Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 19 09:38:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/07_2023/6gen_4396_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/07_2023/6gen_4396.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/6gen_4396/07_2023/6gen_4396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/07_2023/6gen_4396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/07_2023/6gen_4396_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/07_2023/6gen_4396_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 966 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 362 5.49 5 Mg 8 5.21 5 S 118 5.16 5 Be 2 3.05 5 C 26898 2.51 5 N 7881 2.21 5 O 9204 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "M ARG 693": "NH1" <-> "NH2" Residue "M ARG 697": "NH1" <-> "NH2" Residue "M TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 766": "NH1" <-> "NH2" Residue "M PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 787": "NH1" <-> "NH2" Residue "M ARG 815": "NH1" <-> "NH2" Residue "M ARG 833": "NH1" <-> "NH2" Residue "M ARG 926": "NH1" <-> "NH2" Residue "M ARG 956": "NH1" <-> "NH2" Residue "M ARG 967": "NH1" <-> "NH2" Residue "M PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1023": "NH1" <-> "NH2" Residue "M ARG 1133": "NH1" <-> "NH2" Residue "M ASP 1159": "OD1" <-> "OD2" Residue "M ARG 1291": "NH1" <-> "NH2" Residue "M ARG 1313": "NH1" <-> "NH2" Residue "M ARG 1357": "NH1" <-> "NH2" Residue "M PHE 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1387": "NH1" <-> "NH2" Residue "R PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 221": "NH1" <-> "NH2" Residue "R ARG 234": "NH1" <-> "NH2" Residue "R PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 288": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 276": "NH1" <-> "NH2" Residue "T ARG 23": "NH1" <-> "NH2" Residue "T GLU 37": "OE1" <-> "OE2" Residue "T TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 191": "NH1" <-> "NH2" Residue "T ARG 258": "NH1" <-> "NH2" Residue "T ARG 348": "NH1" <-> "NH2" Residue "T ARG 392": "NH1" <-> "NH2" Residue "T ARG 413": "NH1" <-> "NH2" Residue "T GLU 441": "OE1" <-> "OE2" Residue "T TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 52": "NH1" <-> "NH2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "U ARG 122": "NH1" <-> "NH2" Residue "U TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 204": "NH1" <-> "NH2" Residue "U PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 266": "NH1" <-> "NH2" Residue "U ARG 311": "NH1" <-> "NH2" Residue "U ARG 333": "NH1" <-> "NH2" Residue "U ASP 349": "OD1" <-> "OD2" Residue "U ARG 397": "NH1" <-> "NH2" Residue "U ARG 413": "NH1" <-> "NH2" Residue "U GLU 421": "OE1" <-> "OE2" Residue "U ARG 425": "NH1" <-> "NH2" Residue "U ARG 435": "NH1" <-> "NH2" Residue "U TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V ARG 191": "NH1" <-> "NH2" Residue "V ARG 258": "NH1" <-> "NH2" Residue "V ARG 348": "NH1" <-> "NH2" Residue "V ARG 392": "NH1" <-> "NH2" Residue "V ARG 413": "NH1" <-> "NH2" Residue "V GLU 441": "OE1" <-> "OE2" Residue "V TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 69": "NH1" <-> "NH2" Residue "W ARG 122": "NH1" <-> "NH2" Residue "W TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 204": "NH1" <-> "NH2" Residue "W PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 266": "NH1" <-> "NH2" Residue "W ARG 311": "NH1" <-> "NH2" Residue "W ARG 333": "NH1" <-> "NH2" Residue "W ASP 349": "OD1" <-> "OD2" Residue "W ARG 397": "NH1" <-> "NH2" Residue "W ARG 413": "NH1" <-> "NH2" Residue "W GLU 421": "OE1" <-> "OE2" Residue "W ARG 425": "NH1" <-> "NH2" Residue "W ARG 435": "NH1" <-> "NH2" Residue "W TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X GLU 37": "OE1" <-> "OE2" Residue "X TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 191": "NH1" <-> "NH2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X ARG 348": "NH1" <-> "NH2" Residue "X ARG 392": "NH1" <-> "NH2" Residue "X ARG 413": "NH1" <-> "NH2" Residue "X GLU 441": "OE1" <-> "OE2" Residue "X TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 69": "NH1" <-> "NH2" Residue "Y ARG 122": "NH1" <-> "NH2" Residue "Y TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 204": "NH1" <-> "NH2" Residue "Y PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Y PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 266": "NH1" <-> "NH2" Residue "Y ARG 311": "NH1" <-> "NH2" Residue "Y ARG 333": "NH1" <-> "NH2" Residue "Y ASP 349": "OD1" <-> "OD2" Residue "Y ARG 397": "NH1" <-> "NH2" Residue "Y ARG 413": "NH1" <-> "NH2" Residue "Y GLU 421": "OE1" <-> "OE2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 44481 Number of models: 1 Model: "" Number of chains: 29 Chain: "Z" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 655 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'TRANS': 130} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 131 Planarities with less than four sites: {'UNK:plan-1': 131} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 651 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 3525 Classifications: {'DNA': 173} Link IDs: {'rna3p': 172} Chain: "J" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 3568 Classifications: {'DNA': 173} Link IDs: {'rna3p': 172} Chain: "M" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5398 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 19, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 167 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1695 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 3 Chain: "T" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3391 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3299 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3336 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3325 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3410 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 436} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23819 SG CYS S 244 49.911 70.845 117.679 1.00 74.04 S ATOM 23839 SG CYS S 247 46.584 68.555 114.591 1.00 61.50 S ATOM 23955 SG CYS S 264 47.615 71.995 114.554 1.00 90.14 S ATOM 23980 SG CYS S 268 45.500 71.489 117.455 1.00 85.21 S ATOM 23899 SG CYS S 256 52.142 78.661 124.394 1.00 96.12 S ATOM 23920 SG CYS S 259 53.977 75.901 126.523 1.00 80.86 S ATOM 24059 SG CYS S 277 50.955 77.008 128.993 1.00111.59 S Time building chain proxies: 19.62, per 1000 atoms: 0.44 Number of scatterers: 44481 At special positions: 0 Unit cell: (169.83, 199.8, 206.