Starting phenix.real_space_refine on Sat Feb 17 09:34:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpp_32687/02_2024/7wpp_32687_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpp_32687/02_2024/7wpp_32687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpp_32687/02_2024/7wpp_32687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpp_32687/02_2024/7wpp_32687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpp_32687/02_2024/7wpp_32687_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wpp_32687/02_2024/7wpp_32687_neut.pdb" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 276 5.16 5 C 11258 2.51 5 N 3129 2.21 5 O 3583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 34": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "F TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 924": "NH1" <-> "NH2" Residue "F ARG 1035": "NH1" <-> "NH2" Residue "F ARG 1061": "NH1" <-> "NH2" Residue "F ARG 1121": "NH1" <-> "NH2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "H TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 924": "NH1" <-> "NH2" Residue "H ARG 1035": "NH1" <-> "NH2" Residue "H ARG 1061": "NH1" <-> "NH2" Residue "H ARG 1121": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18252 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5427 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 5427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5427 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 675} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 3629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 475, 3623 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 446} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 3692 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.66, per 1000 atoms: 0.64 Number of scatterers: 18252 At special positions: 0 Unit cell: (160.293, 161.391, 149.314, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 276 16.00 O 3583 8.00 N 3129 7.00 C 11258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=116, symmetry=0 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.02 Simple disulfide: pdb=" SG CYS E 210 " - pdb=" SG CYS E 255 " distance=2.03 Simple disulfide: pdb=" SG CYS E 225 " - pdb=" SG CYS E 250 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS E 275 " distance=2.03 Simple disulfide: pdb=" SG CYS E 257 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 265 " - pdb=" SG CYS E 291 " distance=2.03 Simple disulfide: pdb=" SG CYS E 295 " - pdb=" SG CYS E 329 " distance=2.03 Simple disulfide: pdb=" SG CYS E 304 " - pdb=" SG CYS E 325 " distance=2.03 Simple disulfide: pdb=" SG CYS E 308 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 348 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 342 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 372 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 384 " distance=2.03 Simple disulfide: pdb=" SG CYS E 370 " - pdb=" SG CYS E 379 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 524 " distance=2.02 Simple disulfide: pdb=" SG CYS E 410 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS E 418 " - pdb=" SG CYS E 521 " distance=2.03 Simple disulfide: pdb=" SG CYS E 432 " - pdb=" SG CYS E 440 " distance=2.04 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.03 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.02 Simple disulfide: pdb=" SG CYS E 595 " - pdb=" SG CYS E 633 " distance=2.03 Simple disulfide: pdb=" SG CYS E 615 " - pdb=" SG CYS E 621 " distance=2.03 Simple disulfide: pdb=" SG CYS E 623 " - pdb=" SG CYS E 648 " distance=2.02 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 687 " distance=2.03 Simple disulfide: pdb=" SG CYS E 661 " - pdb=" SG CYS E 683 " distance=2.03 Simple disulfide: pdb=" SG CYS E 665 " - pdb=" SG CYS E 679 " distance=2.03 Simple disulfide: pdb=" SG CYS E 669 " - pdb=" SG CYS E 707 " distance=2.03 Simple disulfide: pdb=" SG CYS E 689 " - pdb=" SG CYS E 701 " distance=2.04 Simple disulfide: pdb=" SG CYS E 709 " - pdb=" SG CYS E 731 " distance=2.03 Simple disulfide: pdb=" SG CYS E 729 " - pdb=" SG CYS E 738 " distance=2.03 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 808 " distance=2.03 Simple disulfide: pdb=" SG CYS F 776 " - pdb=" SG CYS F 804 " distance=2.02 Simple disulfide: pdb=" SG CYS F 788 " - pdb=" SG CYS F 799 " distance=2.03 Simple disulfide: pdb=" SG CYS F 792 " - pdb=" SG CYS F 827 " distance=2.03 Simple disulfide: pdb=" SG CYS F 810 " - pdb=" SG CYS F 821 " distance=2.03 Simple disulfide: pdb=" SG CYS F 829 " - pdb=" SG CYS F 851 " distance=2.03 Simple disulfide: pdb=" SG CYS F 846 " - pdb=" SG CYS F 863 " distance=2.03 Simple disulfide: pdb=" SG CYS F 849 " - pdb=" SG CYS F 858 " distance=2.03 Simple disulfide: pdb=" SG CYS F 867 " - pdb=" SG CYS F 996 " distance=2.03 Simple disulfide: pdb=" SG CYS F 889 " - pdb=" SG CYS F1031 " distance=2.03 Simple disulfide: pdb=" SG CYS F 898 " - pdb=" SG CYS F 993 " distance=2.03 Simple disulfide: pdb=" SG CYS F 914 " - pdb=" SG CYS F 921 " distance=2.03 Simple disulfide: pdb=" SG CYS F1046 " - pdb=" SG CYS F1089 " distance=2.03 Simple disulfide: pdb=" SG CYS F1060 " - pdb=" SG CYS F1084 " distance=2.03 Simple disulfide: pdb=" SG CYS F1071 " - pdb=" SG CYS F1111 " distance=2.02 Simple disulfide: pdb=" SG CYS F1091 " - pdb=" SG CYS F1099 " distance=2.04 Simple disulfide: pdb=" SG CYS F1097 " - pdb=" SG CYS H1097 " distance=2.03 Simple disulfide: pdb=" SG CYS F1101 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F1130 " - pdb=" SG CYS F1173 " distance=2.03 Simple disulfide: pdb=" SG CYS F1142 " - pdb=" SG CYS H1142 " distance=2.03 Simple disulfide: pdb=" SG CYS F1149 " - pdb=" SG CYS F1169 " distance=2.03 Simple disulfide: pdb=" SG CYS F1153 " - pdb=" SG CYS F1165 " distance=2.04 Simple disulfide: pdb=" SG CYS F1157 " - pdb=" SG CYS F1196 " distance=2.03 Simple disulfide: pdb=" SG CYS F1177 " - pdb=" SG CYS F1190 " distance=2.03 Simple disulfide: pdb=" SG CYS F1199 " - pdb=" SG CYS F1227 " distance=2.03 Simple disulfide: pdb=" SG CYS F1222 " - pdb=" SG CYS F1237 " distance=2.03 Simple disulfide: pdb=" SG CYS F1225 " - pdb=" SG CYS F1234 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 57 " - pdb=" SG CYS G 200 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 159 " distance=2.02 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 255 " distance=2.02 Simple disulfide: pdb=" SG CYS G 225 " - pdb=" SG CYS G 250 " distance=2.03 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS G 275 " distance=2.03 Simple disulfide: pdb=" SG CYS G 257 " - pdb=" SG CYS G 263 " distance=2.03 Simple disulfide: pdb=" SG CYS G 265 " - pdb=" SG CYS G 291 " distance=2.03 Simple disulfide: pdb=" SG CYS G 295 " - pdb=" SG CYS G 329 " distance=2.03 Simple disulfide: pdb=" SG CYS G 304 " - pdb=" SG CYS G 325 " distance=2.03 Simple disulfide: pdb=" SG CYS G 308 " - pdb=" SG CYS G 321 " distance=2.03 Simple disulfide: pdb=" SG CYS G 312 " - pdb=" SG CYS G 348 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 342 " distance=2.03 Simple disulfide: pdb=" SG CYS G 350 " - pdb=" SG CYS G 372 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 384 " distance=2.02 Simple disulfide: pdb=" SG CYS G 370 " - pdb=" SG CYS G 379 " distance=2.03 Simple disulfide: pdb=" SG CYS G 388 " - pdb=" SG CYS G 524 " distance=2.02 Simple disulfide: pdb=" SG CYS G 410 " - pdb=" SG CYS G 559 " distance=2.03 Simple disulfide: pdb=" SG CYS G 418 " - pdb=" SG CYS G 521 " distance=2.03 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 440 " distance=2.04 Simple disulfide: pdb=" SG CYS G 570 " - pdb=" SG CYS G 613 " distance=2.03 Simple disulfide: pdb=" SG CYS G 584 " - pdb=" SG CYS G 608 " distance=2.02 Simple disulfide: pdb=" SG CYS G 595 " - pdb=" SG CYS G 633 " distance=2.03 Simple disulfide: pdb=" SG CYS G 615 " - pdb=" SG CYS G 621 " distance=2.03 Simple disulfide: pdb=" SG CYS G 623 " - pdb=" SG CYS G 648 " distance=2.02 Simple disulfide: pdb=" SG CYS G 652 " - pdb=" SG CYS G 687 " distance=2.03 Simple disulfide: pdb=" SG CYS G 661 " - pdb=" SG CYS G 683 " distance=2.03 Simple disulfide: pdb=" SG CYS G 665 " - pdb=" SG CYS G 679 " distance=2.03 Simple disulfide: pdb=" SG CYS G 669 " - pdb=" SG CYS G 707 " distance=2.03 Simple disulfide: pdb=" SG CYS G 689 " - pdb=" SG CYS G 701 " distance=2.04 Simple disulfide: pdb=" SG CYS G 709 " - pdb=" SG CYS G 731 " distance=2.03 Simple disulfide: pdb=" SG CYS G 729 " - pdb=" SG CYS G 738 " distance=2.03 Simple disulfide: pdb=" SG CYS H 767 " - pdb=" SG CYS H 808 " distance=2.03 Simple disulfide: pdb=" SG CYS H 776 " - pdb=" SG CYS H 804 " distance=2.02 Simple disulfide: pdb=" SG CYS H 788 " - pdb=" SG CYS H 799 " distance=2.03 Simple disulfide: pdb=" SG CYS H 792 " - pdb=" SG CYS H 827 " distance=2.03 Simple disulfide: pdb=" SG CYS H 810 " - pdb=" SG CYS H 821 " distance=2.04 Simple disulfide: pdb=" SG CYS H 829 " - pdb=" SG CYS H 851 " distance=2.03 Simple disulfide: pdb=" SG CYS H 846 " - pdb=" SG CYS H 863 " distance=2.03 Simple disulfide: pdb=" SG CYS H 849 " - pdb=" SG CYS H 858 " distance=2.03 Simple disulfide: pdb=" SG CYS H 867 " - pdb=" SG CYS H 996 " distance=2.03 Simple disulfide: pdb=" SG CYS H 889 " - pdb=" SG CYS H1031 " distance=2.03 Simple disulfide: pdb=" SG CYS H 898 " - pdb=" SG CYS H 993 " distance=2.03 Simple disulfide: pdb=" SG CYS H 914 " - pdb=" SG CYS H 921 " distance=2.03 Simple disulfide: pdb=" SG CYS H1046 " - pdb=" SG CYS H1089 " distance=2.03 Simple disulfide: pdb=" SG CYS H1060 " - pdb=" SG CYS H1084 " distance=2.03 Simple disulfide: pdb=" SG CYS H1071 " - pdb=" SG CYS H1111 " distance=2.02 Simple disulfide: pdb=" SG CYS H1091 " - pdb=" SG CYS H1099 " distance=2.04 Simple disulfide: pdb=" SG CYS H1101 " - pdb=" SG CYS H1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H1130 " - pdb=" SG CYS H1173 " distance=2.03 Simple disulfide: pdb=" SG CYS H1149 " - pdb=" SG CYS H1169 " distance=2.03 Simple disulfide: pdb=" SG CYS H1153 " - pdb=" SG CYS H1165 " distance=2.03 Simple disulfide: pdb=" SG CYS H1157 " - pdb=" SG CYS H1196 " distance=2.04 Simple disulfide: pdb=" SG CYS H1177 " - pdb=" SG CYS H1190 " distance=2.03 Simple disulfide: pdb=" SG CYS H1199 " - pdb=" SG CYS H1227 " distance=2.03 Simple disulfide: pdb=" SG CYS H1222 " - pdb=" SG CYS H1237 " distance=2.04 Simple disulfide: pdb=" SG CYS H1225 " - pdb=" SG CYS H1234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG E 803 " - " ASN E 156 " " NAG E 804 " - " ASN E 99 " " NAG F1301 " - " ASN F1231 " " NAG F1303 " - " ASN F 857 " " NAG F1304 " - " ASN F1147 " " NAG G 803 " - " ASN G 156 " " NAG G 804 " - " ASN G 99 " " NAG H1301 " - " ASN H1231 " " NAG H1303 " - " ASN H1147 " " NAG H1304 " - " ASN H 857 " Time building additional restraints: 7.60 Conformation dependent library (CDL) restraints added in 4.5 seconds 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4370 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 40 sheets defined 17.4% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'E' and resid 114 through 118 removed outlier: 4.001A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 183 through 189 removed outlier: 3.606A pdb=" N PHE E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 215 through 222 removed outlier: 3.564A pdb=" N LYS E 219 " --> pdb=" O GLY E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 removed outlier: 3.769A pdb=" N SER E 230 " --> pdb=" O GLN E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 252 removed outlier: 3.974A pdb=" N LYS E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.532A pdb=" N LEU E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 514 through 517 Processing helix chain 'E' and resid 545 through 551 Processing helix chain 'E' and resid 568 through 572 Processing helix chain 'E' and resid 573 through 575 No H-bonds generated for 'chain 'E' and resid 573 through 575' Processing helix chain 'E' and resid 576 through 584 removed outlier: 3.809A pdb=" N CYS E 584 " --> pdb=" O SER E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 593 removed outlier: 3.536A pdb=" N PHE E 592 " --> pdb=" O SER E 589 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU E 593 " --> pdb=" O PRO E 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 589 through 593' Processing helix chain 'E' and resid 601 through 613 removed outlier: 3.565A pdb=" N ARG E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR E 610 " --> pdb=" O ARG E 606 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS E 613 " --> pdb=" O ARG E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 637 removed outlier: 4.100A pdb=" N ALA E 627 " --> pdb=" O CYS E 623 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 673 removed outlier: 4.024A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 668 through 673' Processing helix chain 'F' and resid 1017 through 1023 removed outlier: 3.819A pdb=" N ASN F1023 " --> pdb=" O VAL F1019 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1026 No H-bonds generated for 'chain 'F' and resid 1024 through 1026' Processing helix chain 'F' and resid 1049 through 1061 removed outlier: 3.562A pdb=" N ASP F1057 " --> pdb=" O GLN F1053 " (cutoff:3.500A) Processing helix chain 'F' and resid 1062 through 1067 removed outlier: 6.742A pdb=" N ASP F1066 " --> pdb=" O LEU F1063 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL F1067 " --> pdb=" O THR F1064 " (cutoff:3.500A) Processing helix chain 'F' and resid 1068 through 1073 removed outlier: 3.760A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 removed outlier: 3.680A pdb=" N THR F1088 " --> pdb=" O CYS F1084 " (cutoff:3.500A) Processing helix chain 'F' and resid 1100 through 1114 removed outlier: 3.616A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR F1107 " --> pdb=" O THR F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1131 through 1136 removed outlier: 3.659A pdb=" N ARG F1136 " --> pdb=" O GLU F1132 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 118 removed outlier: 4.000A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 155 No H-bonds generated for 'chain 'G' and resid 153 through 155' Processing helix chain 'G' and resid 183 through 189 removed outlier: 3.607A pdb=" N PHE G 187 " --> pdb=" O ASP G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 192 No H-bonds generated for 'chain 'G' and resid 190 through 192' Processing helix chain 'G' and resid 215 through 222 removed outlier: 3.565A pdb=" N LYS G 219 " --> pdb=" O GLY G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.769A pdb=" N SER G 230 " --> pdb=" O GLN G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 252 removed outlier: 3.975A pdb=" N LYS G 252 " --> pdb=" O ALA G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.532A pdb=" N LEU G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 Processing helix chain 'G' and resid 514 through 517 Processing helix chain 'G' and resid 545 through 551 Processing helix chain 'G' and resid 568 through 572 Processing helix chain 'G' and resid 573 through 575 No H-bonds generated for 'chain 'G' and resid 573 through 575' Processing helix chain 'G' and resid 576 through 584 removed outlier: 3.810A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 589 through 593 removed outlier: 3.536A pdb=" N PHE G 592 " --> pdb=" O SER G 589 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU G 593 " --> pdb=" O PRO G 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 589 through 593' Processing helix chain 'G' and resid 601 through 613 removed outlier: 3.565A