Starting phenix.real_space_refine on Sat Feb 17 09:23:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn4_32621/02_2024/7wn4_32621.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn4_32621/02_2024/7wn4_32621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn4_32621/02_2024/7wn4_32621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn4_32621/02_2024/7wn4_32621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn4_32621/02_2024/7wn4_32621.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn4_32621/02_2024/7wn4_32621.pdb" } resolution = 3.4 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= 0.004 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 11242 2.51 5 N 3127 2.21 5 O 3573 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 GLU 90": "OE1" <-> "OE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 278": "OE1" <-> "OE2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E GLU 344": "OE1" <-> "OE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "E GLU 620": "OE1" <-> "OE2" Residue "E GLU 644": "OE1" <-> "OE2" Residue "E GLU 677": "OE1" <-> "OE2" Residue "E GLU 681": "OE1" <-> "OE2" Residue "E GLU 697": "OE1" <-> "OE2" Residue "F ARG 924": "NH1" <-> "NH2" Residue "F GLU 930": "OE1" <-> "OE2" Residue "F GLU 933": "OE1" <-> "OE2" Residue "F ARG 1035": "NH1" <-> "NH2" Residue "F ARG 1061": "NH1" <-> "NH2" Residue "F GLU 1078": "OE1" <-> "OE2" Residue "F GLU 1092": "OE1" <-> "OE2" Residue "F ARG 1121": "NH1" <-> "NH2" Residue "F GLU 1200": "OE1" <-> "OE2" Residue "G ARG 34": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G ARG 202": "NH1" <-> "NH2" Residue "G GLU 223": "OE1" <-> "OE2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G GLU 339": "OE1" <-> "OE2" Residue "G GLU 383": "OE1" <-> "OE2" Residue "G GLU 428": "OE1" <-> "OE2" Residue "G GLU 593": "OE1" <-> "OE2" Residue "G ARG 597": "NH1" <-> "NH2" Residue "G GLU 620": "OE1" <-> "OE2" Residue "G GLU 644": "OE1" <-> "OE2" Residue "G GLU 732": "OE1" <-> "OE2" Residue "H TYR 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 924": "NH1" <-> "NH2" Residue "H GLU 933": "OE1" <-> "OE2" Residue "H GLU 957": "OE1" <-> "OE2" Residue "H GLU 1015": "OE1" <-> "OE2" Residue "H ARG 1035": "NH1" <-> "NH2" Residue "H ARG 1061": "NH1" <-> "NH2" Residue "H GLU 1078": "OE1" <-> "OE2" Residue "H GLU 1092": "OE1" <-> "OE2" Residue "H ARG 1121": "NH1" <-> "NH2" Residue "H TYR 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 18224 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': 1, 'PTRANS': 34, '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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.16, per 1000 atoms: 0.67 Number of scatterers: 18224 At special positions: 0 Unit cell: (159.08, 161.02, 146.47, 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 3573 8.00 N 3127 7.00 C 11242 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=2.02 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 159 " distance=2.04 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=2.02 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=2.02 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 570 " - pdb=" SG CYS E 613 " distance=2.02 Simple disulfide: pdb=" SG CYS E 584 " - pdb=" SG CYS E 608 " distance=2.03 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=2.02 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS F 767 " - pdb=" SG CYS F 808 " distance=2.04 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS F 889 " - pdb=" SG CYS F1031 " distance=2.02 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS F1149 " - pdb=" SG CYS F1169 " distance=2.03 Simple disulfide: pdb=" SG CYS F1153 " - pdb=" SG CYS F1165 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 210 " - pdb=" SG CYS G 255 " distance=2.03 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS G 432 " - pdb=" SG CYS G 440 " distance=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS G 623 " - pdb=" SG CYS G 648 " distance=2.03 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=2.04 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=2.04 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=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS H 889 " - pdb=" SG CYS H1031 " distance=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS H1177 " - pdb=" SG CYS H1190 " distance=2.03 Simple disulfide: pdb=" SG CYS H1199 " - pdb=" SG CYS H1227 " distance=2.02 Simple disulfide: pdb=" SG CYS H1222 " - pdb=" SG CYS H1237 " distance=2.03 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 99 " " NAG E 804 " - " ASN E 156 " " NAG F1302 " - " ASN F 857 " " NAG F1303 " - " ASN F1147 " " NAG G 803 " - " ASN G 99 " " NAG G 804 " - " ASN G 156 " " NAG H1302 " - " ASN H 857 " " NAG H1303 " - " ASN