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 118 16.00 P 362 15.00 Mg 8 11.99 F 6 9.00 O 9204 8.00 N 7881 7.00 C 26898 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.90 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 264 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " Number of angles added : 9 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9030 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 195 helices and 34 sheets defined 42.6% alpha, 10.3% beta 167 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 15.14 Creating SS restraints... Processing helix chain 'Z' and resid 102 through 128 Processing helix chain 'Z' and resid 137 through 141 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 90 through 113 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 90 through 113 Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 31 through 40 Processing helix chain 'C' and resid 50 through 75 removed outlier: 3.518A pdb=" N GLU C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 31 through 40 Processing helix chain 'D' and resid 50 through 75 removed outlier: 3.517A pdb=" N GLU D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 89 Processing helix chain 'E' and resid 18 through 21 No H-bonds generated for 'chain 'E' and resid 18 through 21' Processing helix chain 'E' and resid 28 through 36 Processing helix chain 'E' and resid 48 through 73 Processing helix chain 'E' and resid 81 through 89 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'F' and resid 18 through 21 No H-bonds generated for 'chain 'F' and resid 18 through 21' Processing helix chain 'F' and resid 28 through 36 Processing helix chain 'F' and resid 48 through 73 Processing helix chain 'F' and resid 81 through 89 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'G' and resid 41 through 51 Processing helix chain 'G' and resid 59 through 86 removed outlier: 3.636A pdb=" N GLU G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 107 through 125 Processing helix chain 'H' and resid 41 through 51 Processing helix chain 'H' and resid 59 through 86 removed outlier: 3.636A pdb=" N GLU H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 107 through 124 Processing helix chain 'M' and resid 698 through 711 removed outlier: 4.083A pdb=" N SER M 709 " --> pdb=" O ASN M 705 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU M 710 " --> pdb=" O TRP M 706 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR M 711 " --> pdb=" O LEU M 707 " (cutoff:3.500A) Processing helix chain 'M' and resid 727 through 741 removed outlier: 3.517A pdb=" N ALA M 739 " --> pdb=" O LEU M 735 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS M 740 " --> pdb=" O ALA M 736 " (cutoff:3.500A) Processing helix chain 'M' and resid 757 through 766 removed outlier: 3.955A pdb=" N GLU M 761 " --> pdb=" O LEU M 757 " (cutoff:3.500A) Processing helix chain 'M' and resid 782 through 788 Processing helix chain 'M' and resid 805 through 808 No H-bonds generated for 'chain 'M' and resid 805 through 808' Processing helix chain 'M' and resid 810 through 813 No H-bonds generated for 'chain 'M' and resid 810 through 813' Processing helix chain 'M' and resid 835 through 839 Processing helix chain 'M' and resid 860 through 870 Processing helix chain 'M' and resid 914 through 924 removed outlier: 3.853A pdb=" N HIS M 922 " --> pdb=" O VAL M 918 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN M 923 " --> pdb=" O ALA M 919 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL M 924 " --> pdb=" O LYS M 920 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 970 Processing helix chain 'M' and resid 972 through 974 No H-bonds generated for 'chain 'M' and resid 972 through 974' Processing helix chain 'M' and resid 980 through 993 removed outlier: 4.665A pdb=" N GLN M 988 " --> pdb=" O ASN M 984 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU M 989 " --> pdb=" O CYS M 985 " (cutoff:3.500A) Processing helix chain 'M' and resid 1014 through 1029 removed outlier: 3.753A pdb=" N TYR M1018 " --> pdb=" O VAL M1014 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP M1020 " --> pdb=" O SER M1016 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N VAL M1021 " --> pdb=" O ASP M1017 " (cutoff:3.500A) Processing helix chain 'M' and resid 1047 through 1049 No H-bonds generated for 'chain 'M' and resid 1047 through 1049' Processing helix chain 'M' and resid 1057 through 1063 Processing helix chain 'M' and resid 1071 through 1093 removed outlier: 3.602A pdb=" N LEU M1078 " --> pdb=" O GLU M1074 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU M1080 " --> pdb=" O ASN M1076 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU M1085 " --> pdb=" O THR M1081 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU M1088 " --> pdb=" O GLN M1084 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU M1091 " --> pdb=" O GLU M1087 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA M1092 " --> pdb=" O GLU M1088 " (cutoff:3.500A) Processing helix chain 'M' and resid 1105 through 1133 removed outlier: 3.901A pdb=" N ASP M1117 " --> pdb=" O GLU M1113 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET M1118 " --> pdb=" O GLY M1114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU M1122 " --> pdb=" O MET M1118 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS M1123 " --> pdb=" O LEU M1119 " (cutoff:3.500A) Processing helix chain 'M' and resid 1142 through 1146 Processing helix chain 'M' and resid 1166 through 1172 removed outlier: 3.738A pdb=" N LEU M1171 " --> pdb=" O GLN M1167 " (cutoff:3.500A) Processing helix chain 'M' and resid 1174 through 1180 Processing helix chain 'M' and resid 1193 through 1197 removed outlier: 4.061A pdb=" N LEU M1197 " --> pdb=" O ARG M1193 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1193 through 1197' Processing helix chain 'M' and resid 1209 through 1219 Processing helix chain 'M' and resid 1225 through 1232 Processing helix chain 'M' and resid 1238 through 1243 removed outlier: 4.013A pdb=" N LEU M1241 " --> pdb=" O LYS M1238 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN M1242 " --> pdb=" O SER M1239 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR M1243 " --> pdb=" O LEU M1240 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1238 through 1243' Processing helix chain 'M' and resid 1251 through 1260 Processing helix chain 'M' and resid 1272 through 1285 removed outlier: 4.370A pdb=" N ASP M1276 " --> pdb=" O LYS M1273 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL M1277 " --> pdb=" O VAL M1274 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE M1281 " --> pdb=" O LEU M1278 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU M1282 " --> pdb=" O GLU M1279 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN M1283 " --> pdb=" O GLN M1280 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS M1285 " --> pdb=" O LEU M1282 " (cutoff:3.500A) Processing helix chain 'M' and resid 1299 through 1309 removed outlier: 3.982A pdb=" N ILE M1303 " --> pdb=" O GLU M1299 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE M1308 " --> pdb=" O LEU M1304 " (cutoff:3.500A) Processing helix chain 'M' and resid 1347 through 1355 removed