pdb=" N ARG G 609 " --> pdb=" O LEU G 605 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS G 613 " --> pdb=" O ARG G 609 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 637 removed outlier: 4.100A pdb=" N ALA G 627 " --> pdb=" O CYS G 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 668 through 673 removed outlier: 4.023A pdb=" N LEU G 672 " --> pdb=" O THR G 668 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER G 673 " --> pdb=" O CYS G 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 668 through 673' Processing helix chain 'H' and resid 1017 through 1023 removed outlier: 3.819A pdb=" N ASN H1023 " --> pdb=" O VAL H1019 " (cutoff:3.500A) Processing helix chain 'H' and resid 1024 through 1026 No H-bonds generated for 'chain 'H' and resid 1024 through 1026' Processing helix chain 'H' and resid 1049 through 1061 removed outlier: 3.639A pdb=" N ASP H1057 " --> pdb=" O GLN H1053 " (cutoff:3.500A) Processing helix chain 'H' and resid 1062 through 1067 removed outlier: 6.742A pdb=" N ASP H1066 " --> pdb=" O LEU H1063 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL H1067 " --> pdb=" O THR H1064 " (cutoff:3.500A) Processing helix chain 'H' and resid 1068 through 1073 removed outlier: 3.761A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 removed outlier: 3.681A pdb=" N THR H1088 " --> pdb=" O CYS H1084 " (cutoff:3.500A) Processing helix chain 'H' and resid 1100 through 1114 removed outlier: 3.615A pdb=" N ILE H1104 " --> pdb=" O PHE H1100 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR H1107 " --> pdb=" O THR H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1131 through 1136 removed outlier: 3.659A pdb=" N ARG H1136 " --> pdb=" O GLU H1132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 32 through 37 removed outlier: 3.526A pdb=" N LEU E 150 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'E' and resid 58 through 62 removed outlier: 6.810A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN E 107 " --> pdb=" O GLN E 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 300 through 305 removed outlier: 5.803A pdb=" N TYR E 301 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER E 330 " --> pdb=" O TYR E 301 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN E 303 " --> pdb=" O GLY E 328 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY E 328 " --> pdb=" O GLN E 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AA6, first strand: chain 'E' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'E' and resid 362 through 364 Processing sheet with id=AA8, first strand: chain 'E' and resid 403 through 405 Processing sheet with id=AA9, first strand: chain 'E' and resid 469 through 470 removed outlier: 3.684A pdb=" N GLN E 469 " --> pdb=" O MET E 466 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE E 427 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU E 413 " --> pdb=" O ILE E 427 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR E 429 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN E 411 " --> pdb=" O THR E 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 480 through 484 Processing sheet with id=AB2, first strand: chain 'E' and resid 536 through 537 removed outlier: 3.888A pdb=" N LEU E 541 " --> pdb=" O THR E 537 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 657 through 659 Processing sheet with id=AB4, first strand: chain 'E' and resid 721 through 723 Processing sheet with id=AB5, first strand: chain 'F' and resid 772 through 773 Processing sheet with id=AB6, first strand: chain 'F' and resid 841 through 844 Processing sheet with id=AB7, first strand: chain 'F' and resid 865 through 866 removed outlier: 5.898A pdb=" N LEU F 970 " --> pdb=" O LEU F 966 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 961 " --> pdb=" O SER F 958 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 875 through 876 Processing sheet with id=AB9, first strand: chain 'F' and resid 890 through 895 removed outlier: 7.178A pdb=" N ILE F 907 " --> pdb=" O LEU F 893 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLN F 895 " --> pdb=" O PHE F 905 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE F 905 " --> pdb=" O GLN F 895 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR F 926 " --> pdb=" O LEU F 908 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS F 912 " --> pdb=" O LYS F 922 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS F 922 " --> pdb=" O LYS F 912 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 934 " --> pdb=" O ILE F 927 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU F 933 " --> pdb=" O LYS F 944 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 1144 through 1151 removed outlier: 5.110A pdb=" N TYR F1146 " --> pdb=" O HIS F1174 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N HIS F1174 " --> pdb=" O TYR F1146 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N SER F1148 " --> pdb=" O GLY F1172 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLY F1172 " --> pdb=" O SER F1148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 1182 through 1183 Processing sheet with id=AC3, first strand: chain 'G' and resid 32 through 37 removed outlier: 3.526A pdb=" N LEU G 150 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 42 through 44 Processing sheet with id=AC5, first strand: chain 'G' and resid 58 through 62 removed outlier: 6.810A pdb=" N ILE G 72 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE G 92 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN G 107 " --> pdb=" O GLN G 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 300 through 305 removed outlier: 5.802A pdb=" N TYR G 301 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER G 330 " --> pdb=" O TYR G 301 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLN G 303 " --> pdb=" O GLY G 328 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY G 328 " --> pdb=" O GLN G 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 336 through 337 Processing sheet with id=AC8, first strand: chain 'G' and resid 350 through 351 Processing sheet with id=AC9, first strand: chain 'G' and resid 362 through 364 Processing sheet with id=AD1, first strand: chain 'G' and resid 403 through 405 Processing sheet with id=AD2, first strand: chain 'G' and resid 469 through 470 removed outlier: 3.684A pdb=" N GLN G 469 " --> pdb=" O MET G 466 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N THR G 441 " --> pdb=" O VAL G 430 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL G 430 " --> pdb=" O THR G 441 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 443 " --> pdb=" O GLU G 428 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR G 429 " --> pdb=" O GLN G 411 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLN G 411 " --> pdb=" O THR G 429 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 480 through 484 Processing sheet with id=AD4, first strand: chain 'G' and resid 536 through 537 removed outlier: 3.887A pdb=" N LEU G 541 " --> pdb=" O THR G 537 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 657 through 659 Processing sheet with id=AD6, first strand: chain 'G' and resid 721 through 723 Processing sheet with id=AD7, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AD8, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AD9, first strand: chain 'H' and resid 865 through 866 removed outlier: 5.898A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR H 961 " --> pdb=" O SER H 958 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 875 through 876 Processing sheet with id=AE2, first strand: chain 'H' and resid 890 through 895 removed outlier: 7.177A pdb=" N ILE H 907 " --> pdb=" O LEU H 893 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN H 895 " --> pdb=" O PHE H 905 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE H 905 " --> pdb=" O GLN H 895 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 926 " --> pdb=" O LEU H 908 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS H 912 " --> pdb=" O LYS H 922 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS H 922 " --> pdb=" O LYS H 912 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 934 " --> pdb=" O ILE H 927 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU H 933 " --> pdb=" O LYS H 944 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 1144 through 1151 removed outlier: 5.111A pdb=" N TYR H1146 " --> pdb=" O HIS H1174 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N HIS H1174 " --> pdb=" O TYR H1146 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER H1148 " --> pdb=" O GLY H1172 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLY H1172 " --> pdb=" O SER H1148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 1182 through 1183 446 hydrogen bonds defined for protein. 