440 nonbonded pdb=" O SER F 238 " pdb=" OG SER F 238 " model vdw 2.323 2.440 nonbonded pdb=" O SER G 238 " pdb=" OG SER G 238 " model vdw 2.323 2.440 ... (remaining 128659 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 2.830 Check model and map are aligned: 0.310 Set scattering table: 0.160 Process input model: 43.320 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.007 0.077 17668 Z= 0.435 Angle : 0.996 14.509 24010 Z= 0.516 Chirality : 0.054 0.211 2856 Planarity : 0.008 0.063 2912 Dihedral : 14.553 84.010 6370 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.14), residues: 2128 helix: -2.17 (0.11), residues: 1295 sheet: -1.42 (0.37), residues: 126 loop : -3.91 (0.18), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP G 127 HIS 0.004 0.002 HIS C 319 PHE 0.017 0.002 PHE G 244 TYR 0.017 0.002 TYR C 213 ARG 0.002 0.000 ARG D 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 2.068 Fit side-chains REVERT: A 90 GLN cc_start: 0.8649 (pm20) cc_final: 0.8348 (pm20) REVERT: A 104 TRP cc_start: 0.7793 (t60) cc_final: 0.7411 (t60) REVERT: A 347 CYS cc_start: 0.8199 (m) cc_final: 0.7963 (m) REVERT: B 104 TRP cc_start: 0.7833 (t60) cc_final: 0.7454 (t60) REVERT: B 208 ASN cc_start: 0.8466 (t0) cc_final: 0.8182 (t0) REVERT: B 347 CYS cc_start: 0.8321 (m) cc_final: 0.8108 (m) REVERT: C 37 MET cc_start: 0.7561 (ttp) cc_final: 0.7195 (tmm) REVERT: C 208 ASN cc_start: 0.8683 (t0) cc_final: 0.8369 (t0) REVERT: D 37 MET cc_start: 0.7492 (ttp) cc_final: 0.7203 (tmm) REVERT: D 208 ASN cc_start: 0.8646 (t0) cc_final: 0.8305 (t0) REVERT: F 37 MET cc_start: 0.7362 (ttp) cc_final: 0.7028 (tmm) REVERT: F 104 TRP cc_start: 0.7933 (t60) cc_final: 0.7527 (t60) REVERT: F 208 ASN cc_start: 0.8597 (t0) cc_final: 0.8157 (t0) REVERT: F 307 LYS cc_start: 0.9389 (tptt) cc_final: 0.8986 (tppt) REVERT: G 90 GLN cc_start: 0.8550 (pm20) cc_final: 0.8236 (pm20) REVERT: G 104 TRP cc_start: 0.7665 (t60) cc_final: 0.7354 (t60) REVERT: G 299 PHE cc_start: 0.8528 (t80) cc_final: 0.8307 (t80) REVERT: G 334 PHE cc_start: 0.7409 (t80) cc_final: 0.6874 (t80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2609 time to fit residues: 92.5080 Evaluate side-chains 159 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 20.0000 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 205 ASN A 274 GLN A 280 ASN B 76 GLN B 100 ASN B 205 ASN B 274 GLN B 280 ASN B 319 HIS C 76 GLN C 205 ASN C 274 GLN C 280 ASN C 319 HIS D 76 GLN D 100 ASN D 198 GLN D 205 ASN D 274 GLN D 280 ASN E 76 GLN E 205 ASN E 274 GLN E 280 ASN E 319 HIS F 76 GLN F 100 ASN F 198 GLN F 205 ASN F 274 GLN F 280 ASN G 76 GLN G 205 ASN G 274 GLN G 280 ASN G 319 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17668 Z= 0.150 Angle : 0.581 9.029 24010 Z= 0.288 Chirality : 0.038 0.116 2856 Planarity : 0.006 0.048 2912 Dihedral : 4.465 19.146 2296 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.60 % Allowed : 11.35 % Favored : 87.06 % 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: -1.81 (0.18), residues: 2128 helix: -0.03 (0.14), residues: 1302 sheet: -0.93 (0.41), residues: 126 loop : -3.55 (0.20), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 127 HIS 0.001 0.000 HIS G 319 PHE 0.009 0.001 PHE E 244 TYR 0.013 0.001 TYR A 345 ARG 0.004 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 2.014 Fit side-chains REVERT: A 104 TRP cc_start: 0.7788 (t60) cc_final: 0.7365 (t60) REVERT: A 347 CYS cc_start: 0.8134 (m) cc_final: 0.7896 (m) REVERT: B 104 TRP cc_start: 0.7840 (t60) cc_final: 0.7321 (t60) REVERT: B 208 ASN cc_start: 0.8475 (t0) cc_final: 0.8186 (t0) REVERT: B 347 CYS cc_start: 0.8132 (m) cc_final: 0.7815 (m) REVERT: C 37 MET