outlier: 3.762A pdb=" N CYS M1351 " --> pdb=" O MET M1347 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS M1355 " --> pdb=" O CYS M1351 " (cutoff:3.500A) Processing helix chain 'M' and resid 1375 through 1385 removed outlier: 3.801A pdb=" N LEU M1380 " --> pdb=" O GLU M1376 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS M1381 " --> pdb=" O SER M1377 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN M1385 " --> pdb=" O LYS M1381 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 80 Processing helix chain 'R' and resid 109 through 121 Processing helix chain 'R' and resid 133 through 142 removed outlier: 3.663A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) Proline residue: R 138 - end of helix removed outlier: 5.228A pdb=" N LYS R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N SER R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 133 through 142' Processing helix chain 'R' and resid 220 through 234 Processing helix chain 'R' and resid 243 through 251 Processing helix chain 'R' and resid 260 through 265 Processing helix chain 'R' and resid 308 through 316 removed outlier: 3.969A pdb=" N ILE R 313 " --> pdb=" O GLU R 309 " (cutoff:3.500A) Proline residue: R 314 - end of helix Processing helix chain 'R' and resid 330 through 339 Processing helix chain 'R' and resid 343 through 349 Proline residue: R 347 - end of helix No H-bonds generated for 'chain 'R' and resid 343 through 349' Processing helix chain 'R' and resid 359 through 361 No H-bonds generated for 'chain 'R' and resid 359 through 361' Processing helix chain 'R' and resid 365 through 374 Processing helix chain 'R' and resid 392 through 402 Processing helix chain 'R' and resid 407 through 412 Processing helix chain 'R' and resid 416 through 421 Processing helix chain 'R' and resid 424 through 429 removed outlier: 4.189A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 437 No H-bonds generated for 'chain 'R' and resid 434 through 437' Processing helix chain 'S' and resid 53 through 60 Processing helix chain 'S' and resid 92 through 106 Processing helix chain 'S' and resid 113 through 124 Proline residue: S 117 - end of helix Processing helix chain 'S' and resid 128 through 134 Processing helix chain 'S' and resid 169 through 181 removed outlier: 4.670A pdb=" N SER S 181 " --> pdb=" O LEU S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 202 Processing helix chain 'S' and resid 208 through 213 Processing helix chain 'S' and resid 219 through 226 Processing helix chain 'S' and resid 266 through 270 Processing helix chain 'T' and resid 52 through 66 Processing helix chain 'T' and resid 86 through 96 Processing helix chain 'T' and resid 107 through 110 removed outlier: 3.622A pdb=" N LEU T 110 " --> pdb=" O GLY T 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 107 through 110' Processing helix chain 'T' and resid 117 through 127 Processing helix chain 'T' and resid 183 through 191 Processing helix chain 'T' and resid 216 through 218 No H-bonds generated for 'chain 'T' and resid 216 through 218' Processing helix chain 'T' and resid 249 through 257 Processing helix chain 'T' and resid 265 through 273 Processing helix chain 'T' and resid 282 through 297 Processing helix chain 'T' and resid 313 through 315 No H-bonds generated for 'chain 'T' and resid 313 through 315' Processing helix chain 'T' and resid 318 through 328 removed outlier: 3.578A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 358 No H-bonds generated for 'chain 'T' and resid 356 through 358' Processing helix chain 'T' and resid 361 through 365 Processing helix chain 'T' and resid 377 through 390 Processing helix chain 'T' and resid 397 through 407 Processing helix chain 'T' and resid 412 through 417 Processing helix chain 'T' and resid 419 through 428 removed outlier: 3.742A pdb=" N GLY T 423 " --> pdb=" O LEU T 419 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 445 Processing helix chain 'T' and resid 449 through 457 Processing helix chain 'U' and resid 48 through 63 Processing helix chain 'U' and resid 81 through 92 Processing helix chain 'U' and resid 113 through 123 Processing helix chain 'U' and resid 173 through 181 Processing helix chain 'U' and resid 241 through 249 Processing helix chain 'U' and resid 251 through 253 No H-bonds generated for 'chain 'U' and resid 251 through 253' Processing helix chain 'U' and resid 255 through 259 Processing helix chain 'U' and resid 267 through 283 Processing helix chain 'U' and resid 303 through 314 removed outlier: 4.986A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 342 No H-bonds generated for 'chain 'U' and resid 340 through 342' Processing helix chain 'U' and resid 345 through 349 Processing helix chain 'U' and resid 361 through 374 removed outlier: 3.541A pdb=" N LYS U 365 " --> pdb=" O GLU U 361 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 393 Processing helix chain 'U' and resid 396 through 412 removed outlier: 4.459A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 442 Processing helix chain 'V' and resid 52 through 66 Processing helix chain 'V' and resid 86 through 96 Processing helix chain 'V' and resid 107 through 110 removed outlier: 3.622A pdb=" N LEU V 110 " --> pdb=" O GLY V 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 107 through 110' Processing helix chain 'V' and resid 117 through 127 Processing helix chain 'V' and resid 183 through 191 Processing helix chain 'V' and resid 216 through 218 No H-bonds generated for 'chain 'V' and resid 216 through 218' Processing helix chain 'V' and resid 249 through 257 Processing helix chain 'V' and resid 265 through 273 Processing helix chain 'V' and resid 282 through 297 Processing helix chain 'V' and resid 313 through 315 No H-bonds generated for 'chain 'V' and resid 313 through 315' Processing helix chain 'V' and resid 318 through 328 removed outlier: 3.579A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 358 No H-bonds generated for 'chain 'V' and resid 356 through 358' Processing helix chain 'V' and resid 361 through 365 Processing helix chain 'V' and resid 377 through 390 Processing helix chain 'V' and resid 397 through 407 Processing helix chain 'V' and resid 412 through 417 Processing helix chain 'V' and resid 419 through 428 removed outlier: 3.742A pdb=" N GLY V 423 " --> pdb=" O LEU V 419 " (cutoff:3.500A) Processing helix chain 'V' and resid 436 through 445 Processing helix chain 'V' and resid 449 through 457 Processing helix chain 'W' and resid 48 through 63 Processing helix chain 'W' and resid 81 through 92 Processing helix chain 'W' and resid 113 through 123 Processing helix chain 'W' and resid 173 through 181 Processing helix chain 'W' and resid 241 through 249 Processing helix chain 'W' and resid 251 through 253 No H-bonds generated for 'chain 'W' and resid 251 through 253' Processing helix chain 'W' and resid 255 through 259 