H1147 " Time building additional restraints: 7.03 Conformation dependent library (CDL) restraints added in 4.2 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: 58 helices and 40 sheets defined 21.1% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.657A pdb=" N GLY E 117 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.584A pdb=" N ARG E 236 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 252 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 284 through 290 removed outlier: 4.414A pdb=" N HIS E 288 " --> pdb=" O GLY E 284 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 289 " --> pdb=" O TRP E 285 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 284 through 290' Processing helix chain 'E' and resid 513 through 517 Processing helix chain 'E' and resid 531 through 535 removed outlier: 3.596A pdb=" N ASP E 534 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE E 535 " --> pdb=" O GLY E 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 531 through 535' Processing helix chain 'E' and resid 545 through 552 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 586 removed outlier: 4.079A pdb=" N VAL E 586 " --> pdb=" O GLU E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 598 Proline residue: E 590 - end of helix removed outlier: 4.875A pdb=" N ALA E 594 " --> pdb=" O THR E 591 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS E 596 " --> pdb=" O GLU E 593 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG E 597 " --> pdb=" O ALA E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 615 Processing helix chain 'E' and resid 617 through 637 removed outlier: 3.599A pdb=" N CYS E 623 " --> pdb=" O ARG E 619 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 628 " --> pdb=" O GLY E 624 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG E 636 " --> pdb=" O ALA E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 668 through 674 removed outlier: 4.137A pdb=" N LEU E 672 " --> pdb=" O THR E 668 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 673 " --> pdb=" O CYS E 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 785 through 789 removed outlier: 3.603A pdb=" N THR F 789 " --> pdb=" O LEU F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 791 through 797 removed outlier: 4.323A pdb=" N ASP F 796 " --> pdb=" O CYS F 792 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LEU F 797 " --> pdb=" O GLN F 793 " (cutoff:3.500A) Processing helix chain 'F' and resid 1003 through 1008 removed outlier: 3.604A pdb=" N ASP F1006 " --> pdb=" O GLN F1003 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU F1007 " --> pdb=" O ASN F1004 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR F1008 " --> pdb=" O ASN F1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1003 through 1008' Processing helix chain 'F' and resid 1017 through 1025 Processing helix chain 'F' and resid 1049 through 1061 Processing helix chain 'F' and resid 1062 through 1065 Processing helix chain 'F' and resid 1068 through 1075 removed outlier: 3.606A pdb=" N LYS F1073 " --> pdb=" O GLN F1069 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU F1074 " --> pdb=" O ASP F1070 " (cutoff:3.500A) Processing helix chain 'F' and resid 1077 through 1091 Processing helix chain 'F' and resid 1097 through 1114 removed outlier: 4.382A pdb=" N THR F1103 " --> pdb=" O CYS F1099 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F1104 " --> pdb=" O PHE F1100 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR F1107 " --> pdb=" O THR F1103 " (cutoff:3.500A) Processing helix chain 'F' and resid 1131 through 1136 removed outlier: 3.841A pdb=" N ARG F1136 " --> pdb=" O GLU F1132 " (cutoff:3.500A) Processing helix chain 'F' and resid 1218 through 1222 Processing helix chain 'G' and resid 114 through 118 removed outlier: 4.327A pdb=" N GLY G 117 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 209 through 213 removed outlier: 3.791A pdb=" N ILE G 212 " --> pdb=" O SER G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 231 removed outlier: 4.168A pdb=" N GLY G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS G 225 " --> pdb=" O LEU G 221 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU G 228 " --> pdb=" O GLN G 224 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS G 229 " --> pdb=" O CYS G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 removed outlier: 4.348A pdb=" N ARG G 236 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS G 237 " --> pdb=" O PHE G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 255 removed outlier: 3.996A pdb=" N CYS G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 263 removed outlier: 3.665A pdb=" N CYS G 263 " --> pdb=" O GLY G 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 