Starting phenix.real_space_refine on Mon Mar 18 11:39:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/03_2024/6kfh_9973.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/03_2024/6kfh_9973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/03_2024/6kfh_9973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/03_2024/6kfh_9973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/03_2024/6kfh_9973.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kfh_9973/03_2024/6kfh_9973.pdb" } resolution = 3.6 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 13832 2.51 5 N 3344 2.21 5 O 3568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 54": "OD1" <-> "OD2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 87": "OD1" <-> "OD2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 181": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 123": "NH1" <-> "NH2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 87": "OD1" <-> "OD2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ASP 153": "OD1" <-> "OD2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 181": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 123": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E ASP 153": "OD1" <-> "OD2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 87": "OD1" <-> "OD2" Residue "F TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 123": "NH1" <-> "NH2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 155": "OD1" <-> "OD2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 166": "OE1" <-> "OE2" Residue "F TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 181": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 87": "OD1" <-> "OD2" Residue "G TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 123": "NH1" <-> "NH2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ASP 153": "OD1" <-> "OD2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 181": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "G PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 87": "OD1" <-> "OD2" Residue "H TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H ASP 153": "OD1" <-> "OD2" Residue "H ASP 155": "OD1" <-> "OD2" Residue "H ARG 161": "NH1" <-> "NH2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 181": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "H PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20840 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2605 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 307} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 10.12, per 1000 atoms: 0.49 Number of scatterers: 20840 At special positions: 0 Unit cell: (124.432, 124.432, 108.416, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3568 8.00 N 3344 7.00 C 13832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS B 58 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 76 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS C 248 " distance=2.03 Simple disulfide: pdb=" SG CYS D 58 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 76 " - pdb=" SG CYS D 248 " distance=2.03 Simple disulfide: pdb=" SG CYS E 58 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 76 " - pdb=" SG CYS E 248 " distance=2.03 Simple disulfide: pdb=" SG CYS F 58 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 76 " - pdb=" SG CYS F 248 " distance=2.03 Simple disulfide: pdb=" SG CYS G 58 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 76 " - pdb=" SG CYS G 248 " distance=2.03 Simple disulfide: pdb=" SG CYS H 58 " - pdb=" SG CYS H 265 " distance=2.03 Simple disulfide: pdb=" SG CYS H 76 " - pdb=" SG CYS H 248 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.80 Conformation dependent library (CDL) restraints added in 3.3 seconds 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4880 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 8 sheets defined 71.1% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 removed outlier: 4.455A pdb=" N GLN A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 136 through 152 removed outlier: 3.865A pdb=" N ALA A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 159' Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.516A pdb=" N TYR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 212 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU A 274 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 337 through 350 removed outlier: 3.804A pdb=" N ASP A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.523A pdb=" N TYR A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 357 " --> pdb=" O PRO A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 53 removed outlier: 3.595A pdb=" N VAL B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA B 140 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE B 158 " --> pdb=" O ASP B 155 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 159' Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 212 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU B 274 " --> pdb=" O ASN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE B 282 " --> pdb=" O ILE B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 357 " --> pdb=" O PRO B 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 53 removed outlier: 3.595A pdb=" N VAL C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 removed outlier: 4.455A pdb=" N GLN C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) Proline residue: C 122 - end of helix Processing helix chain 'C' and resid 136 through 152 removed outlier: 3.865A pdb=" N ALA C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE C 158 " --> pdb=" O ASP C 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 159' Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 212 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 269 through 274 removed outlier: 4.040A pdb=" N GLU C 274 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE C 282 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 337 through 350 removed outlier: 3.802A pdb=" N ASP C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU C 357 " --> pdb=" O PRO C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) Proline residue: D 122 - end of helix Processing helix chain 'D' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE D 158 " --> pdb=" O ASP D 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 159' Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 removed outlier: 3.518A pdb=" N TYR D 172 " --> pdb=" O ARG D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 212 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR D 356 " --> pdb=" O ILE D 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU D 357 " --> pdb=" O PRO D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 53 removed outlier: 3.595A pdb=" N VAL E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 removed outlier: 4.455A pdb=" N GLN E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) Proline residue: E 122 - end of helix Processing helix chain 'E' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE E 158 " --> pdb=" O ASP E 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 155 through 159' Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR E 172 " --> pdb=" O ARG E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 212 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 269 through 274 removed outlier: 4.038A pdb=" N GLU E 274 " --> pdb=" O ASN E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 326 through 334 Processing helix chain 'E' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP E 343 " --> pdb=" O LEU E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU E 357 " --> pdb=" O PRO E 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 133 removed outlier: 4.549A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) Proline residue: F 122 - end of helix Processing helix chain 'F' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA F 140 " --> pdb=" O ASP F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 159 removed outlier: 3.603A pdb=" N PHE F 158 " --> pdb=" O ASP F 155 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 155 through 159' Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE F 165 " --> pdb=" O ARG F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 212 Processing helix chain 'F' and resid 223 through 232 Processing helix chain 'F' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE F 282 " --> pdb=" O ILE F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 326 through 334 Processing helix chain 'F' and resid 337 through 350 removed outlier: 3.802A pdb=" N ASP F 343 " --> pdb=" O LEU F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.523A pdb=" N TYR F 356 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LEU F 357 " --> pdb=" O PRO F 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Proline residue: G 122 - end of helix Processing helix chain 'G' and resid 136 through 152 removed outlier: 3.864A pdb=" N ALA G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE G 158 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 155 through 159' Processing helix chain 'G' and resid 160 through 168 removed outlier: 3.576A pdb=" N PHE G 165 " --> pdb=" O ARG G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR G 172 " --> pdb=" O ARG G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 212 Processing helix chain 'G' and resid 223 through 232 Processing helix chain 'G' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU G 274 " --> pdb=" O ASN G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE G 282 " --> pdb=" O ILE G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 326 through 334 Processing helix chain 'G' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP G 343 " --> pdb=" O LEU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR G 356 " --> pdb=" O ILE G 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU G 357 " --> pdb=" O PRO G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 53 removed outlier: 3.596A pdb=" N VAL H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 79 removed outlier: 4.456A pdb=" N GLN H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 133 removed outlier: 4.550A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) Proline residue: H 122 - end of helix Processing helix chain 'H' and resid 136 through 152 removed outlier: 3.865A pdb=" N ALA H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 159 removed outlier: 3.604A pdb=" N PHE H 158 " --> pdb=" O ASP H 155 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 155 through 159' Processing helix chain 'H' and resid 160 through 168 removed outlier: 3.575A pdb=" N PHE H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 181 removed outlier: 3.517A pdb=" N TYR H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 212 Processing helix chain 'H' and resid 223 through 232 Processing helix chain 'H' and resid 269 through 274 removed outlier: 4.039A pdb=" N GLU H 274 " --> pdb=" O ASN H 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 305 removed outlier: 4.001A pdb=" N PHE H 282 " --> pdb=" O ILE H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 326 through 334 Processing helix chain 'H' and resid 337 through 350 removed outlier: 3.803A pdb=" N ASP H 343 " --> pdb=" O LEU H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.524A pdb=" N TYR H 356 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU H 357 " --> pdb=" O PRO H 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA2, first strand: chain 'B' and resid 245 through 246 Processing sheet with id=AA3, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AA4, first strand: chain 'D' and resid 245 through 246 Processing sheet with id=AA5, first strand: chain 'E' and resid 245 through 246 Processing sheet with id=AA6, first strand: chain 'F' and resid 245 through 246 Processing sheet with id=AA7, first strand: chain 'G' and resid 245 through 246 Processing sheet with id=AA8, first strand: chain 'H' and resid 245 through 246 1224 hydrogen bonds defined for protein. 3648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 8.55 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: 6232 1.34 - 1.46: 5580 1.46 - 1.58: 9524 1.58 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 21472 Sorted by residual: bond pdb=" CA ILE G 56 " pdb=" CB ILE G 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.94e+00 bond pdb=" CA ILE F 56 " pdb=" CB ILE F 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.85e+00 bond pdb=" CA ILE E 56 " pdb=" CB ILE E 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.71e+00 bond pdb=" CA ILE C 56 " pdb=" CB ILE C 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.63e+00 bond pdb=" CA ILE A 56 " pdb=" CB ILE A 56 " ideal model delta sigma weight residual 1.553 1.537 0.016 7.40e-03 1.83e+04 4.59e+00 ... (remaining 21467 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.64: 464 106.64 - 113.50: 11740 113.50 - 120.36: 8728 120.36 - 127.21: 8004 127.21 - 134.07: 336 Bond angle restraints: 29272 Sorted by residual: angle pdb=" C TRP C 59 " pdb=" N THR C 60 " pdb=" CA THR C 60 " ideal model delta sigma weight residual 121.95 110.30 11.65 3.74e+00 7.15e-02 9.70e+00 angle pdb=" C TRP F 59 " pdb=" N THR F 60 " pdb=" CA THR F 60 " ideal model delta sigma weight residual 121.95 110.35 11.60 3.74e+00 7.15e-02 9.63e+00 angle pdb=" C TRP H 59 " pdb=" N THR H 60 " pdb=" CA THR H 60 " ideal model delta sigma weight residual 121.95 110.36 11.59 3.74e+00 7.15e-02 9.61e+00 angle pdb=" C TRP B 59 " pdb=" N THR B 60 " pdb=" CA THR B 60 " ideal model delta sigma weight residual 121.95 110.37 11.58 3.74e+00 7.15e-02 9.59e+00 angle pdb=" C TRP A 59 " pdb=" N THR A 60 " pdb=" CA THR A 60 " ideal model delta sigma weight residual 121.95 110.37 11.58 3.74e+00 7.15e-02 9.58e+00 ... (remaining 29267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.88: 10564 15.88 - 31.77: 1284 31.77 - 47.65: 360 47.65 - 63.53: 8 63.53 - 79.41: 24 Dihedral angle restraints: 12240 sinusoidal: 4704 harmonic: 7536 Sorted by residual: dihedral pdb=" CA ASP F 28 " pdb=" C ASP F 28 " pdb=" N ARG F 29 " pdb=" CA ARG F 29 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ASP C 28 " pdb=" C ASP C 28 " pdb=" N ARG C 29 " pdb=" CA ARG C 29 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ASP D 28 " pdb=" C ASP D 28 " pdb=" N ARG D 29 " pdb=" CA ARG D 29 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 12237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1979 0.036 - 0.071: 907 0.071 - 0.107: 237 0.107 - 0.143: 86 0.143 - 0.178: 23 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CA GLU G 274 " pdb=" N GLU G 274 " pdb=" C GLU G 274 " pdb=" CB GLU G 274 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.96e-01 chirality pdb=" CA GLU D 274 " pdb=" N