Processing helix chain 'W' and resid 267 through 283 Processing helix chain 'W' and resid 303 through 314 removed outlier: 4.987A pdb=" N GLU W 314 " --> pdb=" O ASN W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 342 No H-bonds generated for 'chain 'W' and resid 340 through 342' Processing helix chain 'W' and resid 345 through 349 Processing helix chain 'W' and resid 361 through 374 removed outlier: 3.541A pdb=" N LYS W 365 " --> pdb=" O GLU W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 381 through 393 Processing helix chain 'W' and resid 396 through 412 removed outlier: 4.459A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN W 407 " --> pdb=" O ILE W 403 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN W 408 " --> pdb=" O SER W 404 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 429 Processing helix chain 'W' and resid 433 through 442 Processing helix chain 'X' and resid 52 through 66 Processing helix chain 'X' and resid 86 through 96 Processing helix chain 'X' and resid 107 through 110 removed outlier: 3.623A pdb=" N LEU X 110 " --> pdb=" O GLY X 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 107 through 110' Processing helix chain 'X' and resid 117 through 127 Processing helix chain 'X' and resid 183 through 191 Processing helix chain 'X' and resid 216 through 218 No H-bonds generated for 'chain 'X' and resid 216 through 218' Processing helix chain 'X' and resid 249 through 257 Processing helix chain 'X' and resid 265 through 273 Processing helix chain 'X' and resid 282 through 297 Processing helix chain 'X' and resid 313 through 315 No H-bonds generated for 'chain 'X' and resid 313 through 315' Processing helix chain 'X' and resid 318 through 328 removed outlier: 3.578A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 361 through 365 Processing helix chain 'X' and resid 377 through 390 Processing helix chain 'X' and resid 397 through 407 Processing helix chain 'X' and resid 412 through 417 Processing helix chain 'X' and resid 419 through 428 removed outlier: 3.743A pdb=" N GLY X 423 " --> pdb=" O LEU X 419 " (cutoff:3.500A) Processing helix chain 'X' and resid 436 through 445 Processing helix chain 'X' and resid 449 through 457 Processing helix chain 'Y' and resid 48 through 63 Processing helix chain 'Y' and resid 81 through 92 Processing helix chain 'Y' and resid 113 through 123 Processing helix chain 'Y' and resid 173 through 180 Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 251 through 253 No H-bonds generated for 'chain 'Y' and resid 251 through 253' Processing helix chain 'Y' and resid 255 through 259 Processing helix chain 'Y' and resid 267 through 283 Processing helix chain 'Y' and resid 303 through 314 removed outlier: 4.987A pdb=" N GLU Y 314 " --> pdb=" O ASN Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 342 No H-bonds generated for 'chain 'Y' and resid 340 through 342' Processing helix chain 'Y' and resid 345 through 349 Processing helix chain 'Y' and resid 361 through 374 removed outlier: 3.542A pdb=" N LYS Y 365 " --> pdb=" O GLU Y 361 " (cutoff:3.500A) Processing helix chain 'Y' and resid 381 through 393 Processing helix chain 'Y' and resid 396 through 412 removed outlier: 4.459A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN Y 407 " --> pdb=" O ILE Y 403 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 442 Processing sheet with id= A, first strand: chain 'Z' and resid 169 through 171 Processing sheet with id= B, first strand: chain 'M' and resid 798 through 802 removed outlier: 6.709A pdb=" N HIS M 748 " --> pdb=" O CYS M 799 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL M 801 " --> pdb=" O HIS M 748 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE M 750 " --> pdb=" O VAL M 801 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ARG M 847 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LEU M 823 " --> pdb=" O ARG M 847 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU M 849 " --> pdb=" O LEU M 823 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 944 through 946 removed outlier: 6.694A pdb=" N VAL M1364 " --> pdb=" O TYR M 945 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'M' and resid 949 through 951 Processing sheet with id= E, first strand: chain 'M' and resid 1335 through 1338 removed outlier: 4.092A pdb=" N THR M1269 " --> pdb=" O LEU M1319 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET M1290 " --> pdb=" O VAL M1316 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 6 through 9 removed outlier: 3.529A pdb=" N ALA R 28 " --> pdb=" O ILE R 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE R 17 " --> pdb=" O PHE R 26 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 32 through 35 Processing sheet with id= H, first strand: chain 'R' and resid 98 through 101 removed outlier: 6.759A pdb=" N SER R 127 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA R 101 " --> pdb=" O SER R 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE R 129 " --> pdb=" O ALA R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'R' and resid 147 through 151 removed outlier: 5.965A pdb=" N ILE R 353 " --> pdb=" O SER R 386 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS R 355 " --> pdb=" O PRO R 388 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU R 189 " --> pdb=" O VAL R 354 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR R 356 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE R 191 " --> pdb=" O THR R 356 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'R' and resid 286 through 289 removed outlier: 4.084A pdb=" N TYR R 286 " --> pdb=" O VAL R 275 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL R 275 " --> pdb=" O TYR R 286 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 367 through 371 removed outlier: 7.168A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU T 308 " --> pdb=" O VAL T 335 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 130 through 132 removed outlier: 3.690A pdb=" N ARG T 132 " --> pdb=" O GLU T 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU T 302 " --> pdb=" O ARG T 132 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 238 through 243 removed outlier: 3.799A pdb=" N LYS T 241 " --> pdb=" O LYS T 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS T 137 " --> pdb=" O LYS T 241 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU T 135 " --> pdb=" O ILE T 243 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY T 142 " --> pdb=" O ILE T 200 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'T' and resid 166 through 171 removed outlier: 4.520A pdb=" N VAL T 166 " --> pdb=" O LEU T 181 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU T 181 " --> pdb=" O VAL T 166 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'U' and resid 351 through 356 removed outlier: 7.057A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR U 356 " --> pdb=" O LEU U 72 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA U 74 " --> pdb=" O THR U 356 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N GLY U 75 " --> pdb=" O MET U 323 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 230 through 240 Processing sheet with id= Q, first strand: chain 'U' and resid 135 through 138 removed outlier: 3.616A pdb=" N GLY U 138 " --> pdb=" O ILE U 190 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE U 190 " --> pdb=" O GLY U 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY U 203 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'U' and resid 143 through 146 removed outlier: 3.713A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'V' and resid 367 through 371 removed outlier: 7.168A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU V 308 " --> pdb=" O VAL V 335 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'V' and resid 130 through 132 removed outlier: 3.689A pdb=" N ARG V 132 " --> pdb=" O GLU V 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU V 302 " --> pdb=" O ARG V 132 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'V' and resid 238 through 243 removed outlier: 3.798A pdb=" N LYS V 241 " --> pdb=" O LYS V 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS V 137 " --> pdb=" O LYS V 241 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU V 135 " --> pdb=" O ILE V 243 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY V 142 " --> pdb=" O ILE V 200 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'V' and resid 166 through 171 removed outlier: 4.520A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU V 181 " --> pdb=" O VAL V 166 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'W' and resid 351 through 356 removed outlier: 7.057A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR W 356 " --> pdb=" O LEU W 72 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA W 74 " --> pdb=" O THR W 356 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N GLY W 75 " --> pdb=" O MET W 323 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'W' and resid 230 through 240 Processing sheet with id= Y, first strand: chain 'W' and resid 135 through 138 removed outlier: 3.617A pdb=" N GLY W 138 " --> pdb=" O ILE W 190 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE W 190 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'W' and resid 143 through 146 removed outlier: 3.712A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'X' and resid 367 through 371 removed outlier: 7.168A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU X 308 " --> pdb=" O VAL X 335 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'X' and resid 130 through 132 removed outlier: 3.689A pdb=" N ARG X 132 " --> pdb=" O GLU X 302 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU X 302 " --> pdb=" O ARG X 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'X' and resid 238 through 243 removed outlier: 3.799A pdb=" N LYS X 241 " --> pdb=" O LYS X 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS X 137 " --> pdb=" O LYS X 241 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU X 135 " --> pdb=" O ILE X 243 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY X 142 " --> pdb=" O ILE X 200 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU X 203 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL X 209 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'X' and resid 166 through 171 removed outlier: 4.520A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU X 181 " --> pdb=" O VAL X 166 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Y' and resid 351 through 356 removed outlier: 7.056A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR Y 356 " --> pdb=" O LEU Y 72 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA Y 74 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL Y 321 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL Y 73 " --> pdb=" O VAL Y 321 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET Y 323 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLY Y 75 " --> pdb=" O MET Y 323 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Y' and resid 230 through 240 Processing sheet with id= AG, first strand: chain 'Y' and resid 135 through 138 removed outlier: 3.617A pdb=" N GLY Y 138 " --> pdb=" O ILE Y 190 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE Y 190 " --> pdb=" O GLY Y 138 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY Y 203 " --> pdb=" O VAL Y 189 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Y' and resid 143 through 146 removed outlier: 3.712A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) 1361 hydrogen bonds defined for protein. 4005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 421 hydrogen bonds 802 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 294 stacking parallelities Total time for adding SS restraints: 23.47 Time building geometry restraints manager: 19.26 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: 11615 1.34 - 1.46: 9372 1.46 - 1.58: 23975 1.58 - 1.70: 716 1.70 - 1.82: 194 Bond restraints: 45872 Sorted by residual: bond pdb=" C VAL S 116 " pdb=" N PRO S 117 " ideal model delta sigma weight residual 1.337 1.401 -0.065 1.11e-02 8.12e+03 3.39e+01 bond pdb=" BE BEF R 502 " pdb=" F2 BEF R 502 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" BE BEF M1602 " pdb=" F2 BEF M1602 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" BE BEF M1602 " pdb=" F3 BEF M1602 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" BE BEF R 502 " pdb=" F3 BEF R 502 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 45867 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.94: 1935 104.94 - 112.82: 25807 112.82 - 120.71: 20701 120.71 - 128.59: 14678 128.59 - 136.47: 435 Bond angle restraints: 63556 Sorted by residual: angle pdb=" C PHE R 136 " pdb=" N VAL R 137 " pdb=" CA VAL R 137 " ideal model delta sigma weight residual 120.24 124.26 -4.02 6.30e-01 2.52e+00 4.07e+01 angle pdb=" C LEU M 998 " pdb=" N PHE M 999 " pdb=" CA PHE M 999 " ideal model delta sigma weight residual 126.32 135.68 -9.36 1.74e+00 3.30e-01 2.89e+01 angle pdb=" N LYS X 161 " pdb=" CA LYS X 161 " pdb=" C LYS X 161 " ideal model delta sigma weight residual 107.23 115.43 -8.20 1.67e+00 3.59e-01 2.41e+01 angle pdb=" C VAL M1068 " pdb=" N LYS M1069 " pdb=" CA LYS M1069 " ideal model delta sigma weight residual 123.93 131.43 -7.50 1.54e+00 4.22e-01 2.37e+01 angle pdb=" CA TYR X 462 " pdb=" CB TYR X 462 " pdb=" CG TYR X 462 " ideal model delta sigma weight residual 113.90 122.49 -8.59 1.80e+00 3.09e-01 2.28e+01 ... (remaining 63551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 24610 35.71 - 71.42: 2053 71.42 - 107.12: 51 107.12 - 142.83: 11 142.83 - 178.54: 4 Dihedral angle restraints: 26729 sinusoidal: 12778 harmonic: 13951 Sorted by residual: dihedral pdb=" CA GLY T 160 " pdb=" C GLY T 160 " pdb=" N LYS T 161 " pdb=" CA LYS T 161 " ideal model delta harmonic sigma weight residual -180.00 -126.60 -53.40 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ASP X 151 " pdb=" C ASP X 151 " pdb=" N ALA X 152 " pdb=" CA ALA X 152 " ideal model delta harmonic sigma weight residual -180.00 -131.00 -49.00 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA PHE W 221 " pdb=" C PHE W 221 " pdb=" N VAL W 222 " pdb=" CA VAL W 222 " ideal model delta harmonic sigma weight residual 180.00 131.98 48.02 0 5.00e+00 4.00e-02 9.22e+01 ... (remaining 26726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 5700 0.045 - 0.090: 1269 0.090 - 0.135: 423 0.135 - 0.180: 37 0.180 - 0.225: 11 Chirality restraints: 7440 Sorted by residual: chirality pdb=" CA PHE M 999 " pdb=" N PHE M 999 " pdb=" C PHE M 999 " pdb=" CB PHE M 999 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" P DT J 25 " pdb=" OP1 DT J 25 " pdb=" OP2 DT J 25 " pdb=" O5' DT J 25 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ARG M1133 " pdb=" N ARG M1133 " pdb=" C ARG M1133 " pdb=" CB ARG M1133 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 7437 not shown) Planarity restraints: 6874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER W 205 " 0.040 2.00e-02 2.50e+03 8.23e-02 6.77e+01 pdb=" C SER W 205 " -0.142 2.00e-02 2.50e+03 pdb=" O SER W 205 " 0.055 2.00e-02 2.50e+03 pdb=" N PHE W 206 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER Y 205 " 0.035 2.00e-02 2.50e+03 6.97e-02 4.86e+01 pdb=" C SER Y 205 " -0.121 2.00e-02 2.50e+03 pdb=" O SER Y 205 " 0.046 2.00e-02 2.50e+03 pdb=" N PHE Y 206 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP X 151 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C ASP X 151 " 0.070 2.00e-02 2.50e+03 pdb=" O ASP X 151 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA X 152 " -0.024 2.00e-02 2.50e+03 ... (remaining 6871 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 966 2.67 - 3.23: 36963 3.23 - 3.78: 72217 3.78 - 4.34: 94803 4.34 - 4.90: 146159 Nonbonded interactions: 351108 Sorted by model distance: nonbonded pdb=" O3B ADP M1601 " pdb=" BE BEF M1602 " model vdw 2.109 1.936 nonbonded pdb=" O1B ADP R 501 " pdb="MG MG R 503 " model vdw 2.170 2.170 nonbonded pdb=" O3B ADP X 501 " pdb="MG MG Y 501 " model vdw 2.178 2.170 nonbonded pdb=" F3 BEF M1602 " pdb="MG MG M1603 " model vdw 2.192 2.120 nonbonded pdb=" O3B ADP T 501 " pdb="MG MG U 501 " model vdw 2.237 2.170 ... (remaining 351103 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' } ncs_group { reference = (chain 'C' and resid 23 through 102) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 17 through 117) selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 35 through 125) selection = chain 'H' } ncs_group { reference = (chain 'T' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 463 or resid 501)) selection = (chain 'V' and (resid 22 through 161 or (resid 162 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) selection = (chain 'X' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 161 through 163 and (name N or name CA or \ name C or name O or name CB )) or resid 164 through 463 or resid 501)) } ncs_group { reference = (chain 'U' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 222 or (resid 223 and (name N or name C \ A or name C or name O or name CB )) or resid 224 through 459 or resid 502 throug \ h 503)) selection = (chain 'W' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 205 or resid 222 throug \ h 459 or resid 501 through 502)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 205 or resid 222 or (resid 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 through 45 \ 9 or resid 502 through 503)) } 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.250 Construct map_model_manager: 0.040 Extract box with map and model: 15.870 Check model and map are aligned: 0.650 Set scattering table: 0.380 Process input model: 126.320 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 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 : 0.004 0.087 45872 Z= 0.218 Angle : 0.755 14.190 63556 Z= 0.434 Chirality : 0.043 0.225 7440 Planarity : 0.005 0.082 6874 Dihedral : 20.455 178.540 17699 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer Outliers : 8.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.09), residues: 4633 helix: -3.92 (0.05), residues: 2130 sheet: -0.77 (0.20), residues: 580 loop : -2.36 (0.12), residues: 1923 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1505 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 1155 time to evaluate : 4.771 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: 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: 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 outliers start: 350 outliers final: 41 residues processed: 1423 average time/residue: 0.6230 time to fit residues: 1402.5819 Evaluate side-chains 528 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 487 time to evaluate : 4.491 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.4277 time to fit residues: 38.3196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 429 optimal weight: 7.9990 chunk 385 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 398 optimal weight: 0.0670 chunk 154 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 296 optimal weight: 0.8980 chunk 462 optimal weight: 1.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS E 16 GLN E 42 GLN E 113 HIS F 32 HIS F 39 ASN F 42 GLN H 87 ASN H 112 HIS M 782 GLN M 857 GLN ** M 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1082 ASN M1173 ASN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 HIS ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 HIS ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 247 ASN R 251 GLN R 270 HIS R 359 ASN S 261 ASN T 124 ASN ** T 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 263 GLN T 289 ASN T 357 HIS ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 ASN U 36 GLN U 63 ASN U 237 HIS U 252 GLN ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 190 GLN V 245 GLN ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 357 HIS ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 63 ASN W 272 GLN W 401 ASN X 271 GLN X 341 ASN X 357 HIS Y 23 HIS Y 63 ASN Y 230 GLN Y 326 ASN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 45872 Z= 0.206 Angle : 0.700 10.783 63556 Z= 0.359 Chirality : 0.042 0.242 7440 Planarity : 0.005 0.061 6874 Dihedral : 23.702 155.922 8743 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.10), residues: 4633 helix: -1.63 (0.09), residues: 2115 sheet: -0.57 (0.20), residues: 632 loop : -1.86 (0.12), residues: 1886 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 518 time to evaluate : 4.