260 through 263' Processing helix chain 'G' and resid 264 through 278 removed outlier: 3.639A pdb=" N LEU G 268 " --> pdb=" O ALA G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.863A pdb=" N CYS G 348 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 465 through 469 removed outlier: 3.559A pdb=" N GLN G 469 " --> pdb=" O MET G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 514 through 517 Processing helix chain 'G' and resid 545 through 552 Processing helix chain 'G' and resid 568 through 572 removed outlier: 3.720A pdb=" N ALA G 571 " --> pdb=" O ASP G 568 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU G 572 " --> pdb=" O PRO G 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 568 through 572' Processing helix chain 'G' and resid 576 through 584 removed outlier: 3.877A pdb=" N CYS G 584 " --> pdb=" O SER G 580 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 596 Proline residue: G 590 - end of helix removed outlier: 4.911A pdb=" N ALA G 594 " --> pdb=" O THR G 591 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS G 596 " --> pdb=" O GLU G 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 615 Processing helix chain 'G' and resid 617 through 635 removed outlier: 3.825A pdb=" N ALA G 627 " --> pdb=" O CYS G 623 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 707 No H-bonds generated for 'chain 'G' and resid 705 through 707' Processing helix chain 'H' and resid 785 through 789 Processing helix chain 'H' and resid 1003 through 1008 removed outlier: 3.795A pdb=" N ASP H1006 " --> pdb=" O GLN H1003 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU H1007 " --> pdb=" O ASN H1004 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR H1008 " --> pdb=" O ASN H1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1003 through 1008' Processing helix chain 'H' and resid 1017 through 1024 Processing helix chain 'H' and resid 1049 through 1061 Processing helix chain 'H' and resid 1062 through 1065 Processing helix chain 'H' and resid 1068 through 1073 removed outlier: 3.776A pdb=" N LYS H1073 " --> pdb=" O GLN H1069 " (cutoff:3.500A) Processing helix chain 'H' and resid 1077 through 1091 Processing helix chain 'H' and resid 1097 through 1114 removed outlier: 4.771A pdb=" N THR H1103 " --> pdb=" O CYS H1099 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR H1107 " --> pdb=" O THR H1103 " (cutoff:3.500A) Processing helix chain 'H' and resid 1130 through 1134 removed outlier: 3.990A pdb=" N ARG H1133 " --> pdb=" O CYS H1130 " (cutoff:3.500A) Processing helix chain 'H' and resid 1192 through 1196 Processing helix chain 'H' and resid 1218 through 1222 Processing sheet with id=AA1, first strand: chain 'E' and resid 35 through 37 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 60 through 62 removed outlier: 6.782A pdb=" N ILE E 72 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE E 94 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 300 through 305 removed outlier: 4.173A pdb=" N CYS E 304 " --> pdb=" O VAL E 326 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL E 326 " --> pdb=" O CYS E 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 337 through 338 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 455 through 458 removed outlier: 5.084A pdb=" N THR E 441 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL E 430 " --> pdb=" O THR E 441 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER E 443 " --> pdb=" O GLU E 428 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE E 425 " --> pdb=" O LEU E 414 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 465 through 466 removed outlier: 3.515A pdb=" N GLN E 469 " --> pdb=" O MET E 466 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 475 through 476 removed outlier: 3.514A pdb=" N GLN E 483 " --> pdb=" O ARG E 491 " (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 841 through 844 Processing sheet with id=AB6, first strand: chain 'F' and resid 865 through 866 removed outlier: 4.727A pdb=" N TRP F 974 " --> pdb=" O ILE F 962 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 874 through 876 Processing sheet with id=AB8, first strand: chain 'F' and resid 890 through 891 Processing sheet with id=AB9, first strand: chain 'F' and resid 928 through 929 removed outlier: 3.612A pdb=" N VAL F 929 " --> pdb=" O GLY F 932 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 936 through 937 Processing sheet with id=AC2, first strand: chain 'F' and resid 1144 through 1146 removed outlier: 3.663A pdb=" N ARG F1145 " --> pdb=" O HIS F1174 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 1150 through 1151 Processing sheet with id=AC4, first strand: chain 'G' and resid 33 through 35 Processing sheet with id=AC5, first