GLU D 274 " pdb=" C GLU D 274 " pdb=" CB GLU D 274 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" CA GLU F 274 " pdb=" N GLU F 274 " pdb=" C GLU F 274 " pdb=" CB GLU F 274 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 3229 not shown) Planarity restraints: 3584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 305 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C LYS G 305 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS G 305 " 0.009 2.00e-02 2.50e+03 pdb=" N THR G 306 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 305 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LYS H 305 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS H 305 " 0.009 2.00e-02 2.50e+03 pdb=" N THR H 306 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 305 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LYS F 305 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS F 305 " 0.009 2.00e-02 2.50e+03 pdb=" N THR F 306 " 0.008 2.00e-02 2.50e+03 ... (remaining 3581 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5610 2.78 - 3.31: 20640 3.31 - 3.84: 33880 3.84 - 4.37: 37027 4.37 - 4.90: 64227 Nonbonded interactions: 161384 Sorted by model distance: nonbonded pdb=" O ASN F 31 " pdb=" OG1 THR F 35 " model vdw 2.255 2.440 nonbonded pdb=" O ASN E 31 " pdb=" OG1 THR E 35 " model vdw 2.255 2.440 nonbonded pdb=" O ASN G 31 " pdb=" OG1 THR G 35 " model vdw 2.255 2.440 nonbonded pdb=" O ASN D 31 " pdb=" OG1 THR D 35 " model vdw 2.255 2.440 nonbonded pdb=" O ASN B 31 " pdb=" OG1 THR B 35 " model vdw 2.255 2.440 ... (remaining 161379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.470 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 50.890 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.120 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 0.050 21472 Z= 0.449 Angle : 0.735 11.650 29272 Z= 0.389 Chirality : 0.045 0.178 3232 Planarity : 0.003 0.021 3584 Dihedral : 14.752 79.413 7312 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.26 % Favored : 87.74 % Rotamer: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % 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: -3.15 (0.15), residues: 2480 helix: -0.95 (0.11), residues: 1680 sheet: -5.11 (0.18), residues: 40 loop : -4.48 (0.16), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 68 HIS 0.004 0.001 HIS G 50 PHE 0.012 0.002 PHE D 119 TYR 0.008 0.001 TYR A 172 ARG 0.003 0.000 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 772 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8209 (m-30) cc_final: 0.7900 (m-30) REVERT: A 54 ASP cc_start: 0.7573 (p0) cc_final: 0.7340 (p0) REVERT: A 67 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7432 (mm-40) REVERT: A 103 GLN cc_start: 0.7094 (pt0) cc_final: 0.6744 (pt0) REVERT: A 107 TRP cc_start: 0.8173 (m100) cc_final: 0.7858 (m-10) REVERT: A 142 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8959 (mtpp) REVERT: A 145 ASP cc_start: 0.8700 (t70) cc_final: 0.8461 (t0) REVERT: A 198 TRP cc_start: 0.8621 (t-100) cc_final: 0.8241 (t-100) REVERT: A 226 ILE cc_start: 0.7735 (mm) cc_final: 0.7449 (mm) REVERT: A 241 HIS cc_start: 0.8118 (p90) cc_final: 0.7639 (p-80) REVERT: A 313 LYS cc_start: 0.8845 (mtpt) cc_final: 0.8580 (mtmm) REVERT: B 28 ASP cc_start: 0.8118 (m-30) cc_final: 0.7786 (m-30) REVERT: B 103 GLN cc_start: 0.6822 (pt0) cc_final: 0.6601 (pt0) REVERT: B 107 TRP cc_start: 0.7935 (m100) cc_final: 0.7706 (m-10) REVERT: B 145 ASP cc_start: 0.8691 (t70) cc_final: 0.8362 (t0) REVERT: B 313 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8516 (mtmm) REVERT: B 353 PRO cc_start: 0.9454 (Cg_endo) cc_final: 0.9203 (Cg_exo) REVERT: C 45 LEU cc_start: 0.8259 (tp) cc_final: 0.8031 (tp) REVERT: C 49 SER cc_start: 0.9049 (t) cc_final: 0.8744 (m) REVERT: C 103 GLN cc_start: 0.7088 (pt0) cc_final: 0.6714 (pt0) REVERT: C 107 TRP cc_start: 0.8226 (m100) cc_final: 0.7850 (m-10) REVERT: C 154 LYS cc_start: 0.8644 (mttt) cc_final: 0.8442 (mttt) REVERT: C 157 LYS cc_start: 0.7931 (mmtt) cc_final: 0.7716 (mtmm) REVERT: C 198 TRP cc_start: 0.8577 (t-100) cc_final: 0.8150 (t-100) REVERT: C 361 MET cc_start: 0.9464 (mtp) cc_final: 0.9224 (mtm) REVERT: D 23 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7988 (mmtm) REVERT: D 103 GLN cc_start: 0.6794 (pt0) cc_final: 0.6579 (pt0) REVERT: D 107 TRP cc_start: 0.8123 (m100) cc_final: 0.7899 (m-10) REVERT: D 303 CYS cc_start: 0.7983 (t) cc_final: 0.7654 (t) REVERT: D 313 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8378 (mtmm) REVERT: E 59 TRP cc_start: 0.7497 (t-100) cc_final: 0.7278 (t60) REVERT: E 103 GLN cc_start: 0.6976 (pt0) cc_final: 0.6669 (pt0) REVERT: E 107 TRP cc_start: 0.8177 (m100) cc_final: 0.7835 (m-10) REVERT: E 142 LYS cc_start: 0.9192 (mtmm) cc_final: 0.8992 (mtmt) REVERT: E 307 LYS cc_start: 0.8375 (mttt) cc_final: 0.8117 (tmtt) REVERT: E 313 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8517 (mtmm) REVERT: E 361 MET cc_start: 0.9426 (mtp) cc_final: 0.9197 (mtm) REVERT: F 23 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7917 (mmtm) REVERT: F 313 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8485 (mtmm) REVERT: F 353 PRO cc_start: 0.9477 (Cg_endo) cc_final: 0.9263 (Cg_exo) REVERT: G 28 ASP cc_start: 0.8136 (m-30) cc_final: 0.7817 (m-30) REVERT: G 54 ASP cc_start: 0.7497 (p0) cc_final: 0.7260 (p0) REVERT: G 103 GLN cc_start: 0.7069 (pt0) cc_final: 0.6725 (pt0) REVERT: G 107 TRP cc_start: 0.8141 (m100) cc_final: 0.7832 (m-10) REVERT: G 142 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8941 (mtpp) REVERT: G 145 ASP cc_start: 0.8778 (t70) cc_final: 0.8565 (t0) REVERT: G 177 ILE cc_start: 0.9366 (mm) cc_final: 0.9148 (mt) REVERT: G 198 TRP cc_start: 0.8711 (t-100) cc_final: 0.8405 (t-100) REVERT: G 226 ILE cc_start: 0.7693 (mm) cc_final: 0.7408 (mm) REVERT: G 241 HIS cc_start: 0.8117 (p90) cc_final: 0.7640 (p-80) REVERT: G 313 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8493 (mtmm) REVERT: G 361 MET cc_start: 0.9396 (mtp) cc_final: 0.9185 (mtm) REVERT: H 23 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7967 (mmtm) REVERT: H 107 TRP cc_start: 0.8017 (m100) cc_final: 0.7768 (m-10) REVERT: H 145 ASP cc_start: 0.8732 (t70) cc_final: 0.8486 (t0) REVERT: H 313 LYS cc_start: 0.8775 (mtpt) cc_final: 0.8493 (mtmm) REVERT: H 325 ILE cc_start: 0.8524 (mp) cc_final: 0.8319 (mm) outliers start: 0 outliers final: 0 residues processed: 772 average time/residue: 0.3275 time to fit residues: 378.1722 Evaluate side-chains 556 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 225 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN A 232 GLN A 247 HIS ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 151 ASN B 199 GLN B 212 GLN B 232 GLN B 247 HIS ** B 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN C 212 GLN C 232 GLN C 247 HIS C 329 GLN D 199 GLN D 212 GLN D 232 GLN D 247 HIS ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN D 329 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN E 232 GLN E 247 HIS ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN F 63 GLN F 212 GLN F 232 GLN F 247 HIS ** F 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 GLN G 50 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 212 GLN G 232 GLN G 247 HIS ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN H 199 GLN H 212 GLN H 232 GLN H 247 HIS ** H 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21472 