cc_start: 0.7447 (ttp) cc_final: 0.7174 (tmm) REVERT: C 208 ASN cc_start: 0.8651 (t0) cc_final: 0.8331 (t0) REVERT: D 208 ASN cc_start: 0.8632 (t0) cc_final: 0.8238 (t0) REVERT: E 30 LEU cc_start: 0.7756 (mt) cc_final: 0.7510 (mp) REVERT: E 208 ASN cc_start: 0.8509 (t0) cc_final: 0.8215 (t0) REVERT: E 345 TYR cc_start: 0.7603 (t80) cc_final: 0.7381 (t80) REVERT: F 29 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7725 (mtm-85) REVERT: F 104 TRP cc_start: 0.7849 (t60) cc_final: 0.7597 (t60) REVERT: F 208 ASN cc_start: 0.8602 (t0) cc_final: 0.8122 (t0) REVERT: G 90 GLN cc_start: 0.8549 (pm20) cc_final: 0.8287 (pm20) REVERT: G 304 ASP cc_start: 0.7018 (p0) cc_final: 0.6799 (p0) outliers start: 31 outliers final: 16 residues processed: 229 average time/residue: 0.2348 time to fit residues: 87.8371 Evaluate side-chains 176 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 160 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 205 ASN A 280 ASN B 89 GLN B 205 ASN C 89 GLN C 205 ASN D 89 GLN D 205 ASN D 280 ASN E 89 GLN E 205 ASN F 89 GLN F 205 ASN F 280 ASN G 89 GLN G 205 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 17668 Z= 0.422 Angle : 0.695 9.501 24010 Z= 0.353 Chirality : 0.042 0.167 2856 Planarity : 0.006 0.057 2912 Dihedral : 4.727 21.620 2296 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.04 % Allowed : 13.56 % Favored : 83.39 % 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: -1.12 (0.19), residues: 2128 helix: 0.58 (0.15), residues: 1309 sheet: -0.86 (0.42), residues: 126 loop : -3.41 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP D 85 HIS 0.003 0.002 HIS D 134 PHE 0.015 0.002 PHE B 244 TYR 0.020 0.002 TYR A 213 ARG 0.003 0.000 ARG D 300 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 183 time to evaluate : 2.192 Fit side-chains REVERT: A 37 MET cc_start: 0.7579 (tmm) cc_final: 0.7337 (tmm) REVERT: A 89 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7301 (mm110) REVERT: B 37 MET cc_start: 0.7310 (tmm) cc_final: 0.6934 (tmm) REVERT: B 208 ASN cc_start: 0.8485 (t0) cc_final: 0.8191 (t0) REVERT: B 347 CYS cc_start: 0.8304 (m) cc_final: 0.8019 (m) REVERT: C 37 MET cc_start: 0.7739 (ttp) cc_final: 0.7359 (tmm) REVERT: C 89 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7296 (mm110) REVERT: C 208 ASN cc_start: 0.8656 (t0) cc_final: 0.8311 (t0) REVERT: D 37 MET cc_start: 0.7380 (tmm) cc_final: 0.7133 (tmm) REVERT: D 89 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7230 (mm110) REVERT: D 208 ASN cc_start: 0.8600 (t0) cc_final: 0.8234 (t0) REVERT: E 208 ASN cc_start: 0.8588 (t0) cc_final: 0.8275 (t0) REVERT: E 345 TYR cc_start: 0.7820 (t80) cc_final: 0.7616 (t80) REVERT: F 89 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7436 (mm110) REVERT: F 208 ASN cc_start: 0.8564 (t0) cc_final: 0.8139 (t0) REVERT: G 89 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7397 (mm110) REVERT: G 299 PHE cc_start: 0.8440 (t80) cc_final: 0.8083 (t80) outliers start: 59 outliers final: 44 residues processed: 221 average time/residue: 0.2651 time to fit residues: 92.4590 Evaluate side-chains 212 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 163 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 258 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 205 ASN B 205 ASN C 205 ASN C 280 ASN D 205 ASN E 198 GLN E 205 ASN F 205 ASN G 205 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17668 Z= 0.152 Angle : 0.557 9.802 24010 Z= 0.276 Chirality : 0.037 0.117 2856 Planarity : 0.005 0.043 2912 Dihedral : 4.222 20.875 2296 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.60 % Allowed : 16.55 