strand: chain 'G' and resid 42 through 44 Processing sheet with id=AC6, first strand: chain 'G' and resid 59 through 62 removed outlier: 5.651A pdb=" N LEU G 60 " --> pdb=" O GLY G 74 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY G 74 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 62 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER G 83 " --> pdb=" O ASP G 75 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 300 through 305 removed outlier: 4.438A pdb=" N CYS G 304 " --> pdb=" O VAL G 326 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL G 326 " --> pdb=" O CYS G 304 " (cutoff:3.500A) 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 386 through 389 Processing sheet with id=AD2, first strand: chain 'G' and resid 395 through 398 Processing sheet with id=AD3, first strand: chain 'G' and resid 454 through 458 removed outlier: 6.881A pdb=" N GLU G 428 " --> pdb=" O ARG G 442 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL G 444 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL G 426 " --> pdb=" O VAL G 444 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL G 446 " --> pdb=" O SER G 424 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER G 424 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA G 415 " --> pdb=" O ILE G 425 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE G 427 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU G 413 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 7.351A 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=AD4, first strand: chain 'G' and resid 657 through 658 Processing sheet with id=AD5, first strand: chain 'G' and resid 693 through 695 Processing sheet with id=AD6, first strand: chain 'H' and resid 772 through 773 Processing sheet with id=AD7, first strand: chain 'H' and resid 815 through 817 Processing sheet with id=AD8, first strand: chain 'H' and resid 829 through 830 Processing sheet with id=AD9, first strand: chain 'H' and resid 841 through 844 Processing sheet with id=AE1, first strand: chain 'H' and resid 865 through 866 removed outlier: 4.614A pdb=" N LEU H 970 " --> pdb=" O LEU H 966 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 874 through 876 Processing sheet with id=AE3, first strand: chain 'H' and resid 890 through 891 Processing sheet with id=AE4, first strand: chain 'H' and resid 1144 through 1151 removed outlier: 4.101A pdb=" N CYS H1149 " --> pdb=" O VAL H1170 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N VAL H1170 " --> pdb=" O CYS H1149 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1151 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: 6.38 Time building geometry restraints manager: 7.63 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: 6170 1.34 - 1.47: 4292 1.47 - 1.59: 7840 1.59 - 1.72: 1 1.72 - 1.84: 320 Bond restraints: 18623 Sorted by residual: bond pdb=" CA ASP F 975 " pdb=" C ASP F 975 " ideal model delta sigma weight residual 1.524 1.461 0.063 1.66e-02 3.63e+03 1.46e+01 bond pdb=" CA ASP H 975 " pdb=" C ASP H 975 " ideal model delta sigma weight residual 1.525 1.473 0.052 1.38e-02 5.25e+03 1.41e+01 bond pdb=" N VAL H 850 " pdb=" CA VAL H 850 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.85e+00 bond pdb=" N VAL E 102 " pdb=" CA VAL E 102 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.20e-02 6.94e+03 8.61e+00 bond pdb=" N CYS H 851 " pdb=" CA CYS H 851 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.15e-02 7.56e+03 7.97e+00 ... (remaining 18618 not shown) Histogram of bond angle deviations from ideal: 97.24 - 104.64: 372 104.64 - 112.03: 8779 112.03 - 119.43: 6464 119.43 - 126.82: 9395 126.82 - 134.22: 261 Bond angle restraints: 25271 Sorted by residual: angle pdb=" C TRP H 974 " pdb=" N ASP H 975 " pdb=" CA ASP H 975 " ideal model delta sigma weight residual 122.83 113.38 9.45 1.54e+00 4.22e-01 3.77e+01 angle pdb=" N VAL H1230 " pdb=" CA VAL H1230 " pdb=" C VAL H1230 " ideal model delta sigma weight residual 113.71 109.22 4.49 9.50e-01 1.11e+00 2.23e+01 angle pdb=" CA PRO H1038 " pdb=" N PRO H1038 " pdb=" CD PRO H1038 " ideal model delta sigma weight residual 112.00 105.61 6.39 1.40e+00 5.10e-01 2.08e+01 angle pdb=" N LYS E 157 " pdb=" CA LYS E 157 " pdb=" C LYS E 157 " ideal model delta sigma weight residual 113.55 107.82 5.73 1.26e+00 6.30e-01 2.07e+01 angle pdb=" C TRP F 974 " pdb=" N ASP F 975 " pdb=" CA ASP F 975 " ideal model delta sigma weight residual 122.65 115.35 7.30 1.66e+00 3.63e-01 1.93e+01 ... (remaining 25266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10352 17.94 - 35.88: 1008 35.88 - 53.81: 206 53.81 - 71.75: 46 71.75 - 89.69: 31 Dihedral angle restraints: 11643 sinusoidal: 4819 harmonic: 6824 Sorted by residual: dihedral pdb=" CA MET E 111 " pdb=" C MET E 111 " pdb=" N PRO E 112 " pdb=" CA PRO E 112 " ideal model delta harmonic sigma weight residual 180.00 121.65 58.35 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CB CYS E 65 " pdb=" SG CYS E 65 " pdb=" SG CYS E 159 " pdb=" CB CYS E 159 " ideal model delta sinusoidal sigma weight residual -86.00 2.79 -88.79 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS H1130 " pdb=" SG CYS H1130 " pdb=" SG CYS H1173 " pdb=" CB CYS H1173 " ideal model delta sinusoidal sigma weight residual -86.00 -173.61 87.61 1 1.00e+01 1.00e-02 9.20e+01 ... (remaining 11640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2728 0.146 - 0.292: 26 0.292 - 0.438: 1 0.438 - 0.584: 1 0.584 - 0.730: 1 Chirality restraints: 2757 Sorted by residual: chirality pdb=" C1 NAG G 804 " pdb=" ND2 ASN G 156 " pdb=" C2 NAG G 804 " pdb=" O5 NAG G 804 " both_signs ideal model delta sigma weight residual False -2.40 -1.67 -0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" C1 NAG F1302 " pdb=" ND2 ASN F 857 " pdb=" C2 NAG F1302 " pdb=" O5 NAG F1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.87 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" C1 NAG G 803 " pdb=" ND2 ASN G 99 " pdb=" C2 NAG G 803 " pdb=" O5 NAG G 803 " both_signs ideal model delta sigma weight residual False -2.40 -2.72 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2754 not shown) Planarity restraints: 3366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H1037 " 0.075 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO H1038 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO H1038 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO H1038 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 804 " 0.045 2.00e-02 2.50e+03 3.67e-02 1.69e+01 pdb=" C7 NAG G 804 " -0.011 2.00e-02 2.50e+03 pdb=" C8 NAG G 804 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG G 804 " -0.059 2.00e-02 2.50e+03 pdb=" O7 NAG G 804 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H1303 " 0.044 2.00e-02 2.50e+03 3.65e-02 1.67e+01 pdb=" C7 NAG H1303 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG H1303 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG H1303 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG H1303 " -0.008 2.00e-02 2.50e+03 ... (remaining 3363 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 622 2.69 - 3.24: 18203 3.24 - 3.79: 27201 3.79 - 4.35: 35952 4.35 - 4.90: 60491 Nonbonded interactions: 142469 Sorted by model distance: nonbonded pdb=" OH TYR F 883 " pdb=" O LEU F 995 " model vdw 2.137 2.440 nonbonded pdb=" NE2 GLN G 431 " pdb=" O ASP G 435 " model vdw 2.164 2.520 nonbonded pdb=" OG SER H1129 " pdb=" OE1 GLU H1131 " model vdw 2.177 2.440 nonbonded pdb=" OG1 THR E 311 " pdb=" OE1 GLN E 313 " model vdw 2.183 2.440 nonbonded pdb=" O THR E 668 " pdb=" OG SER E 671 " model vdw 2.190 2.440 ... (remaining 142464 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 1303)) selection = (chain 'H' and (resid 767 through 1052 or resid 1054 through 1241 or resid 1301 \ through 1303)) } 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.460 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 53.220 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 18623 Z= 0.495 Angle : 0.956 9.453 25271 Z= 0.570 Chirality : 0.054 0.730 2757 Planarity : 0.006 0.110 3358 Dihedral : 14.185 89.689 6925 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.54 % Favored : 86.29 % Rotamer: Outliers : 0.15 % Allowed : 0.44 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.16), residues: 2365 helix: -0.74 (0.28), residues: 335 sheet: -2.69 (0.27), residues: 364 loop : -2.26 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 502 HIS 0.008 0.001 HIS G 726 PHE 0.019 0.002 PHE F1021 TYR 0.026 0.002 TYR E 711 ARG 0.019 0.001 ARG E 597 *********************** 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 225 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 223 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 593 GLU cc_start: 0.8162 (tp30) cc_final: 0.7927 (mm-30) REVERT: F 1049 ASN cc_start: 0.7047 (t0) cc_final: 0.6780 (t0) REVERT: G 111 MET cc_start: 0.9140 (ttt) cc_final: 0.8808 (ttt) REVERT: G 280 MET cc_start: 0.8270 (tmm) cc_final: 0.7677 (tmm) REVERT: G 737 HIS cc_start: 0.6647 (m90) cc_final: 0.6416 (m90) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.3374 time to fit residues: 114.6724 Evaluate side-chains 173 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 112 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 HIS E 526 ASN G 104 GLN ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 832 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18623 Z= 0.311 Angle : 0.704 8.009 25271 Z= 0.363 Chirality : 0.047 0.177 2757 Planarity : 0.005 