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 72 residues processed: 625 average time/residue: 0.5780 time to fit residues: 596.4937 Evaluate side-chains 453 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 381 time to evaluate : 4.293 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.4091 time to fit residues: 61.0780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 256 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 384 optimal weight: 2.9990 chunk 314 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 463 optimal weight: 0.9990 chunk 500 optimal weight: 1.9990 chunk 412 optimal weight: 0.5980 chunk 459 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 371 optimal weight: 8.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN G 112 HIS H 70 ASN M 702 GLN M 712 ASN M 730 GLN M 808 GLN M 873 GLN ** M1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1226 GLN M1285 HIS ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 HIS ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 455 GLN V 94 GLN V 124 ASN ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN V 341 ASN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 289 ASN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 326 ASN Y 408 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 45872 Z= 0.205 Angle : 0.655 12.128 63556 Z= 0.336 Chirality : 0.041 0.261 7440 Planarity : 0.004 0.052 6874 Dihedral : 23.574 150.568 8743 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 3.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.11), residues: 4633 helix: -0.40 (0.10), residues: 2112 sheet: -0.34 (0.21), residues: 621 loop : -1.60 (0.13), residues: 1900 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 417 time to evaluate : 4.690 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 51 residues processed: 509 average time/residue: 0.5498 time to fit residues: 468.6508 Evaluate side-chains 394 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 343 time to evaluate : 4.566 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.4078 time to fit residues: 45.0569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 457 optimal weight: 0.9990 chunk 348 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 464 optimal weight: 10.0000 chunk 492 optimal weight: 1.9990 chunk 242 optimal weight: 20.0000 chunk 440 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN F 42 GLN M 712 ASN M 873 GLN M1044 ASN M1070 ASN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1356 HIS ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 GLN R 374 GLN R 384 HIS R 422 HIS S 261 ASN S 273 ASN ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 155 GLN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 256 ASN V 394 GLN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 299 HIS ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 205 ASN ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN X 357 HIS ** X 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 252 GLN ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.086 45872 Z= 0.347 Angle : 0.815 13.326 63556 Z= 0.422 Chirality : 0.045 0.208 7440 Planarity : 0.006 0.073 6874 Dihedral : 23.637 150.235 8743 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 22.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 4.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.31 (0.11), residues: 4633 helix: -0.23 (0.11), residues: 2121 sheet: -0.62 (0.20), residues: 628 loop : -1.61 (0.13), residues: 1884 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 391 time to evaluate : 4.843 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 outliers start: 181 outliers final: 73 residues processed: 538 average time/residue: 0.5621 time to fit residues: 505.4802 Evaluate side-chains 384 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 311 time to evaluate : 4.403 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.4264 time to fit residues: 63.3247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 409 optimal weight: 0.0980 chunk 279 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 366 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 419 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 251 optimal weight: 8.9990 chunk 441 optimal weight: 0.3980 chunk 124 optimal weight: 9.9990 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1070 ASN M1249 GLN M1263 HIS ** M1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 HIS ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 394 GLN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 HIS ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 416 ASN W 455 GLN ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 237 HIS Y 455 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.7880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.104 45872 Z= 0.410 Angle : 0.866 16.498 63556 Z= 0.449 Chirality : 0.048 0.293 7440 Planarity : 0.006 0.077 6874 Dihedral : 23.876 148.628 8743 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.87 % Favored : 94.11 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.53 (0.12), residues: 4633 helix: -0.30 (0.11), residues: 2081 sheet: -0.73 (0.21), residues: 606 loop : -1.83 (0.13), residues: 1946 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 330 time to evaluate : 4.754 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 outliers start: 146 outliers final: 73 residues processed: 448 average time/residue: 0.5936 time to fit residues: 443.3676 Evaluate side-chains 359 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 286 time to evaluate : 4.663 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.4288 time to fit residues: 64.3464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 165 optimal weight: 5.9990 chunk 443 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 288 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 492 optimal weight: 0.0870 chunk 408 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 162 optimal weight: 0.2980 chunk 258 optimal weight: 0.