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.19), residues: 2128 helix: 1.08 (0.15), residues: 1302 sheet: -0.58 (0.45), residues: 126 loop : -3.17 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 74 HIS 0.001 0.001 HIS G 319 PHE 0.020 0.001 PHE A 299 TYR 0.012 0.001 TYR G 213 ARG 0.003 0.000 ARG E 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 186 time to evaluate : 1.922 Fit side-chains REVERT: A 104 TRP cc_start: 0.8006 (t60) cc_final: 0.7794 (t60) REVERT: B 208 ASN cc_start: 0.8454 (t0) cc_final: 0.8141 (t0) REVERT: B 347 CYS cc_start: 0.8226 (m) cc_final: 0.7872 (m) REVERT: C 37 MET cc_start: 0.7476 (ttp) cc_final: 0.7114 (tmm) REVERT: C 208 ASN cc_start: 0.8600 (t0) cc_final: 0.8283 (t0) REVERT: D 37 MET cc_start: 0.7151 (tmm) cc_final: 0.6915 (tmm) REVERT: D 208 ASN cc_start: 0.8620 (t0) cc_final: 0.8229 (t0) REVERT: E 208 ASN cc_start: 0.8498 (t0) cc_final: 0.8193 (t0) REVERT: E 345 TYR cc_start: 0.7762 (t80) cc_final: 0.7539 (t80) REVERT: F 208 ASN cc_start: 0.8492 (t0) cc_final: 0.8049 (t0) REVERT: G 299 PHE cc_start: 0.8365 (t80) cc_final: 0.7966 (t80) outliers start: 31 outliers final: 19 residues processed: 207 average time/residue: 0.2570 time to fit residues: 84.1057 Evaluate side-chains 186 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 343 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 319 HIS B 205 ASN C 205 ASN D 205 ASN D 319 HIS E 205 ASN F 89 GLN F 205 ASN F 319 HIS G 205 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17668 Z= 0.160 Angle : 0.542 9.747 24010 Z= 0.268 Chirality : 0.037 0.125 2856 Planarity : 0.004 0.042 2912 Dihedral : 3.947 20.251 2296 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 2.53 % Allowed : 16.55 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 2128 helix: 1.37 (0.16), residues: 1309 sheet: -0.30 (0.47), residues: 126 loop : -2.96 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 85 HIS 0.001 0.001 HIS F 106 PHE 0.017 0.001 PHE B 299 TYR 0.012 0.001 TYR G 213 ARG 0.004 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 190 time to evaluate : 2.095 Fit side-chains REVERT: A 104 TRP cc_start: 0.7971 (t60) cc_final: 0.7727 (t60) REVERT: B 208 ASN cc_start: 0.8453 (t0) cc_final: 0.8122 (t0) REVERT: B 347 CYS cc_start: 0.8154 (m) cc_final: 0.7775 (m) REVERT: C 37 MET cc_start: 0.7386 (ttp) cc_final: 0.6814 (tmm) REVERT: C 208 ASN cc_start: 0.8685 (t0) cc_final: 0.8324 (t0) REVERT: D 208 ASN cc_start: 0.8626 (t0) cc_final: 0.8216 (t0) REVERT: E 208 ASN cc_start: 0.8512 (t0) cc_final: 0.8177 (t0) REVERT: E 345 TYR cc_start: 0.7701 (t80) cc_final: 0.7445 (t80) REVERT: F 208 ASN cc_start: 0.8478 (t0) cc_final: 0.8019 (t0) REVERT: G 299 PHE cc_start: 0.8460 (t80) cc_final: 0.8052 (t80) outliers start: 49 outliers final: 35 residues processed: 228 average time/residue: 0.2515 time to fit residues: 90.8640 Evaluate side-chains 214 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 205 ASN B 205 ASN C 89 GLN C 205 ASN D 89 GLN D 205 ASN E 205 ASN F 89 GLN F 205 ASN F 280 ASN G 89 GLN G 205 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17668 Z= 0.224 Angle : 0.574 9.605 24010 Z= 0.287 Chirality : 0.038 0.129 2856 Planarity : 0.005 0.042 2912 Dihedral : 4.021 20.144 2296 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.30 % Allowed : 17.38 % Favored : 79.32 % 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: -0.04 (0.20), residues: 2128 helix: 1.40 (0.16), residues: 1309 sheet: -0.25 (0.47), residues: 126 loop : -2.92 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.002 0.001 HIS D 319 PHE 0.017 0.001 PHE B 299 TYR 0.016 0.001 TYR C 213 ARG 0.004 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 182 