1163 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.46 Time building geometry restraints manager: 8.02 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: 6156 1.34 - 1.47: 4334 1.47 - 1.59: 7841 1.59 - 1.71: 0 1.71 - 1.84: 320 Bond restraints: 18651 Sorted by residual: bond pdb=" N LYS G 157 " pdb=" CA LYS G 157 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 9.20e+00 bond pdb=" N CYS H 858 " pdb=" CA CYS H 858 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.17e-02 7.31e+03 7.88e+00 bond pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.21e-02 6.83e+03 7.81e+00 bond pdb=" N PHE E 155 " pdb=" CA PHE E 155 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.30e-02 5.92e+03 7.20e+00 bond pdb=" N ASN E 156 " pdb=" CA ASN E 156 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.05e+00 ... (remaining 18646 not shown) Histogram of bond angle deviations from ideal: 97.52 - 104.94: 384 104.94 - 112.37: 8454 112.37 - 119.79: 7411 119.79 - 127.21: 8775 127.21 - 134.64: 285 Bond angle restraints: 25309 Sorted by residual: angle pdb=" C THR E 175 " pdb=" N GLN E 176 " pdb=" CA GLN E 176 " ideal model delta sigma weight residual 120.60 132.28 -11.68 1.60e+00 3.91e-01 5.33e+01 angle pdb=" C ALA E 267 " pdb=" N LEU E 268 " pdb=" CA LEU E 268 " ideal model delta sigma weight residual 120.29 130.62 -10.33 1.42e+00 4.96e-01 5.29e+01 angle pdb=" C ALA G 267 " pdb=" N LEU G 268 " pdb=" CA LEU G 268 " ideal model delta sigma weight residual 120.29 130.62 -10.33 1.42e+00 4.96e-01 5.29e+01 angle pdb=" C THR G 175 " pdb=" N GLN G 176 " pdb=" CA GLN G 176 " ideal model delta sigma weight residual 120.60 132.22 -11.62 1.60e+00 3.91e-01 5.28e+01 angle pdb=" C LEU G 228 " pdb=" N LYS G 229 " pdb=" CA LYS G 229 " ideal model delta sigma weight residual 121.81 134.64 -12.83 1.83e+00 2.99e-01 4.91e+01 ... (remaining 25304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10938 17.94 - 35.88: 563 35.88 - 53.82: 127 53.82 - 71.75: 41 71.75 - 89.69: 16 Dihedral angle restraints: 11685 sinusoidal: 4861 harmonic: 6824 Sorted by residual: dihedral pdb=" CB CYS E 312 " pdb=" SG CYS E 312 " pdb=" SG CYS E 348 " pdb=" CB CYS E 348 " ideal model delta sinusoidal sigma weight residual 93.00 173.03 -80.03 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS G 312 " pdb=" SG CYS G 312 " pdb=" SG CYS G 348 " pdb=" CB CYS G 348 " ideal model delta sinusoidal sigma weight residual 93.00 172.99 -79.99 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS F 810 " pdb=" SG CYS F 810 " pdb=" SG CYS F 821 " pdb=" CB CYS F 821 " ideal model delta sinusoidal sigma weight residual 93.00 172.08 -79.08 1 1.00e+01 1.00e-02 7.78e+01 ... (remaining 11682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.304: 2711 0.304 - 0.608: 20 0.608 - 0.911: 27 0.911 - 1.215: 0 1.215 - 1.519: 9 Chirality restraints: 2767 Sorted by residual: chirality pdb=" CB THR G 181 " pdb=" CA THR G 181 " pdb=" OG1 THR G 181 " pdb=" CG2 THR G 181 " both_signs ideal model delta sigma weight residual False 2.55 1.03 1.52 2.00e-01 2.50e+01 5.77e+01 chirality pdb=" CB THR E 181 " pdb=" CA THR E 181 " pdb=" OG1 THR E 181 " pdb=" CG2 THR E 181 " both_signs ideal model delta sigma weight residual False 2.55 1.04 1.52 2.00e-01 2.50e+01 5.74e+01 chirality pdb=" CB THR E 175 " pdb=" CA THR E 175 " pdb=" OG1 THR E 175 " pdb=" CG2 THR E 175 " both_signs ideal model delta sigma weight residual False 2.55 1.07 1.49 2.00e-01 2.50e+01 5.52e+01 ... (remaining 2764 not shown) Planarity restraints: 3370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 804 " 0.333 2.00e-02 2.50e+03 2.88e-01 1.03e+03 pdb=" C7 NAG E 804 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG E 804 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG E 804 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG E 804 " 0.208 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H1303 " 0.323 2.00e-02 2.50e+03 2.77e-01 9.62e+02 pdb=" C7 NAG H1303 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG H1303 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG H1303 " -0.490 2.00e-02 2.50e+03 pdb=" O7 NAG H1303 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 803 " -0.301 2.00e-02 2.50e+03 2.52e-01 7.97e+02 pdb=" C7 NAG E 803 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG E 803 " -0.193 2.00e-02 2.50e+03 pdb=" N2 NAG E 803 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG E 803 " -0.017 2.00e-02 2.50e+03 ... (remaining 3367 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 221 2.61 - 3.18: 16044 3.18 - 3.76: 26595 3.76 - 4.33: 37449 4.33 - 4.90: 61322 Nonbonded interactions: 141631 Sorted by model distance: nonbonded pdb=" OG SER F1009 " pdb=" OD1 ASN F1011 " model vdw 2.041 2.440 nonbonded pdb=" OG SER H1009 " pdb=" OD1 ASN H1011 " model vdw 2.041 2.440 nonbonded pdb=" O GLU E 270 " pdb=" OG1 THR E 274 " model vdw 2.057 2.440 nonbonded pdb=" O GLU G 270 " pdb=" OG1 THR G 274 " model vdw 2.058 2.440 nonbonded pdb=" O SER F1093 " pdb=" OG SER H1093 " model vdw 2.068 2.440 ... (remaining 141626 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 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and (resid 767 through 1052 or resid 1054 through 1241 or resid 1301 \ through 1304)) selection = (chain 'H' and (resid 767 through 1052 or resid 1054 through 1241 or resid 1301 \ through 1304)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.230 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 52.950 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.009 0.073 18651 Z= 0.578 Angle : 1.171 13.739 25309 Z= 0.629 Chirality : 0.139 1.519 2767 Planarity : 0.012 0.288 3360 Dihedral : 10.808 89.693 6967 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.98 % Favored : 89.89 % Rotamer: Outliers : 0.74 % Allowed : 2.31 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.14), residues: 2365 helix: -3.60 (0.18), residues: 325 sheet: -2.90 (0.21), residues: 426 loop : -2.84 (0.13), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP H 974 HIS 0.010 0.002 HIS E 596 PHE 0.026 0.003 PHE G 535 TYR 0.038 0.003 TYR G 527 ARG 0.011 0.001 ARG H 960 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 589 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 TYR cc_start: 0.7943 (m-80) cc_final: 0.7401 (m-80) REVERT: E 217 MET cc_start: 0.2897 (mtp) cc_final: 0.1206 (ptt) REVERT: F 897 TYR cc_start: 0.7804 (m-10) cc_final: 0.7529 (m-80) REVERT: F 1028 SER cc_start: 0.8280 (p) cc_final: 0.7798 (t) REVERT: G 217 MET cc_start: 0.1917 (mtp) cc_final: 0.1432 (ptt) REVERT: G 233 VAL cc_start: 0.7387 (p) cc_final: 0.7053 (t) REVERT: G 343 VAL cc_start: 0.7235 (p) cc_final: 0.6498 (m) REVERT: H 793 GLN cc_start: 0.6705 (pp30) cc_final: 0.6504 (tm-30) REVERT: H 795 