Z= 0.231 Angle : 0.614 6.694 29272 Z= 0.319 Chirality : 0.042 0.160 3232 Planarity : 0.004 0.062 3584 Dihedral : 5.066 22.727 2752 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 2.90 % Allowed : 20.47 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2480 helix: 0.24 (0.12), residues: 1696 sheet: None (None), residues: 0 loop : -4.09 (0.17), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 68 HIS 0.011 0.001 HIS G 50 PHE 0.018 0.001 PHE G 242 TYR 0.019 0.001 TYR C 301 ARG 0.007 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 613 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7555 (p0) cc_final: 0.7249 (p0) REVERT: A 103 GLN cc_start: 0.7046 (pt0) cc_final: 0.6721 (pt0) REVERT: A 107 TRP cc_start: 0.8075 (m100) cc_final: 0.7798 (m-10) REVERT: A 142 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8954 (mtpp) REVERT: A 145 ASP cc_start: 0.8647 (t70) cc_final: 0.8379 (t0) REVERT: A 313 LYS cc_start: 0.8735 (mtpt) cc_final: 0.8506 (mtmm) REVERT: B 130 ILE cc_start: 0.9201 (tp) cc_final: 0.8628 (tp) REVERT: B 145 ASP cc_start: 0.8575 (t70) cc_final: 0.8308 (t0) REVERT: B 313 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8434 (mtmm) REVERT: B 353 PRO cc_start: 0.9389 (Cg_endo) cc_final: 0.9188 (Cg_exo) REVERT: C 45 LEU cc_start: 0.8126 (tp) cc_final: 0.7845 (tp) REVERT: C 49 SER cc_start: 0.8966 (t) cc_final: 0.8679 (m) REVERT: C 103 GLN cc_start: 0.7121 (pt0) cc_final: 0.6741 (pt0) REVERT: C 107 TRP cc_start: 0.8083 (m100) cc_final: 0.7809 (m-10) REVERT: C 154 LYS cc_start: 0.8683 (mttt) cc_final: 0.8431 (mttt) REVERT: D 103 GLN cc_start: 0.6797 (pt0) cc_final: 0.6595 (pt0) REVERT: D 130 ILE cc_start: 0.9167 (tp) cc_final: 0.8618 (tp) REVERT: D 157 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7723 (mtmm) REVERT: D 159 LYS cc_start: 0.8029 (mptt) cc_final: 0.7787 (mptt) REVERT: D 303 CYS cc_start: 0.7922 (t) cc_final: 0.7622 (t) REVERT: D 313 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8364 (mtmm) REVERT: E 59 TRP cc_start: 0.7542 (t-100) cc_final: 0.7337 (t60) REVERT: E 103 GLN cc_start: 0.6951 (pt0) cc_final: 0.6595 (pt0) REVERT: E 107 TRP cc_start: 0.8116 (m100) cc_final: 0.7847 (m-10) REVERT: E 142 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8916 (mtpp) REVERT: E 157 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7672 (mtmm) REVERT: E 313 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8392 (mtmm) REVERT: E 334 LEU cc_start: 0.7838 (tp) cc_final: 0.7601 (tp) REVERT: F 313 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8445 (mtmm) REVERT: G 54 ASP cc_start: 0.7679 (p0) cc_final: 0.7359 (p0) REVERT: G 103 GLN cc_start: 0.7029 (pt0) cc_final: 0.6649 (pt0) REVERT: G 107 TRP cc_start: 0.8087 (m100) cc_final: 0.7812 (m-10) REVERT: G 142 LYS cc_start: 0.9218 (mtmm) cc_final: 0.8931 (mtpp) REVERT: G 145 ASP cc_start: 0.8714 (t70) cc_final: 0.8461 (t0) REVERT: G 177 ILE cc_start: 0.9352 (mm) cc_final: 0.9142 (mt) REVERT: G 313 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8459 (mtmm) REVERT: G 329 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8283 (pt0) REVERT: G 332 SER cc_start: 0.9276 (t) cc_final: 0.9000 (p) REVERT: H 107 TRP cc_start: 0.7910 (m100) cc_final: 0.7705 (m-10) REVERT: H 313 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8458 (mtmm) outliers start: 64 outliers final: 52 residues processed: 657 average time/residue: 0.3160 time to fit residues: 316.5701 Evaluate side-chains 593 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 539 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 303 CYS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 329 GLN Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 243 optimal weight: 0.0040 chunk 200 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 180 optimal weight: 0.0770 overall best weight: 1.0156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN B 314 ASN C 50 HIS C 329 GLN E 50 HIS ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN G 50 HIS ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN G 329 GLN H 314 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21472 Z= 0.165 Angle : 0.583 8.880 29272 Z= 0.299 Chirality : 0.041 0.173 3232 Planarity : 0.003 0.039 3584 Dihedral : 4.710 19.790 2752 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.49 % Allowed : 22.87 % Favored : 73.64 % 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: -0.98 (0.17), residues: 2480 helix: 0.68 (0.12), residues: 1720 sheet: -4.35 (0.31), residues: 40 loop : -3.83 (0.18), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 68 HIS 0.019 0.002 HIS G 50 PHE 0.012 0.001 PHE B 51 TYR 0.016 0.001 TYR C 301 ARG 0.003 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 612 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7566 (p0) cc_final: 0.7245 (p0) REVERT: A 107 TRP cc_start: 0.7951 (m100) cc_final: 0.7750 (m-10) REVERT: A 145 ASP cc_start: 0.8575 (t70) cc_final: 0.8326 (t0) REVERT: B 50 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7313 (p-80) REVERT: B 145 ASP cc_start: 0.8549 (t70) cc_final: 0.8300 (t0) REVERT: B 156 ASP cc_start: 0.8525 (t0) cc_final: 0.8293 (t0) REVERT: B 159 LYS cc_start: 0.7982 (mptt) cc_final: 0.7681 (mptt) REVERT: B 264 LEU cc_start: 0.8784 (tp) cc_final: 0.8477 (tt) REVERT: C 49 SER cc_start: 0.8911 (t) cc_final: 0.8615 (m) REVERT: C 103 GLN cc_start: 0.7020 (pt0) cc_final: 0.6613 (pt0) REVERT: C 107 TRP cc_start: 0.8007 (m100) cc_final: 0.7746 (m-10) REVERT: C 186 ARG cc_start: 0.6710 (mtp180) cc_final: 0.6378 (mtp85) REVERT: D 28 ASP cc_start: 0.7529 (m-30) cc_final: 0.7278 (m-30) REVERT: D 130 ILE cc_start: 0.9136 (tp) cc_final: 0.8584 (tp) REVERT: D 136 ASP cc_start: 0.8409 (p0) cc_final: 0.8174 (p0) REVERT: D 156 ASP cc_start: 0.8762 (t0) cc_final: 0.8389 (t0) REVERT: D 159 LYS cc_start: 0.7941 (mptt) cc_final: 0.7721 (mptt) REVERT: D 313 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8262 (mtmm) REVERT: E 103 GLN cc_start: 0.6849 (pt0) cc_final: 0.6483 (pt0) REVERT: E 226 ILE cc_start: 0.7388 (mm) cc_final: 0.7151 (mt) REVERT: E 313 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8400 (mtmm) REVERT: F 130 ILE cc_start: 0.9260 (tp) cc_final: 0.8824 (tp) REVERT: F 157 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7774 (mtmm) REVERT: F 159 LYS cc_start: 0.7917 (mptt) cc_final: 0.7626 (mptt) REVERT: F 264 LEU cc_start: 0.8681 (tp) cc_final: 0.8383 (tt) REVERT: F 313 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8380 (mtmm) REVERT: G 54 ASP cc_start: 0.7672 (p0) cc_final: 0.7361 (p0) REVERT: G 107 TRP cc_start: 0.7976 (m100) cc_final: 0.7769 (m-10) REVERT: G 142 LYS cc_start: 0.9199 (mtmm) cc_final: 0.8924 (mtpp) REVERT: G 145 ASP cc_start: 0.8652 (t70) cc_final: 0.8390 (t0) REVERT: G 313 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8473 (mtmm) REVERT: G 332 SER cc_start: 0.9286 (t) cc_final: 0.9033 (p) REVERT: G 361 MET cc_start: 0.9292 (mtp) cc_final: 0.9028 (mtm) REVERT: H 130 ILE cc_start: 0.9236 (tp) cc_final: 0.8824 (tp) REVERT: H 264 LEU cc_start: 0.8683 (tp) cc_final: 0.8394 (tt) REVERT: H 313 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8419 (mtmm) REVERT: H 332 SER cc_start: 0.9020 (t) cc_final: 0.8781 (p) outliers start: 77 outliers final: 54 residues processed: 662 average time/residue: 0.3036 time to fit residues: 308.1027 Evaluate side-chains 579 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 