time to evaluate : 2.039 Fit side-chains REVERT: A 89 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7252 (mm110) REVERT: A 280 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8335 (t0) REVERT: B 208 ASN cc_start: 0.8464 (t0) cc_final: 0.8116 (t0) REVERT: B 347 CYS cc_start: 0.8250 (m) cc_final: 0.7868 (m) REVERT: C 37 MET cc_start: 0.7406 (ttp) cc_final: 0.6993 (tmm) REVERT: C 89 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7213 (mm110) REVERT: C 208 ASN cc_start: 0.8619 (t0) cc_final: 0.8282 (t0) REVERT: D 16 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6605 (pp) REVERT: D 208 ASN cc_start: 0.8588 (t0) cc_final: 0.8204 (t0) REVERT: E 16 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6767 (pp) REVERT: E 208 ASN cc_start: 0.8511 (t0) cc_final: 0.8185 (t0) REVERT: E 345 TYR cc_start: 0.7758 (t80) cc_final: 0.7507 (t80) REVERT: F 16 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6494 (pp) REVERT: F 208 ASN cc_start: 0.8496 (t0) cc_final: 0.8107 (t0) REVERT: G 16 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6661 (pp) REVERT: G 299 PHE cc_start: 0.8484 (t80) cc_final: 0.8128 (t80) REVERT: G 304 ASP cc_start: 0.7314 (p0) cc_final: 0.7069 (p0) outliers start: 64 outliers final: 42 residues processed: 234 average time/residue: 0.2376 time to fit residues: 89.6838 Evaluate side-chains 223 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 174 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 343 LYS Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 113 optimal weight: 0.1980 chunk 202 optimal weight: 0.7980 chunk 126 optimal weight: 0.0980 chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 205 ASN C 205 ASN C 280 ASN D 89 GLN D 205 ASN E 205 ASN F 205 ASN G 205 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17668 Z= 0.129 Angle : 0.525 9.345 24010 Z= 0.258 Chirality : 0.037 0.122 2856 Planarity : 0.004 0.042 2912 Dihedral : 3.727 20.260 2296 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.96 % Allowed : 18.67 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 2128 helix: 1.66 (0.16), residues: 1302 sheet: -0.14 (0.48), residues: 126 loop : -2.76 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 104 HIS 0.001 0.001 HIS B 106 PHE 0.019 0.001 PHE E 299 TYR 0.015 0.001 TYR D 345 ARG 0.003 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 1.780 Fit side-chains REVERT: A 104 TRP cc_start: 0.7902 (t60) cc_final: 0.7636 (t60) REVERT: B 208 ASN cc_start: 0.8439 (t0) cc_final: 0.8150 (t0) REVERT: B 347 CYS cc_start: 0.8063 (m) cc_final: 0.7641 (m) REVERT: C 16 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6332 (pp) REVERT: C 208 ASN cc_start: 0.8664 (t0) cc_final: 0.8291 (t0) REVERT: D 208 ASN cc_start: 0.8612 (t0) cc_final: 0.8210 (t0) REVERT: E 208 ASN cc_start: 0.8456 (t0) cc_final: 0.8088 (t0) REVERT: E 345 TYR cc_start: 0.7699 (t80) cc_final: 0.7410 (t80) REVERT: F 208 ASN cc_start: 0.8452 (t0) cc_final: 0.7990 (t0) REVERT: F 280 ASN cc_start: 0.8347 (t0) cc_final: 0.8015 (t0) REVERT: G 299 PHE cc_start: 0.8422 (t80) cc_final: 0.8158 (t80) REVERT: G 304 ASP cc_start: 0.7197 (p0) cc_final: 0.6942 (p0) outliers start: 38 outliers final: 29 residues processed: 218 average time/residue: 0.2404 time to fit residues: 84.0993 Evaluate side-chains 210 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 334 PHE Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 0.3980 chunk 60 optimal weight: 0.0670 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 0.0980 chunk 137 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 205 ASN C 205 ASN D 89 GLN D 205 ASN D 280 ASN E 205 ASN F 205 ASN G 205 