TYR cc_start: 0.7587 (t80) cc_final: 0.7264 (t80) REVERT: H 842 VAL cc_start: 0.8520 (m) cc_final: 0.8300 (p) outliers start: 14 outliers final: 1 residues processed: 593 average time/residue: 1.2422 time to fit residues: 826.5115 Evaluate side-chains 255 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 181 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 0.0980 chunk 184 optimal weight: 0.0040 chunk 71 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 303 GLN E 368 ASN E 374 ASN F 942 ASN F 952 HIS ** F1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1168 GLN F1221 HIS G 78 ASN G 277 GLN G 452 HIS G 460 HIS ** G 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1013 GLN H1069 GLN H1113 GLN H1221 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18651 Z= 0.189 Angle : 0.690 12.036 25309 Z= 0.348 Chirality : 0.050 0.739 2767 Planarity : 0.005 0.049 3360 Dihedral : 6.458 59.366 2773 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.09 % Favored : 93.82 % Rotamer: Outliers : 3.97 % Allowed : 14.08 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.15), residues: 2365 helix: -1.62 (0.25), residues: 329 sheet: -1.96 (0.23), residues: 430 loop : -2.19 (0.14), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 974 HIS 0.005 0.001 HIS G 95 PHE 0.018 0.002 PHE H 878 TYR 0.026 0.001 TYR G 711 ARG 0.007 0.001 ARG G 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 277 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 649 GLU cc_start: 0.5688 (pt0) cc_final: 0.5186 (mm-30) REVERT: F 1161 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6387 (pm20) REVERT: G 695 MET cc_start: 0.6444 (mmp) cc_final: 0.6020 (mmp) REVERT: G 728 MET cc_start: 0.6906 (tmm) cc_final: 0.6600 (tmm) REVERT: H 795 TYR cc_start: 0.7582 (t80) cc_final: 0.7315 (t80) REVERT: H 842 VAL cc_start: 0.8516 (m) cc_final: 0.8266 (p) REVERT: H 862 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7839 (t) REVERT: H 947 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6718 (ptm) REVERT: H 1035 ARG cc_start: 0.7201 (mmt180) cc_final: 0.6875 (mmt180) REVERT: H 1061 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7611 (mpt90) outliers start: 80 outliers final: 26 residues processed: 327 average time/residue: 1.1079 time to fit residues: 414.0799 Evaluate side-chains 221 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 712 ASP Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 1088 THR Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 75 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 497 ASP Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1061 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 214 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 chunk 191 optimal weight: 0.0170 chunk 212 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 172 optimal weight: 8.9990 overall best weight: 4.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 HIS E 189 ASN E 322 GLN E 393 GLN E 419 GLN F 817 HIS F1013 GLN F1113 GLN F1174 HIS F1226 HIS G 95 HIS G 189 ASN G 303 GLN G 596 HIS ** H1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1113 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 18651 Z= 0.412 Angle : 0.806 12.222 25309 Z= 0.407 Chirality : 0.056 0.701 2767 Planarity : 0.006 0.052 3360 Dihedral : 6.614 58.135 2773 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.78 % Favored : 92.17 % Rotamer: Outliers : 5.54 % Allowed : 15.45 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.16), residues: 2365 helix: -0.48 (0.27), residues: 307 sheet: -1.41 (0.24), residues: 434 loop : -1.90 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 199 HIS 0.006 0.002 HIS E 484 PHE 0.038 0.003 PHE H 999 TYR 0.033 0.003 TYR H 897 ARG 0.006 0.001 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 220 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6537 (pm20) REVERT: E 217 MET cc_start: 0.2963 (OUTLIER) cc_final: 0.1214 (ppp) REVERT: E 294 VAL cc_start: 0.7676 (OUTLIER) cc_final: 0.7409 (m) REVERT: E 302 ARG cc_start: 0.7443 (ttm170) cc_final: 0.7210 (ttp-170) REVERT: E 313 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: E 347 GLU cc_start: 0.7278 (tp30) cc_final: 0.7005 (tp30) REVERT: E 649 GLU cc_start: 0.6227 (pt0) cc_final: 0.5390 (mm-30) REVERT: E 712 ASP cc_start: 0.6590 (t0) cc_final: 0.6080 (t0) REVERT: E 728 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6812 (tpp) REVERT: F 793 GLN cc_start: 0.6931 (pp30) cc_final: 0.6650 (tm-30) REVERT: F 912 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8006 (mptt) REVERT: F 920 LYS cc_start: 0.5921 (OUTLIER) cc_final: 0.5435 (mtmt) REVERT: G 313 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6648 (mp10) REVERT: G 416 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7938 (ttm170) REVERT: G 496 GLU cc_start: 0.6948 (pm20) cc_final: 0.6713 (pm20) REVERT: G 564 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8460 (tptp) REVERT: H 795 TYR cc_start: 0.7670 (t80) cc_final: 0.7287 (t80) REVERT: H 802 MET cc_start: 0.5508 (OUTLIER) cc_final: 0.5180 (mpt) REVERT: H 842 VAL cc_start: 0.8706 (m) cc_final: 0.8403 (p) REVERT: H 947 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6862 (ptm) REVERT: H 1061 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7564 (mpt90) REVERT: H 1092 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6125 (mp0) outliers start: 112 outliers final: 42 residues processed: 302 average time/residue: 1.2231 time to fit residues: 417.1701 Evaluate side-chains 232 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 728 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 821 CYS Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1087 ASP Chi-restraints excluded: chain F residue 1088 THR Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain G residue 78 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 416 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 802 MET Chi-restraints excluded: chain H residue 848 THR Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 927 ILE Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 0.0970 chunk 215 optimal weight: 0.6980 chunk 228 optimal weight: 5.9990 chunk 112 optimal weight: 0.0770 chunk 204 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.3740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN F 952 HIS F1188 GLN G 78 ASN G 453 ASN ** H1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18651 Z= 0.194 Angle : 0.633 8.582 25309 Z= 0.319 Chirality : 0.048 0.546 2767 Planarity : 0.004 0.046 3360 Dihedral : 6.031 57.532 2773 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.01 % Favored : 93.91 % Rotamer: Outliers : 4.22 % Allowed : 17.36 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.16), residues: 2365 helix: -0.09 (0.28), residues: 333 sheet: -1.13 (0.24), residues: 436 loop : -1.72 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 974 HIS 0.003 0.001 HIS E 596 PHE 0.019 0.002 PHE H 999 TYR 0.016 0.001 TYR H 897 ARG 0.009 0.000 ARG G 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 199 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 649 GLU cc_start: 0.6266 (pt0) cc_final: 0.5399 (mm-30) REVERT: F 793 GLN cc_start: 0.6884 (pp30) cc_final: 0.6608 (tm-30) REVERT: F 912 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7946 (mptt) REVERT: G 107 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7092 (pp30) REVERT: G 280 MET cc_start: 0.7627 (ttm) cc_final: 0.7321 (ttm) REVERT: G 313 GLN cc_start: 0.6783 (mp10) cc_final: 0.6201 (mp-120) REVERT: G 344 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: G 373 ARG cc_start: 0.7349 (ttm110) cc_final: 0.7132 (ttm110) REVERT: G 387 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7210 (mt-10) REVERT: G 564 