524 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 127 LYS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 107 optimal weight: 0.0060 chunk 151 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 chunk 239 optimal weight: 0.0020 chunk 118 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.5208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21472 Z= 0.182 Angle : 0.577 10.288 29272 Z= 0.295 Chirality : 0.041 0.191 3232 Planarity : 0.003 0.041 3584 Dihedral : 4.587 18.407 2752 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.85 % Allowed : 26.22 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2480 helix: 0.90 (0.12), residues: 1720 sheet: None (None), residues: 0 loop : -3.61 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 59 HIS 0.015 0.002 HIS E 50 PHE 0.016 0.001 PHE C 51 TYR 0.022 0.001 TYR F 300 ARG 0.005 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 565 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7532 (p0) cc_final: 0.7244 (p0) REVERT: A 107 TRP cc_start: 0.8015 (m100) cc_final: 0.7792 (m-10) REVERT: A 145 ASP cc_start: 0.8595 (t70) cc_final: 0.8322 (t0) REVERT: A 264 LEU cc_start: 0.8733 (tp) cc_final: 0.8340 (tt) REVERT: B 50 HIS cc_start: 0.7697 (OUTLIER) cc_final: 0.6583 (p-80) REVERT: B 130 ILE cc_start: 0.9138 (tp) cc_final: 0.8638 (tp) REVERT: B 145 ASP cc_start: 0.8533 (t70) cc_final: 0.8283 (t0) REVERT: B 264 LEU cc_start: 0.8762 (tp) cc_final: 0.8460 (tt) REVERT: C 103 GLN cc_start: 0.7021 (pt0) cc_final: 0.6646 (pt0) REVERT: C 107 TRP cc_start: 0.8017 (m100) cc_final: 0.7757 (m-10) REVERT: C 301 TYR cc_start: 0.8395 (t80) cc_final: 0.8060 (t80) REVERT: D 28 ASP cc_start: 0.7472 (m-30) cc_final: 0.7257 (m-30) REVERT: D 67 GLN cc_start: 0.6916 (mp10) cc_final: 0.6713 (mp10) REVERT: D 130 ILE cc_start: 0.9175 (tp) cc_final: 0.8679 (tp) REVERT: D 159 LYS cc_start: 0.7911 (mptt) cc_final: 0.7686 (mptt) REVERT: D 264 LEU cc_start: 0.8556 (tp) cc_final: 0.8272 (tt) REVERT: D 313 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8306 (mtmm) REVERT: E 54 ASP cc_start: 0.7556 (p0) cc_final: 0.7142 (p0) REVERT: E 264 LEU cc_start: 0.8799 (tp) cc_final: 0.8499 (tt) REVERT: E 313 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8475 (mtmm) REVERT: E 325 ILE cc_start: 0.8842 (mm) cc_final: 0.8630 (mm) REVERT: F 130 ILE cc_start: 0.9150 (tp) cc_final: 0.8669 (tp) REVERT: F 156 ASP cc_start: 0.8552 (t0) cc_final: 0.8178 (t0) REVERT: F 157 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7803 (mtmm) REVERT: F 159 LYS cc_start: 0.7971 (mptt) cc_final: 0.7688 (mptt) REVERT: F 264 LEU cc_start: 0.8635 (tp) cc_final: 0.8336 (tt) REVERT: F 313 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8397 (mtmm) REVERT: G 54 ASP cc_start: 0.7487 (p0) cc_final: 0.7238 (p0) REVERT: G 142 LYS cc_start: 0.9210 (mtmm) cc_final: 0.8929 (mtpp) REVERT: G 145 ASP cc_start: 0.8612 (t70) cc_final: 0.8355 (t0) REVERT: G 303 CYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7861 (t) REVERT: G 313 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8491 (mtmm) REVERT: G 332 SER cc_start: 0.9358 (t) cc_final: 0.9056 (p) REVERT: G 361 MET cc_start: 0.9300 (mtp) cc_final: 0.9064 (mtm) REVERT: H 28 ASP cc_start: 0.7478 (m-30) cc_final: 0.7253 (m-30) REVERT: H 130 ILE cc_start: 0.9091 (tp) cc_final: 0.8655 (tp) REVERT: H 264 LEU cc_start: 0.8685 (tp) cc_final: 0.8400 (tt) REVERT: H 313 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8388 (mtmm) REVERT: H 332 SER cc_start: 0.9028 (t) cc_final: 0.8781 (p) outliers start: 85 outliers final: 66 residues processed: 624 average time/residue: 0.2970 time to fit residues: 288.1387 Evaluate side-chains 591 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 523 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 303 CYS Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 0.3980 chunk 136 optimal weight: 7.9990 chunk 3 optimal weight: 0.0570 chunk 178 optimal weight: 0.4980 chunk 98 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.5902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21472 Z= 0.183 Angle : 0.570 10.489 29272 Z= 0.290 Chirality : 0.041 0.179 3232 Planarity : 0.003 0.042 3584 Dihedral : 4.461 17.302 2752 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.57 % Allowed : 27.58 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2480 helix: 1.09 (0.13), residues: 1720 sheet: -4.04 (0.39), residues: 40 loop : -3.55 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 59 HIS 0.009 0.001 HIS E 50 PHE 0.015 0.001 PHE A 330 TYR 0.024 0.001 TYR D 120 ARG 0.004 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 586 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.7481 (p0) cc_final: 0.7268 (p0) REVERT: A 107 TRP cc_start: 0.8031 (m100) cc_final: 0.7830 (m-10) REVERT: A 145 ASP cc_start: 0.8604 (t70) cc_final: 0.8334 (t0) REVERT: A 303 CYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7934 (t) REVERT: B 28 ASP cc_start: 0.7450 (m-30) cc_final: 0.7171 (m-30) REVERT: B 50 HIS cc_start: 0.7663 (OUTLIER) cc_final: 0.6536 (p-80) REVERT: B 130 ILE cc_start: 0.9114 (tp) cc_final: 0.8572 (tp) REVERT: B 145 ASP cc_start: 0.8513 (t70) cc_final: 0.8280 (t0) REVERT: B 274 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.5974 (mp0) REVERT: B 325 ILE cc_start: 0.8611 (mm) cc_final: 0.8393 (mm) REVERT: C 107 TRP cc_start: 0.8051 (m100) cc_final: 0.7813 (m-10) REVERT: C 303 CYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7871 (t) REVERT: D 28 ASP cc_start: 0.7489 (m-30) cc_final: 0.7289 (m-30) REVERT: D 130 ILE cc_start: 0.9201 (tp) cc_final: 0.8680 (tp) REVERT: D 156 ASP cc_start: 0.8831 (t0) cc_final: 0.8443 (t0) REVERT: D 159 LYS cc_start: 0.7881 (mptt) cc_final: 0.7659 (mptt) REVERT: D 264 LEU cc_start: 0.8506 (tp) cc_final: 0.8033 (tt) REVERT: D 274 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.6503 (mp0) REVERT: D 313 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8251 (mtmm) REVERT: D 325 ILE cc_start: 0.8602 (mm) cc_final: 0.8386 (mm) REVERT: E 28 ASP cc_start: 0.7258 (m-30) cc_final: 0.7004 (m-30) REVERT: E 54 ASP cc_start: 0.7613 (p0) cc_final: 0.7222 (p0) REVERT: F 156 ASP cc_start: 0.8545 (t0) cc_final: 0.8272 (t0) REVERT: F 159 LYS cc_start: 0.8019 (mptt) cc_final: 0.7706 (mptt) REVERT: F 264 LEU cc_start: 0.8549 (tp) cc_final: 0.8287 (tt) REVERT: F 274 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6300 (mp0) REVERT: F 313 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8377 (mtmm) REVERT: G 28 ASP cc_start: 0.7496 (m-30) cc_final: 0.7178 (m-30) REVERT: G 54 ASP cc_start: 0.7466 (p0) cc_final: 0.7225 (p0) REVERT: G 142 LYS cc_start: 0.9191 (mtmm) cc_final: 0.8918 (mtpp) REVERT: G 145 ASP cc_start: 0.8610 (t70) cc_final: 0.8350 (t0) REVERT: G 157 LYS cc_start: 0.7528 (mmtt) cc_final: 0.6925 (mmtm) REVERT: G 332 SER cc_start: 0.9342 (t) cc_final: 0.9022 (p) REVERT: G 361 MET cc_start: 0.9266 (mtp) cc_final: 0.9031 (mtm) REVERT: H 50 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.6984 (p90) REVERT: H 130 ILE cc_start: 0.9089 (tp) cc_final: 0.8597 (tp) REVERT: H 136 ASP cc_start: 0.8331 (p0) cc_final: 0.8052 (p0) REVERT: H 264 LEU cc_start: 0.8609 (tp) cc_final: 0.8360 (tt) REVERT: H 274 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: H 313 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8395 (mtmm) REVERT: H 332 SER cc_start: 0.9042 (t) cc_final: 0.8737 (p) REVERT: H 334 LEU cc_start: 0.7644 (tp) cc_final: 0.7366 (tt) outliers start: 101 outliers final: 66 residues processed: 658 average time/residue: 0.3052 time to fit residues: 313.1572 Evaluate side-chains 615 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 541 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 239 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21472 Z= 0.195 Angle : 0.575 8.289 29272 Z= 0.294 Chirality : 0.041 0.188 3232 Planarity : 0.003 0.045 3584 Dihedral : 4.408 17.104 2752 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.94 % Allowed : 29.35 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2480 helix: 1.18 (0.13), residues: 1720 sheet: -3.97 (0.41), residues: 40 loop : -3.52 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 236 HIS 0.005 0.001 HIS E 50 PHE 0.011 0.001 PHE H 51 TYR 0.026 0.001 TYR B 120 ARG 0.004 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 570 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7400 (m-30) cc_final: 0.7134 (m-30) REVERT: A 107 TRP cc_start: 0.8038 (m100) cc_final: 0.7824 (m-10) REVERT: A 145 ASP cc_start: 0.8616 (t70) cc_final: 0.8351 (t0) REVERT: A 274 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.6147 (mp0) REVERT: A 303 CYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7941 (t) REVERT: B 28 ASP cc_start: 0.7463 (m-30) cc_final: 0.7215 (m-30) REVERT: B 50 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.6633 (p-80) REVERT: B 136 ASP cc_start: 0.8342 (p0) cc_final: 0.8078 (p0) REVERT: B 145 ASP cc_start: 0.8516 (t70) cc_final: 0.8281 (t0) REVERT: B 274 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.5947 (mp0) REVERT: B 325 ILE cc_start: 0.8613 (mm) cc_final: 0.8411 (mm) REVERT: C 107 TRP cc_start: 0.8064 (m100) cc_final: 0.7833 (m-10) REVERT: C 274 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.6178 (mp0) REVERT: C 303 CYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7853 (t) REVERT: D 28 ASP cc_start: 0.7484 (m-30) cc_final: 0.7270 (m-30) REVERT: D 130 ILE cc_start: 0.9202 (tp) cc_final: 0.8730 (tp) REVERT: D 156 ASP cc_start: 0.8817 (t0) cc_final: 0.8560 (t0) REVERT: D 274 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6149 (mp0) REVERT: D 313 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8393 (mtmm) REVERT: E 28 ASP cc_start: 0.7235 (m-30) cc_final: 0.6979 (m-30) REVERT: E 54 ASP cc_start: 0.7615 (p0) cc_final: 0.7216 (p0) REVERT: E 274 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: E 361 MET cc_start: 0.9080 (mtp) cc_final: 0.8696 (ttm) REVERT: F 130 ILE cc_start: 0.9126 (tp) cc_final: 0.8632 (tp) REVERT: F 156 ASP cc_start: 0.8516 (t0) cc_final: 0.8157 (t0) REVERT: F 159 LYS cc_start: 0.8026 (mptt) cc_final: 0.7673 (mptt) REVERT: F 264 LEU cc_start: 0.8530 (tp) cc_final: 0.8284 (tt) REVERT: F 274 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.6219 (mp0) REVERT: F 313 LYS cc_start: 0.8602 (mtpt) cc_final: 0.8365 (mtmm) REVERT: G 28 ASP cc_start: 0.7453 (m-30) cc_final: 0.7152 (m-30) REVERT: G 54 ASP cc_start: 0.7491 (p0) cc_final: 0.7277 (p0) REVERT: G 145 ASP cc_start: 0.8604 (t70) cc_final: 0.8360 (t0) REVERT: G 157 LYS cc_start: 0.7519 (mmtt) cc_final: 0.6851 (mmtm) REVERT: G 236 TRP cc_start: 0.7976 (p90) cc_final: 0.7754 (p90) REVERT: G 313 LYS cc_start: 0.8981 (mtmm) cc_final: 0.8711 (mtmm) REVERT: G 332 SER cc_start: 0.9359 (t) cc_final: 0.9021 (p) REVERT: G 361 MET cc_start: 0.9265 (mtp) cc_final: 0.9032 (mtm) REVERT: H 50 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7073 (p90) REVERT: H 130 ILE cc_start: 0.9062 (tp) cc_final: 0.8637 (tp) REVERT: H 136 ASP cc_start: 0.8335 (p0) cc_final: 0.8033 (p0) REVERT: H 264 LEU cc_start: 0.8634 (tp) cc_final: 0.8413 (tt) REVERT: H 274 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.6256 (mp0) REVERT: H 303 CYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7741 (t) REVERT: H 332 SER cc_start: 0.9039 (t) cc_final: 0.8739 (p) outliers start: 109 outliers final: 79 residues processed: 644 average time/residue: 0.2718 time to fit residues: 276.9920 Evaluate side-chains 625 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 534 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 299 ILE Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 175 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 239 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21472 Z= 0.174 Angle : 0.589 11.353 29272 Z= 0.297 Chirality : 0.040 0.170 3232 Planarity : 0.003 0.044 3584 Dihedral : 4.368 16.474 2752 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.39 % Allowed : 30.66 % Favored : 64.95 % 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: -0.11 (0.17), residues: 2480 helix: 1.28 (0.13), residues: 1720 sheet: None (None), residues: 0 loop : -3.44 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 236 HIS 0.010 0.001 HIS H 50 PHE 0.013 0.001 PHE A 330 TYR 0.027 0.001 TYR B 120 ARG 0.003 0.000 ARG C 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 598 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.7305 (m-30) cc_final: 0.7060 (m-30) REVERT: A 145 ASP cc_start: 0.8678 (t70) cc_final: 0.8406 (t0) REVERT: A 274 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.6016 (mp0) REVERT: A 303 CYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7890 (t) REVERT: A 361 MET cc_start: 0.9335 (mtp) cc_final: 0.9065 (mtm) REVERT: B 28 ASP cc_start: 0.7461 (m-30) cc_final: 0.7255 (m-30) REVERT: B 50 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.6778 (p-80) REVERT: B 130 ILE cc_start: 0.9107 (tp) cc_final: 0.8626 (tp) REVERT: B 145 ASP cc_start: 0.8513 (t70) cc_final: 0.8276 (t0) REVERT: B 274 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.5834 (mp0) REVERT: B 325 ILE cc_start: 0.8593 (mm) cc_final: 0.8377 (mm) REVERT: C 274 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.6151 (mp0) REVERT: C 303 CYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7830 (t) REVERT: D 130 ILE cc_start: 0.9167 (tp) cc_final: 0.8732 (tp) REVERT: D 136 ASP cc_start: 0.8340 (p0) cc_final: 0.8032 (p0) REVERT: D 264 LEU cc_start: 0.8487 (tp) cc_final: 0.8073 (tt) REVERT: D 274 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.6162 (mp0) REVERT: E 274 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: E 361 MET cc_start: 0.9049 (mtp) cc_final: 0.8707 (ttm) REVERT: F 67 GLN cc_start: 0.7134 (mp10) cc_final: 0.6836 (mp10) REVERT: F 136 ASP cc_start: 0.8366 (p0) cc_final: 0.8047 (p0) REVERT: F 156 ASP cc_start: 0.8504 (t0) cc_final: 0.8172 (t0) REVERT: F 159 LYS cc_start: 0.7990 (mptt) cc_final: 0.7655 (mptt) REVERT: F 264 LEU cc_start: 0.8493 (tp) cc_final: 0.8266 (tt) REVERT: F 274 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.6204 (mp0) REVERT: F 303 CYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7682 (t) REVERT: F 313 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8373 (mtmm) REVERT: G 28 ASP cc_start: 0.7323 (m-30) cc_final: 0.7096 (m-30) REVERT: G 54 ASP cc_start: 0.7489 (p0) cc_final: 0.7268 (p0) REVERT: G 145 ASP cc_start: 0.8627 (t70) cc_final: 0.8377 (t0) REVERT: G 157 LYS cc_start: 0.7710 (mmtt) cc_final: 0.7040 (mmtm) REVERT: G 274 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: G 313 LYS cc_start: 0.8954 (mtmm) cc_final: 0.8673 (mtmm) REVERT: G 331 PHE cc_start: 0.8576 (m-80) cc_final: 0.8243 (m-80) REVERT: G 332 SER cc_start: 0.9348 (t) cc_final: 0.8997 (p) REVERT: H 130 ILE cc_start: 0.9086 (tp) cc_final: 0.8625 (tp) REVERT: H 136 ASP cc_start: 0.8319 (p0) cc_final: 0.8041 (p0) REVERT: H 274 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6211 (mp0) REVERT: H 313 LYS cc_start: 0.8824 (mtmm) cc_final: 0.8528 (mtmm) REVERT: H 332 SER cc_start: 0.9045 (t) cc_final: 0.8698 (p) outliers start: 97 outliers final: 78 residues processed: 657 average time/residue: 0.2805 time to fit residues: 292.2177 Evaluate side-chains 660 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 570 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 50 HIS Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 142 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 118 optimal weight: 0.3980 chunk 22 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 217 optimal weight: 8.