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17668 Z= 0.133 Angle : 0.524 9.122 24010 Z= 0.258 Chirality : 0.037 0.116 2856 Planarity : 0.004 0.042 2912 Dihedral : 3.606 19.077 2296 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.01 % Allowed : 18.77 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 2128 helix: 1.81 (0.15), residues: 1309 sheet: -0.07 (0.47), residues: 126 loop : -2.66 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 104 HIS 0.002 0.001 HIS B 106 PHE 0.021 0.001 PHE B 299 TYR 0.019 0.001 TYR A 345 ARG 0.004 0.000 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 187 time to evaluate : 2.067 Fit side-chains REVERT: B 16 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6390 (pp) REVERT: B 208 ASN cc_start: 0.8438 (t0) cc_final: 0.8116 (t0) REVERT: B 347 CYS cc_start: 0.8087 (m) cc_final: 0.7650 (m) REVERT: C 16 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6334 (pp) REVERT: C 208 ASN cc_start: 0.8661 (t0) cc_final: 0.8275 (t0) REVERT: D 208 ASN cc_start: 0.8637 (t0) cc_final: 0.8190 (t0) REVERT: E 208 ASN cc_start: 0.8457 (t0) cc_final: 0.8074 (t0) REVERT: F 208 ASN cc_start: 0.8459 (t0) cc_final: 0.7977 (t0) REVERT: G 16 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6618 (pp) REVERT: G 90 GLN cc_start: 0.8486 (pm20) cc_final: 0.8212 (pm20) REVERT: G 299 PHE cc_start: 0.8416 (t80) cc_final: 0.8152 (t80) REVERT: G 304 ASP cc_start: 0.7206 (p0) cc_final: 0.6989 (p0) outliers start: 39 outliers final: 28 residues processed: 215 average time/residue: 0.2536 time to fit residues: 86.5251 Evaluate side-chains 210 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 334 PHE Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.6980 chunk 176 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 205 ASN B 205 ASN C 89 GLN C 205 ASN C 280 ASN D 89 GLN D 205 ASN E 205 ASN F 205 ASN G 205 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17668 Z= 0.206 Angle : 0.563 9.499 24010 Z= 0.281 Chirality : 0.038 0.126 2856 Planarity : 0.004 0.042 2912 Dihedral : 3.761 19.007 2296 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 1.91 % Allowed : 18.82 % Favored : 79.27 % 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: 0.52 (0.20), residues: 2128 helix: 1.83 (0.15), residues: 1309 sheet: -0.02 (0.48), residues: 126 loop : -2.66 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.002 0.001 HIS D 319 PHE 0.014 0.001 PHE F 299 TYR 0.016 0.001 TYR D 345 ARG 0.004 0.000 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 177 time to evaluate : 1.987 Fit side-chains REVERT: B 16 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6426 (pp) REVERT: B 208 ASN cc_start: 0.8386 (t0) cc_final: 0.8044 (t0) REVERT: B 347 CYS cc_start: 0.8195 (m) cc_final: 0.7794 (m) REVERT: C 16 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6335 (pp) REVERT: C 37 MET cc_start: 0.7339 (ttp) cc_final: 0.7010 (tmm) REVERT: C 208 ASN cc_start: 0.8618 (t0) cc_final: 0.8271 (t0) REVERT: D 16 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6632 (pp) REVERT: D 208 ASN cc_start: 0.8605 (t0) cc_final: 0.8194 (t0) REVERT: E 16 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6698 (pp) REVERT: E 208 ASN cc_start: 0.8494 (t0) cc_final: 0.8127 (t0) REVERT: F 208 ASN cc_start: 0.8483 (t0) cc_final: 0.8009 (t0) REVERT: G 16 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6650 (pp) REVERT: G 299 PHE cc_start: 0.8431 (t80) cc_final: 0.8137 (t80) REVERT: G 304 ASP cc_start: 0.7173 (p0) cc_final: 0.6951 (p0) outliers start: 37 outliers final: 31 residues processed: 205 average time/residue: 0.2381 time to fit residues: 80.1786 Evaluate side-chains 212 