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8504 (tptp) REVERT: G 609 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7615 (mtt-85) REVERT: H 795 TYR cc_start: 0.7598 (t80) cc_final: 0.7391 (t80) REVERT: H 802 MET cc_start: 0.5380 (OUTLIER) cc_final: 0.5024 (mpt) REVERT: H 842 VAL cc_start: 0.8562 (m) cc_final: 0.8346 (p) REVERT: H 862 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8276 (t) REVERT: H 947 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6815 (ptm) REVERT: H 1061 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7683 (mpt90) outliers start: 85 outliers final: 42 residues processed: 259 average time/residue: 1.1758 time to fit residues: 345.7296 Evaluate side-chains 228 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 179 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 ASN Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 804 CYS Chi-restraints excluded: chain F residue 821 CYS Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 1135 LEU Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 344 GLU Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 802 MET Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 978 LEU Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1124 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.0870 chunk 129 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 157 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 3.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN F1188 GLN G 313 GLN G 368 ASN ** H1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18651 Z= 0.306 Angle : 0.703 10.458 25309 Z= 0.354 Chirality : 0.051 0.591 2767 Planarity : 0.005 0.047 3360 Dihedral : 6.234 57.829 2773 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.57 % Favored : 92.39 % Rotamer: Outliers : 5.05 % Allowed : 17.36 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.16), residues: 2365 helix: 0.33 (0.29), residues: 305 sheet: -0.79 (0.25), residues: 430 loop : -1.63 (0.14), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 553 HIS 0.004 0.001 HIS E 421 PHE 0.024 0.002 PHE H 999 TYR 0.024 0.002 TYR H 897 ARG 0.006 0.001 ARG G 643 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 193 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 217 MET cc_start: 0.2994 (OUTLIER) cc_final: 0.1433 (ppp) REVERT: E 313 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: E 346 THR cc_start: 0.7535 (m) cc_final: 0.7319 (p) REVERT: E 543 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: E 712 ASP cc_start: 0.6909 (t0) cc_final: 0.6623 (t0) REVERT: F 793 GLN cc_start: 0.7206 (pp30) cc_final: 0.6925 (tm-30) REVERT: F 912 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7965 (mptt) REVERT: F 937 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.6944 (p90) REVERT: F 1051 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7251 (tmm) REVERT: G 107 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.6916 (pp30) REVERT: G 313 GLN cc_start: 0.6558 (OUTLIER) cc_final: 0.6162 (mp-120) REVERT: G 496 GLU cc_start: 0.6967 (pm20) cc_final: 0.6732 (pm20) REVERT: G 564 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8451 (tptp) REVERT: H 795 TYR cc_start: 0.7628 (t80) cc_final: 0.7335 (t80) REVERT: H 862 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8277 (t) REVERT: H 947 MET cc_start: 0.7316 (OUTLIER) cc_final: 0.6801 (ptm) REVERT: H 1061 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7557 (mpt90) REVERT: H 1092 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6019 (mp0) outliers start: 102 outliers final: 49 residues processed: 262 average time/residue: 1.1607 time to fit residues: 345.8235 Evaluate side-chains 241 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 180 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 804 CYS Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 912 LYS Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1051 MET Chi-restraints excluded: chain F residue 1148 SER Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 479 ASP Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1124 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 75 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN G 78 ASN G 452 HIS ** H1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 18651 Z= 0.442 Angle : 0.810 9.847 25309 Z= 0.409 Chirality : 0.056 0.687 2767 Planarity : 0.006 0.052 3360 Dihedral : 6.713 59.448 2773 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.99 % Favored : 91.96 % Rotamer: Outliers : 5.25 % Allowed : 17.80 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.16), residues: 2365 helix: -0.11 (0.28), residues: 323 sheet: -0.76 (0.26), residues: 410 loop : -1.72 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 553 HIS 0.006 0.001 HIS G 556 PHE 0.030 0.003 PHE H 999 TYR 0.029 0.002 TYR E 710 ARG 0.010 0.001 ARG G 643 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 182 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6591 (mt0) REVERT: E 217 MET cc_start: 0.2696 (OUTLIER) cc_final: 0.1208 (ppp) REVERT: E 313 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7325 (mp10) REVERT: E 483 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: E 543 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6751 (mt-10) REVERT: F 816 ARG cc_start: 0.7421 (mtp85) cc_final: 0.7188 (ttp80) REVERT: F 920 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5632 (mtmt) REVERT: F 1030 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6764 (pm20) REVERT: F 1051 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7210 (tmm) REVERT: G 107 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.6934 (pp30) REVERT: G 416 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7983 (ttm170) REVERT: G 564 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8444 (tptp) REVERT: G 660 GLN cc_start: 0.6933 (tp40) cc_final: 0.6145 (mm110) REVERT: H 771 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.4061 (mtm) REVERT: H 795 TYR cc_start: 0.7742 (t80) cc_final: 0.7503 (t80) REVERT: H 947 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6902 (ptm) REVERT: H 1061 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7578 (mpt90) REVERT: H 1092 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6090 (mp0) REVERT: H 1154 GLN cc_start: 0.5788 (OUTLIER) cc_final: 0.5494 (tp-100) outliers start: 106 outliers final: 65 residues processed: 262 average time/residue: 1.2099 time to fit residues: 359.9334 Evaluate side-chains 243 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 162 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 483 GLN Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 786 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 804 CYS Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1030 GLN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1051 MET Chi-restraints excluded: chain F residue 1148 SER Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 416 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 564 LYS Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain H residue 771 MET Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 927 ILE Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1124 THR Chi-restraints excluded: chain H residue 1154 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 192 optimal weight: 0.2980 chunk 127 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN E 660 GLN G 78 ASN ** H1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18651 Z= 0.290 Angle : 0.706 9.354 25309 Z= 0.356 Chirality : 0.051 0.615 2767 Planarity : 0.005 0.052 3360 Dihedral : 6.390 58.139 2773 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.19 % Favored : 92.77 % Rotamer: Outliers : 5.15 % Allowed : 18.49 