0.082 3358 Dihedral : 5.917 54.082 2730 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.41 % Favored : 89.47 % Rotamer: Outliers : 1.08 % Allowed : 8.34 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.75 (0.16), residues: 2365 helix: -0.19 (0.28), residues: 333 sheet: -2.62 (0.27), residues: 360 loop : -2.13 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 222 HIS 0.018 0.001 HIS E 452 PHE 0.020 0.002 PHE E 579 TYR 0.028 0.001 TYR E 711 ARG 0.007 0.000 ARG E 597 *********************** 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 208 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8083 (pp) cc_final: 0.7766 (mt) REVERT: E 476 LEU cc_start: 0.7999 (tt) cc_final: 0.7706 (mp) REVERT: E 740 MET cc_start: 0.6799 (mmm) cc_final: 0.6587 (tpt) REVERT: G 111 MET cc_start: 0.9099 (ttt) cc_final: 0.8704 (ttt) REVERT: G 280 MET cc_start: 0.8263 (tmm) cc_final: 0.7501 (tmm) outliers start: 21 outliers final: 15 residues processed: 196 average time/residue: 0.3441 time to fit residues: 103.1832 Evaluate side-chains 182 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 684 LEU Chi-restraints excluded: chain E residue 719 GLU Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain G residue 374 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 799 CYS Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1187 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 145 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 214 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 172 optimal weight: 0.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1215 ASN F1226 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 ASN ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1069 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18623 Z= 0.182 Angle : 0.608 8.109 25271 Z= 0.312 Chirality : 0.044 0.166 2757 Planarity : 0.005 0.107 3358 Dihedral : 5.456 59.564 2730 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.43 % Favored : 90.48 % Rotamer: Outliers : 1.57 % Allowed : 11.28 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.04 % 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: -2.53 (0.16), residues: 2365 helix: -0.11 (0.27), residues: 355 sheet: -2.36 (0.27), residues: 358 loop : -1.99 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 199 HIS 0.015 0.001 HIS E 452 PHE 0.016 0.001 PHE H1100 TYR 0.024 0.001 TYR E 711 ARG 0.008 0.000 ARG E 597 *********************** 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 238 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 207 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 111 MET cc_start: 0.9023 (ttt) cc_final: 0.8606 (ttt) REVERT: G 333 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: G 644 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7450 (mt-10) outliers start: 31 outliers final: 16 residues processed: 227 average time/residue: 0.2932 time to fit residues: 101.7517 Evaluate side-chains 197 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 719 GLU Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 772 VAL Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 374 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 935 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 23 optimal weight: 0.0770 chunk 102 optimal weight: 0.9980 chunk 144 optimal weight: 0.0370 chunk 215 optimal weight: 2.9990 chunk 228 optimal weight: 20.0000 chunk 112 optimal weight: 0.0470 chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 overall best weight: 0.2452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 18623 Z= 0.157 Angle : 0.597 10.198 25271 Z= 0.304 Chirality : 0.043 0.295 2757 Planarity : 0.005 0.101 3358 Dihedral : 5.123 56.613 2730 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.59 % Favored : 91.37 % Rotamer: Outliers : 1.67 % Allowed : 12.90 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.31 (0.17), residues: 2365 helix: 0.01 (0.27), residues: 367 sheet: -2.12 (0.27), residues: 366 loop : -1.86 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 502 HIS 0.021 0.001 HIS E 452 PHE 0.018 0.001 PHE G 735 TYR 0.026 0.001 TYR H 897 ARG 0.009 0.000 ARG E 597 *********************** 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 245 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8018 (pp) cc_final: 0.7698 (mt) REVERT: E 581 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7326 (mm-30) REVERT: G 111 MET cc_start: 0.8949 (ttt) cc_final: 0.8571 (ttt) REVERT: G 226 GLN cc_start: 0.7704 (mm-40) cc_final: 0.7495 (mm-40) REVERT: G 280 MET cc_start: 0.8255 (tmm) cc_final: 0.8005 (tmm) REVERT: G 333 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6827 (tp30) outliers start: 33 outliers final: 21 residues processed: 