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21472 Z= 0.166 Angle : 0.585 10.422 29272 Z= 0.295 Chirality : 0.040 0.195 3232 Planarity : 0.003 0.042 3584 Dihedral : 4.267 16.251 2752 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.48 % Allowed : 31.84 % Favored : 63.68 % 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: -0.00 (0.17), residues: 2480 helix: 1.35 (0.13), residues: 1728 sheet: -3.96 (0.44), residues: 40 loop : -3.33 (0.19), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 236 HIS 0.004 0.001 HIS G 50 PHE 0.022 0.001 PHE G 51 TYR 0.028 0.001 TYR H 120 ARG 0.003 0.000 ARG E 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 607 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8609 (t70) cc_final: 0.8334 (t0) REVERT: A 274 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: A 361 MET cc_start: 0.9295 (mtp) cc_final: 0.9073 (mtm) REVERT: B 130 ILE cc_start: 0.8937 (tp) cc_final: 0.8466 (tp) REVERT: B 136 ASP cc_start: 0.8304 (p0) cc_final: 0.8035 (p0) REVERT: B 145 ASP cc_start: 0.8512 (t70) cc_final: 0.8272 (t0) REVERT: B 274 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: B 325 ILE cc_start: 0.8477 (mm) cc_final: 0.8273 (mm) REVERT: C 274 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: C 291 SER cc_start: 0.9217 (t) cc_final: 0.8725 (m) REVERT: C 303 CYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7799 (t) REVERT: D 130 ILE cc_start: 0.9144 (tp) cc_final: 0.8692 (tp) REVERT: D 136 ASP cc_start: 0.8315 (p0) cc_final: 0.7988 (p0) REVERT: D 156 ASP cc_start: 0.8652 (t0) cc_final: 0.8052 (t70) REVERT: D 208 TYR cc_start: 0.7740 (t80) cc_final: 0.7493 (t80) REVERT: D 274 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6090 (mp0) REVERT: D 313 LYS cc_start: 0.8807 (mtmm) cc_final: 0.8538 (mtmm) REVERT: E 274 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.6097 (mp0) REVERT: E 361 MET cc_start: 0.9060 (mtp) cc_final: 0.8688 (ttm) REVERT: F 67 GLN cc_start: 0.7060 (mp10) cc_final: 0.6760 (mp10) REVERT: F 130 ILE cc_start: 0.9187 (tp) cc_final: 0.8704 (tp) REVERT: F 136 ASP cc_start: 0.8325 (p0) cc_final: 0.8021 (p0) REVERT: F 159 LYS cc_start: 0.7812 (mptt) cc_final: 0.7550 (mptt) REVERT: F 274 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: F 303 CYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7733 (t) REVERT: G 54 ASP cc_start: 0.7489 (p0) cc_final: 0.7261 (p0) REVERT: G 145 ASP cc_start: 0.8615 (t70) cc_final: 0.8376 (t0) REVERT: G 157 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7022 (mmtm) REVERT: G 236 TRP cc_start: 0.7884 (p90) cc_final: 0.7657 (p90) REVERT: G 274 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.6106 (mp0) REVERT: G 313 LYS cc_start: 0.8932 (mtmm) cc_final: 0.8639 (mtmm) REVERT: G 331 PHE cc_start: 0.8585 (m-80) cc_final: 0.8296 (m-80) REVERT: G 332 SER cc_start: 0.9320 (t) cc_final: 0.8963 (p) REVERT: H 130 ILE cc_start: 0.8940 (tp) cc_final: 0.8491 (tp) REVERT: H 136 ASP cc_start: 0.8328 (p0) cc_final: 0.8020 (p0) REVERT: H 264 LEU cc_start: 0.8525 (tp) cc_final: 0.8320 (tt) REVERT: H 274 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: H 303 CYS cc_start: 0.8053 (OUTLIER) cc_final: 0.7712 (t) REVERT: H 313 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8527 (mtmm) REVERT: H 332 SER cc_start: 0.9023 (t) cc_final: 0.8684 (p) outliers start: 99 outliers final: 78 residues processed: 664 average time/residue: 0.2866 time to fit residues: 299.0649 Evaluate side-chains 657 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 568 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 222 optimal weight: 7.9990 chunk 134 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 174 optimal weight: 6.9990 chunk 68 optimal weight: 0.2980 chunk 201 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 221 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN A 329 GLN B 63 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21472 Z= 0.218 Angle : 0.606 10.321 29272 Z= 0.306 Chirality : 0.041 0.190 3232 Planarity : 0.003 0.044 3584 Dihedral : 4.340 17.243 2752 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 4.57 % Allowed : 31.84 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2480 helix: 1.30 (0.12), residues: 1728 sheet: -3.96 (0.47), residues: 40 loop : -3.30 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 236 HIS 0.005 0.001 HIS H 50 PHE 0.021 0.001 PHE B 51 TYR 0.029 0.001 TYR H 120 ARG 0.004 0.000 ARG D 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 562 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8667 (t70) cc_final: 0.8397 (t0) REVERT: A 274 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.6057 (mp0) REVERT: B 130 ILE cc_start: 0.9161 (tp) cc_final: 0.8620 (tp) REVERT: B 136 ASP cc_start: 0.8322 (p0) cc_final: 0.8067 (p0) REVERT: B 145 ASP cc_start: 0.8544 (t70) cc_final: 0.8299 (t0) REVERT: B 188 MET cc_start: 0.8353 (mmm) cc_final: 0.8114 (mtp) REVERT: B 274 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.5882 (mp0) REVERT: B 325 ILE cc_start: 0.8471 (mm) cc_final: 0.8233 (mm) REVERT: C 274 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.6100 (mp0) REVERT: C 303 CYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7890 (t) REVERT: D 130 ILE cc_start: 0.9053 (tp) cc_final: 0.8585 (tp) REVERT: D 208 TYR cc_start: 0.7786 (t80) cc_final: 0.7535 (t80) REVERT: D 274 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: D 313 LYS cc_start: 0.8798 (mtmm) cc_final: 0.8505 (mtmm) REVERT: E 274 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.6110 (mp0) REVERT: E 361 MET cc_start: 0.9089 (mtp) cc_final: 0.8741 (ttm) REVERT: F 28 ASP cc_start: 0.7408 (m-30) cc_final: 0.7184 (m-30) REVERT: F 67 GLN cc_start: 0.7010 (mp10) cc_final: 0.6743 (mp10) REVERT: F 136 ASP cc_start: 0.8312 (p0) cc_final: 0.7976 (p0) REVERT: F 274 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.6171 (mp0) REVERT: F 303 CYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7761 (t) REVERT: F 313 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8505 (mtmm) REVERT: G 145 ASP cc_start: 0.8637 (t70) cc_final: 0.8395 (t0) REVERT: G 157 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7016 (mmtm) REVERT: G 236 TRP cc_start: 0.7941 (p90) cc_final: 0.7708 (p90) REVERT: G 274 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: G 313 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8622 (mtmm) REVERT: G 332 SER cc_start: 0.9338 (t) cc_final: 0.8971 (p) REVERT: H 28 ASP cc_start: 0.7400 (m-30) cc_final: 0.7179 (m-30) REVERT: H 130 ILE cc_start: 0.9129 (tp) cc_final: 0.8619 (tp) REVERT: H 136 ASP cc_start: 0.8276 (p0) cc_final: 0.7961 (p0) REVERT: H 157 LYS cc_start: 0.7554 (mmtt) cc_final: 0.6800 (mmtp) REVERT: H 188 MET cc_start: 0.8363 (mmm) cc_final: 0.8134 (mtp) REVERT: H 274 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.6176 (mp0) REVERT: H 303 CYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7739 (t) REVERT: H 313 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8501 (mtmm) REVERT: H 332 SER cc_start: 0.9078 (t) cc_final: 0.8679 (p) outliers start: 101 outliers final: 83 residues processed: 626 average time/residue: 0.2802 time to fit residues: 277.3424 Evaluate side-chains 647 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 553 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 50 HIS Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 292 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 50 HIS Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 65 ASN Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 0.9990 chunk 143 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 196 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 63 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 ASN H 50 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21472 Z= 0.163 Angle : 0.615 11.217 29272 Z= 0.308 Chirality : 0.040 0.184 3232 Planarity : 0.003 0.042 3584 Dihedral : 4.229 16.570 2752 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.53 % Allowed : 32.97 % Favored : 63.50 % 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: 0.08 (0.17), residues: 2480 helix: 1.39 (0.13), residues: 1728 sheet: -4.04 (0.45), residues: 40 loop : -3.22 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 236 HIS 0.005 0.001 HIS H 50 PHE 0.017 0.001 PHE B 147 TYR 0.027 0.001 TYR B 120 ARG 0.007 0.000 ARG B 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4960 Ramachandran restraints generated. 2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 573 time to evaluate : 2.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8622 (t70) cc_final: 0.8392 (t0) REVERT: A 264 LEU cc_start: 0.8599 (tp) cc_final: 0.8393 (tp) REVERT: A 274 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.6054 (mp0) REVERT: A 361 MET cc_start: 0.9294 (mtp) cc_final: 0.9051 (mtm) REVERT: B 130 ILE cc_start: 0.9142 (tp) cc_final: 0.8613 (tp) REVERT: B 136 ASP cc_start: 0.8245 (p0) cc_final: 0.7989 (p0) REVERT: B 145 ASP cc_start: 0.8507 (t70) cc_final: 0.8261 (t0) REVERT: B 264 LEU cc_start: 0.8477 (tp) cc_final: 0.8187 (tt) REVERT: B 274 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.5864 (mp0) REVERT: B 325 ILE cc_start: 0.8556 (mm) cc_final: 0.8355 (mm) REVERT: C 264 LEU cc_start: 0.8495 (tp) cc_final: 0.8251 (tp) REVERT: C 274 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.6096 (mp0) REVERT: C 291 SER cc_start: 0.9235 (t) cc_final: 0.8693 (m) REVERT: C 303 CYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7836 (t) REVERT: D 130 ILE cc_start: 0.9152 (tp) cc_final: 0.8760 (tp) REVERT: D 208 TYR cc_start: 0.7758 (t80) cc_final: 0.7509 (t80) REVERT: D 274 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: D 313 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8520 (mtmm) REVERT: E 151 ASN cc_start: 0.8445 (p0) cc_final: 0.8158 (m-40) REVERT: E 274 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.6033 (mp0) REVERT: E 291 SER cc_start: 0.9250 (t) cc_final: 0.8711 (m) REVERT: E 361 MET cc_start: 0.9059 (mtp) cc_final: 0.8717 (ttm) REVERT: F 67 GLN cc_start: 0.6983 (mp10) cc_final: 0.6717 (mp10) REVERT: F 130 ILE cc_start: 0.9102 (tp) cc_final: 0.8652 (tp) REVERT: F 136 ASP cc_start: 0.8306 (p0) cc_final: 0.7988 (p0) REVERT: F 188 MET cc_start: 0.8299 (mmm) cc_final: 0.8066 (mtp) REVERT: F 274 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: F 303 CYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7744 (t) REVERT: F 313 LYS cc_start: 0.8828 (mtmm) cc_final: 0.8507 (mtmm) REVERT: G 145 ASP cc_start: 0.8667 (t70) cc_final: 0.8427 (t0) REVERT: G 157 LYS cc_start: 0.7708 (mmtt) cc_final: 0.6988 (mmtm) REVERT: G 274 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6069 (mp0) REVERT: G 313 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8638 (mtmm) REVERT: G 331 PHE cc_start: 0.8555 (m-80) cc_final: 0.8302 (m-80) REVERT: G 332 SER cc_start: 0.9323 (t) cc_final: 0.8909 (p) REVERT: H 130 ILE cc_start: 0.9160 (tp) cc_final: 0.8721 (tp) REVERT: H 136 ASP cc_start: 0.8291 (p0) cc_final: 0.7988 (p0) REVERT: H 274 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.6093 (mp0) REVERT: H 303 CYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7689 (t) REVERT: H 313 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8535 (mtmm) REVERT: H 332 SER cc_start: 0.9036 (t) cc_final: 0.8649 (p) outliers start: 78 outliers final: 64 residues processed: 621 average time/residue: 0.2810 time to fit residues: 276.9883 Evaluate side-chains 632 residues out of total 2248 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 557 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 50 HIS Chi-restraints excluded: chain B residue 63 GLN Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 235 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 50 HIS Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 274 GLU Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 274 GLU Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 341 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 ASP Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 235 ASP Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 268 THR Chi-restraints excluded: chain F residue 274 GLU Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 303 CYS Chi-restraints excluded: chain F residue 341 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 74 GLN Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 235 ASP Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 274 GLU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 303 CYS Chi-restraints excluded: chain H residue 341 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 181 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 202 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 173 optimal weight: 0.0870 overall best weight: 0.8298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN B 63 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN ** F 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.131119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.108959 restraints weight = 29835.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.112810 restraints weight = 16269.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.115434 restraints weight = 10926.308| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21472 Z= 0.173 Angle : 0.639 12.355 29272 Z= 0.315 Chirality : 0.040 0.179 3232 Planarity : 0.003 0.061 3584 Dihedral : 4.228 15.740 2752 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 3.58 % Allowed : 33.79 % Favored : 62.64 % 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: 0.12 (0.17), residues: 2480 helix: 1.43 (0.13), residues: 1728 sheet: -4.10 (0.45), residues: 40 loop : -3.20 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP F 236 HIS 0.005 0.001 HIS H 50 PHE 0.019 0.001 PHE F 51 TYR 0.028 0.001 TYR H 120 ARG 0.014 0.000 ARG D 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5059.33 seconds wall clock time: 91 minutes 10.36 seconds (5470.36 seconds total)