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN F 42 GLN H 70 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 873 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN R 114 HIS S 273 ASN ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 47 GLN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 455 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.7764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 45872 Z= 0.185 Angle : 0.677 13.926 63556 Z= 0.344 Chirality : 0.042 0.211 7440 Planarity : 0.004 0.052 6874 Dihedral : 23.548 149.028 8743 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.88 (0.12), residues: 4633 helix: 0.39 (0.11), residues: 2090 sheet: -0.77 (0.20), residues: 629 loop : -1.57 (0.13), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 365 time to evaluate : 4.704 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 outliers start: 54 outliers final: 16 residues processed: 400 average time/residue: 0.5596 time to fit residues: 374.3704 Evaluate side-chains 322 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 306 time to evaluate : 4.599 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4004 time to fit residues: 18.1745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 474 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 280 optimal weight: 8.9990 chunk 359 optimal weight: 3.9990 chunk 278 optimal weight: 0.7980 chunk 414 optimal weight: 10.0000 chunk 275 optimal weight: 4.9990 chunk 490 optimal weight: 0.9980 chunk 307 optimal weight: 8.9990 chunk 299 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 373 GLN ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.8348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 45872 Z= 0.259 Angle : 0.720 17.182 63556 Z= 0.367 Chirality : 0.042 0.260 7440 Planarity : 0.005 0.055 6874 Dihedral : 23.448 148.510 8743 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.90 (0.12), residues: 4633 helix: 0.39 (0.11), residues: 2100 sheet: -0.75 (0.21), residues: 605 loop : -1.62 (0.13), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 314 time to evaluate : 4.642 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 outliers start: 68 outliers final: 26 residues processed: 360 average time/residue: 0.5773 time to fit residues: 351.4360 Evaluate side-chains 322 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 296 time to evaluate : 4.681 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.4468 time to fit residues: 27.4018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 303 optimal weight: 0.8980 chunk 195 optimal weight: 0.1980 chunk 293 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 311 optimal weight: 6.9990 chunk 334 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 385 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 873 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.8916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 45872 Z= 0.254 Angle : 0.720 13.580 63556 Z= 0.367 Chirality : 0.043 0.315 7440 Planarity : 0.005 0.087 6874 Dihedral : 23.438 148.432 8743 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.95 (0.12), residues: 4633 helix: 0.37 (0.11), residues: 2109 sheet: -0.87 (0.20), residues: 611 loop : -1.65 (0.13), residues: 1913 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 324 time to evaluate : 5.017 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 outliers start: 54 outliers final: 29 residues processed: 360 average time/residue: 0.6020 time to fit residues: 360.6996 Evaluate side-chains 318 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 289 time to evaluate : 4.742 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4866 time to fit residues: 31.4394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 446 optimal weight: 6.9990 chunk 470 optimal weight: 0.0770 chunk 428 optimal weight: 7.9990 chunk 457 optimal weight: 0.4980 chunk 469 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 199 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 413 optimal weight: 0.2980 chunk 432 optimal weight: 9.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 HIS F 42 GLN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 10 ASN ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 359 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 416 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.8854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 45872 Z= 0.173 Angle : 0.680 14.179 63556 Z= 0.339 Chirality : 0.041 0.330 7440 Planarity : 0.004 0.055 6874 Dihedral : 23.246 149.004 8743 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4633 helix: 0.69 (0.11), residues: 2107 sheet: -0.73 (0.21), residues: 597 loop : -1.51 (0.14), residues: 1929 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 342 time to evaluate : 4.998 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 outliers start: 18 outliers final: 6 residues processed: 353 average time/residue: 0.5999 time to fit residues: 355.5867 Evaluate side-chains 310 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 304 time to evaluate : 4.525 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5775 time to fit residues: 11.8686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 455 optimal weight: 8.9990 chunk 300 optimal weight: 2.9990 chunk 483 optimal weight: 0.5980 chunk 295 optimal weight: 0.2980 chunk 229 optimal weight: 8.9990 chunk 336 optimal weight: 9.9990 chunk 507 optimal weight: 4.9990 chunk 466 optimal weight: 9.9990 chunk 403 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 311 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 GLN ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 238 HIS ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.9350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 45872 Z= 0.275 Angle : 0.744 15.059 63556 Z= 0.377 Chirality : 0.043 0.327 7440 Planarity : 0.005 0.081 6874 Dihedral : 23.300 148.542 8743 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.79 (0.12), residues: 4633 helix: 0.55 (0.11), residues: 2105 sheet: -0.88 (0.20), residues: 605 loop : -1.59 (0.14), residues: 1923 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 303 time to evaluate : 4.508 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 outliers start: 17 outliers final: 9 residues processed: 316 average time/residue: 0.6225 time to fit residues: 332.0489 Evaluate side-chains 293 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 284 time to evaluate : 4.525 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5163 time to fit residues: 14.1116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 247 optimal weight: 0.7980 chunk 320 optimal weight: 0.0670 chunk 430 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 372 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 415 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN H 87 ASN M 744 ASN ** M 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.086438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.071080 restraints weight = 346404.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.072619 restraints weight = 207437.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.073622 restraints weight = 141669.563| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.9343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 45872 Z= 0.181 Angle : 0.691 16.735 63556 Z= 0.344 Chirality : 0.042 0.400 7440 Planarity : 0.004 0.068 6874 Dihedral : 23.214 148.931 8743 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.54 (0.12), residues: 4633 helix: 0.78 (0.11), residues: 2088 sheet: -0.77 (0.20), residues: 597 loop : -1.47 (0.14), residues: 1948 =============================================================================== Job complete usr+sys time: 9765.97 seconds wall clock time: 178 minutes 13.24 seconds (10693.24 seconds total)