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.16), residues: 2365 helix: 0.01 (0.28), residues: 325 sheet: -0.71 (0.26), residues: 418 loop : -1.64 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 222 HIS 0.004 0.001 HIS E 596 PHE 0.021 0.002 PHE H 999 TYR 0.020 0.002 TYR H 897 ARG 0.007 0.001 ARG G 643 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 174 time to evaluate : 2.138 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: E 217 MET cc_start: 0.2720 (OUTLIER) cc_final: 0.2482 (pmt) REVERT: E 302 ARG cc_start: 0.7686 (ttp-170) cc_final: 0.7014 (ttt-90) REVERT: E 313 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: E 356 ARG cc_start: 0.7525 (tpt170) cc_final: 0.7185 (mmt-90) REVERT: E 483 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: E 543 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6737 (mt-10) REVERT: F 1030 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6909 (pm20) REVERT: F 1229 VAL cc_start: 0.4023 (OUTLIER) cc_final: 0.3673 (t) REVERT: G 107 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6889 (pp30) REVERT: G 660 GLN cc_start: 0.7038 (tp40) cc_final: 0.6192 (mm110) REVERT: H 771 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.4084 (mtm) REVERT: H 795 TYR cc_start: 0.7707 (t80) cc_final: 0.7480 (t80) REVERT: H 842 VAL cc_start: 0.8597 (m) cc_final: 0.8354 (p) REVERT: H 862 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8332 (t) REVERT: H 947 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6828 (ptm) REVERT: H 1061 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7630 (mpt90) REVERT: H 1092 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.5968 (mp0) outliers start: 104 outliers final: 64 residues processed: 251 average time/residue: 1.1085 time to fit residues: 317.7215 Evaluate side-chains 236 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 160 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 466 MET Chi-restraints excluded: chain E residue 483 GLN Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 804 CYS Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 854 ARG Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1030 GLN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1148 SER Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 613 CYS Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain H residue 771 MET Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1124 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN F1215 ASN G 78 ASN G 452 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 18651 Z= 0.404 Angle : 0.787 10.974 25309 Z= 0.397 Chirality : 0.054 0.644 2767 Planarity : 0.006 0.054 3360 Dihedral : 6.695 59.015 2773 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.16 % Favored : 91.79 % Rotamer: Outliers : 5.49 % Allowed : 18.49 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2365 helix: -0.12 (0.28), residues: 325 sheet: -0.66 (0.26), residues: 398 loop : -1.66 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 222 HIS 0.005 0.001 HIS E 452 PHE 0.026 0.003 PHE H 999 TYR 0.024 0.002 TYR E 710 ARG 0.006 0.001 ARG G 643 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 173 time to evaluate : 2.112 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: E 107 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6570 (mt0) REVERT: E 161 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8567 (mp) REVERT: E 217 MET cc_start: 0.2530 (OUTLIER) cc_final: 0.2223 (pmt) REVERT: E 302 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.7121 (ttt-90) REVERT: E 313 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: E 543 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6827 (mt-10) REVERT: F 816 ARG cc_start: 0.7423 (mtp85) cc_final: 0.7198 (ttp80) REVERT: F 920 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5760 (mtpt) REVERT: F 1030 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7014 (pm20) REVERT: F 1051 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7140 (tmm) REVERT: F 1078 GLU cc_start: 0.7655 (tp30) cc_final: 0.7445 (tp30) REVERT: F 1229 VAL cc_start: 0.4433 (OUTLIER) cc_final: 0.4108 (t) REVERT: G 107 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6804 (pp30) REVERT: G 313 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5849 (mp-120) REVERT: G 564 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8436 (tptp) REVERT: G 605 LEU cc_start: 0.8734 (tp) cc_final: 0.8520 (tp) REVERT: G 660 GLN cc_start: 0.6972 (tp40) cc_final: 0.6132 (mm110) REVERT: H 771 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.4029 (ttm) REVERT: H 795 TYR cc_start: 0.7725 (t80) cc_final: 0.7514 (t80) REVERT: H 947 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6974 (ptm) REVERT: H 1061 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7572 (mpt90) REVERT: H 1092 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6027 (mp0) REVERT: H 1154 GLN cc_start: 0.5962 (OUTLIER) cc_final: 0.5697 (tp-100) outliers start: 111 outliers final: 71 residues processed: 256 average time/residue: 1.2163 time to fit residues: 352.2985 Evaluate side-chains 255 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 167 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 107 GLN Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 854 ARG Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain F residue 947 MET Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1030 GLN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1051 MET Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1148 SER Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 444 VAL Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 564 LYS Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 613 CYS Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain H residue 771 MET Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 898 CYS Chi-restraints excluded: chain H residue 911 ASN Chi-restraints excluded: chain H residue 927 ILE Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1124 THR Chi-restraints excluded: chain H residue 1154 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 200 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN G 78 ASN G 288 HIS H 793 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18651 Z= 0.295 Angle : 0.714 10.220 25309 Z= 0.359 Chirality : 0.051 0.593 2767 Planarity : 0.005 0.053 3360 Dihedral : 6.393 58.463 2773 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.81 % Favored : 93.15 % Rotamer: Outliers : 4.90 % Allowed : 19.13 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.16), residues: 2365 helix: 0.03 (0.28), residues: 325 sheet: -0.43 (0.28), residues: 352 loop : -1.60 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 222 HIS 0.004 0.001 HIS E 596 PHE 0.020 0.002 PHE H 999 TYR 0.019 0.002 TYR H 897 ARG 0.006 0.001 ARG G 643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 174 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 217 MET cc_start: 0.2712 (OUTLIER) cc_final: 0.2501 (pmt) REVERT: E 280 MET cc_start: 0.7588 (ttm) cc_final: 0.7300 (tmm) REVERT: E 302 ARG cc_start: 0.7634 (ttp-170) cc_final: 0.7081 (ttt-90) REVERT: E 313 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: E 483 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8197 (pt0) REVERT: E 543 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6777 (mt-10) REVERT: F 920 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5632 (mtmt) REVERT: F 1030 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: F 1051 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7143 (tmm) REVERT: F 1229 VAL cc_start: 0.4245 (OUTLIER) cc_final: 0.3951 (t) REVERT: G 107 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.6885 (pp30) REVERT: G 364 SER cc_start: 