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 280 ASN Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 334 PHE Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 192 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 132 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 205 ASN C 205 ASN C 280 ASN D 89 GLN D 205 ASN E 205 ASN F 205 ASN G 205 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17668 Z= 0.255 Angle : 0.592 9.523 24010 Z= 0.298 Chirality : 0.039 0.136 2856 Planarity : 0.005 0.043 2912 Dihedral : 3.949 20.013 2296 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.11 % Allowed : 18.67 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 2128 helix: 1.77 (0.15), residues: 1309 sheet: -0.05 (0.47), residues: 126 loop : -2.70 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 104 HIS 0.003 0.001 HIS D 319 PHE 0.023 0.001 PHE E 299 TYR 0.017 0.001 TYR C 345 ARG 0.005 0.000 ARG D 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 183 time to evaluate : 2.055 Fit side-chains REVERT: A 104 TRP cc_start: 0.7798 (t60) cc_final: 0.7312 (t60) REVERT: B 16 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6466 (pp) REVERT: B 208 ASN cc_start: 0.8407 (t0) cc_final: 0.8055 (t0) REVERT: B 347 CYS cc_start: 0.8294 (m) cc_final: 0.7909 (m) REVERT: C 16 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6315 (pp) REVERT: C 37 MET cc_start: 0.7384 (ttp) cc_final: 0.6995 (tmm) REVERT: C 208 ASN cc_start: 0.8616 (t0) cc_final: 0.8266 (t0) REVERT: D 16 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6630 (pp) REVERT: D 208 ASN cc_start: 0.8597 (t0) cc_final: 0.8191 (t0) REVERT: E 208 ASN cc_start: 0.8534 (t0) cc_final: 0.8190 (t0) REVERT: F 16 LEU cc_start: 0.6819 (OUTLIER) cc_final: 0.6346 (pp) REVERT: F 208 ASN cc_start: 0.8530 (t0) cc_final: 0.8125 (t0) REVERT: G 16 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6787 (pp) REVERT: G 299 PHE cc_start: 0.8485 (t80) cc_final: 0.8140 (t80) REVERT: G 304 ASP cc_start: 0.7268 (p0) cc_final: 0.6997 (p0) outliers start: 41 outliers final: 33 residues processed: 216 average time/residue: 0.2316 time to fit residues: 82.7963 Evaluate side-chains 214 residues out of total 1974 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 176 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 40 CYS Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 62 THR Chi-restraints excluded: chain G residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.0870 chunk 51 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 171 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 30 optimal weight: 30.0000 chunk 146 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 205 ASN B 205 ASN C 205 ASN D 89 GLN D 205 ASN E 205 ASN F 205 ASN G 205 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.168746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117369 restraints weight = 23010.527| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.77 r_work: 0.3140 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17668 Z= 0.140 Angle : 0.536 9.381 24010 Z= 0.265 Chirality : 0.037 0.113 2856 Planarity : 0.004 0.042 2912 Dihedral : 3.659 20.125 2296 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.65 % Allowed : 19.24 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 2128 helix: 1.93 (0.15), residues: 1302 sheet: -0.06 (0.47), residues: 126 loop : -2.61 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 104 HIS 0.002 0.001 HIS B 106 PHE 0.015 0.001 PHE F 299 TYR 0.021 0.001 TYR E 345 ARG 0.004 0.000 ARG D 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3136.01 seconds wall clock time: 58 minutes 34.69 seconds (3514.69 seconds total)