0.8546 (p) cc_final: 0.8261 (t) REVERT: G 605 LEU cc_start: 0.8706 (tp) cc_final: 0.8479 (tp) REVERT: G 609 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7656 (mtt-85) REVERT: G 660 GLN cc_start: 0.6967 (tp40) cc_final: 0.6036 (mm110) REVERT: H 771 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.4167 (mtm) REVERT: H 795 TYR cc_start: 0.7761 (t80) cc_final: 0.7547 (t80) REVERT: H 862 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8347 (t) REVERT: H 947 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6897 (ptm) REVERT: H 1061 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7642 (mpt90) REVERT: H 1092 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5999 (mp0) REVERT: H 1154 GLN cc_start: 0.5896 (OUTLIER) cc_final: 0.5627 (tp-100) outliers start: 99 outliers final: 65 residues processed: 242 average time/residue: 1.1626 time to fit residues: 321.8542 Evaluate side-chains 248 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 167 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 483 GLN Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 771 MET Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 870 ILE Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 920 LYS Chi-restraints excluded: chain F residue 937 PHE Chi-restraints excluded: chain F residue 947 MET Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1030 GLN Chi-restraints excluded: chain F residue 1050 ILE Chi-restraints excluded: chain F residue 1051 MET Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1148 SER Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1161 GLU Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 394 SER Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 501 ASP Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 613 CYS Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain G residue 739 THR Chi-restraints excluded: chain H residue 771 MET Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 898 CYS Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 982 VAL Chi-restraints excluded: chain H residue 1034 THR Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1092 GLU Chi-restraints excluded: chain H residue 1124 THR Chi-restraints excluded: chain H residue 1154 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 40.0000 chunk 106 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 235 optimal weight: 0.0470 chunk 216 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN F1072 ASN G 78 ASN G 313 GLN H 793 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18651 Z= 0.172 Angle : 0.628 9.507 25309 Z= 0.314 Chirality : 0.047 0.521 2767 Planarity : 0.005 0.050 3360 Dihedral : 5.891 59.947 2773 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.68 % Allowed : 20.55 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.16), residues: 2365 helix: 0.30 (0.29), residues: 327 sheet: -0.08 (0.28), residues: 364 loop : -1.52 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 222 HIS 0.003 0.001 HIS F 817 PHE 0.012 0.001 PHE E 76 TYR 0.013 0.001 TYR H 988 ARG 0.006 0.000 ARG G 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4730 Ramachandran restraints generated. 2365 Oldfield, 0 Emsley, 2365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 184 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 302 ARG cc_start: 0.7409 (ttp-170) cc_final: 0.6843 (ttt-90) REVERT: E 313 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7319 (mp10) REVERT: E 341 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7437 (pp) REVERT: E 543 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: F 1051 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.6848 (tmm) REVERT: F 1187 LEU cc_start: 0.5627 (mt) cc_final: 0.5371 (mp) REVERT: F 1229 VAL cc_start: 0.4162 (OUTLIER) cc_final: 0.3880 (t) REVERT: G 116 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8502 (mmtm) REVERT: G 197 GLU cc_start: 0.7328 (mp0) cc_final: 0.7063 (mp0) REVERT: G 280 MET cc_start: 0.7621 (ttm) cc_final: 0.7360 (ttm) REVERT: G 416 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7886 (ttm170) REVERT: G 609 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7659 (mtt-85) REVERT: H 795 TYR cc_start: 0.7675 (t80) cc_final: 0.7431 (t80) REVERT: H 862 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8337 (t) REVERT: H 947 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6722 (ptm) REVERT: H 1061 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7751 (mpt90) REVERT: H 1154 GLN cc_start: 0.5696 (OUTLIER) cc_final: 0.5402 (tp-100) outliers start: 74 outliers final: 44 residues processed: 234 average time/residue: 1.2018 time to fit residues: 318.6372 Evaluate side-chains 225 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 169 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 329 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 420 ASP Chi-restraints excluded: chain E residue 422 SER Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 543 GLU Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 685 GLU Chi-restraints excluded: chain F residue 822 VAL Chi-restraints excluded: chain F residue 829 CYS Chi-restraints excluded: chain F residue 862 VAL Chi-restraints excluded: chain F residue 982 VAL Chi-restraints excluded: chain F residue 1051 MET Chi-restraints excluded: chain F residue 1143 GLU Chi-restraints excluded: chain F residue 1148 SER Chi-restraints excluded: chain F residue 1156 THR Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 130 SER Chi-restraints excluded: chain G residue 161 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 416 ARG Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 476 LEU Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 515 VAL Chi-restraints excluded: chain G residue 567 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 584 CYS Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 609 ARG Chi-restraints excluded: chain G residue 613 CYS Chi-restraints excluded: chain G residue 616 SER Chi-restraints excluded: chain G residue 622 LEU Chi-restraints excluded: chain G residue 683 CYS Chi-restraints excluded: chain G residue 707 CYS Chi-restraints excluded: chain H residue 776 CYS Chi-restraints excluded: chain H residue 862 VAL Chi-restraints excluded: chain H residue 928 LEU Chi-restraints excluded: chain H residue 947 MET Chi-restraints excluded: chain H residue 982 VAL Chi-restraints excluded: chain H residue 1061 ARG Chi-restraints excluded: chain H residue 1081 LEU Chi-restraints excluded: chain H residue 1124 THR Chi-restraints excluded: chain H residue 1154 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 187 optimal weight: 0.1980 chunk 78 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 164 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1013 GLN G 78 ASN G 313 GLN H 793 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.169556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.124006 restraints weight = 23546.794| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.12 r_work: 0.3225 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18651 Z= 0.209 Angle : 0.646 9.603 25309 Z= 0.323 Chirality : 0.048 0.527 2767 Planarity : 0.005 0.052 3360 Dihedral : 5.939 59.526 2773 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.63 % Allowed : 20.84 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.16), residues: 2365 helix: 0.34 (0.29), residues: 327 sheet: -0.21 (0.28), residues: 352 loop : -1.44 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 222 HIS 0.003 0.001 HIS H 874 PHE 0.017 0.002 PHE H 999 TYR 0.016 0.001 TYR H 897 ARG 0.006 0.000 ARG G 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7088.08 seconds wall clock time: 127 minutes 25.50 seconds (7645.50 seconds total)