236 average time/residue: 0.2891 time to fit residues: 105.4964 Evaluate side-chains 198 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 374 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 589 SER Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 844 ILE Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 194 optimal weight: 0.4980 chunk 157 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 204 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** F 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1226 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 901 ASN ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18623 Z= 0.190 Angle : 0.602 10.558 25271 Z= 0.306 Chirality : 0.044 0.224 2757 Planarity : 0.005 0.095 3358 Dihedral : 5.013 56.607 2730 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.80 % Favored : 91.16 % Rotamer: Outliers : 2.11 % Allowed : 13.49 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.20 (0.17), residues: 2365 helix: 0.06 (0.27), residues: 371 sheet: -2.08 (0.27), residues: 372 loop : -1.77 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 502 HIS 0.023 0.001 HIS E 452 PHE 0.034 0.001 PHE E 70 TYR 0.019 0.001 TYR F 897 ARG 0.010 0.000 ARG E 597 *********************** 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 220 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8137 (pp) cc_final: 0.7730 (mt) REVERT: E 581 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7313 (mm-30) REVERT: G 111 MET cc_start: 0.8977 (ttt) cc_final: 0.8609 (ttt) REVERT: G 280 MET cc_start: 0.8257 (tmm) cc_final: 0.8006 (tmm) REVERT: G 333 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6818 (tp30) REVERT: H 1055 MET cc_start: 0.7503 (mmm) cc_final: 0.7294 (mtm) outliers start: 42 outliers final: 28 residues processed: 208 average time/residue: 0.2885 time to fit residues: 93.7146 Evaluate side-chains 197 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 381 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 936 LEU Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 374 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 844 ILE Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 20.0000 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 228 optimal weight: 20.0000 chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 20.0000 chunk 119 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 452 HIS ** F 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 901 ASN ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18623 Z= 0.229 Angle : 0.615 15.163 25271 Z= 0.312 Chirality : 0.045 0.301 2757 Planarity : 0.005 0.094 3358 Dihedral : 5.031 57.319 2730 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.67 % Favored : 91.29 % Rotamer: Outliers : 2.16 % Allowed : 14.52 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.16 (0.17), residues: 2365 helix: 0.16 (0.27), residues: 367 sheet: -2.01 (0.27), residues: 364 loop : -1.77 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP G 502 HIS 0.023 0.001 HIS E 452 PHE 0.027 0.001 PHE E 70 TYR 0.029 0.001 TYR E 711 ARG 0.011 0.000 ARG E 597 *********************** 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 222 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 179 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8183 (pp) cc_final: 0.7838 (mt) REVERT: E 282 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7787 (pp) REVERT: E 581 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7333 (mm-30) REVERT: G 111 MET cc_start: 0.8941 (ttt) cc_final: 0.8594 (ttt) REVERT: G 280 MET cc_start: 0.8289 (tmm) cc_final: 0.8039 (tmm) REVERT: G 333 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6948 (tp30) outliers start: 43 outliers final: 32 residues processed: 207 average time/residue: 0.3053 time to fit residues: 97.5035 Evaluate side-chains 206 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 898 CYS Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 374 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 844 ILE Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL 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: 8.9990 chunk 130 optimal weight: 8.9990 chunk 166 optimal weight: 0.0060 chunk 129 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 227 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 556 HIS ** F 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 18623 Z= 0.369 Angle : 0.682 10.665 25271 Z= 0.348 Chirality : 0.048 0.267 2757 Planarity : 0.005 0.098 3358 Dihedral : 5.406 59.040 2730 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.74 % Favored : 89.21 % Rotamer: Outliers : 2.26 % Allowed : 15.01 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.27 (0.17), residues: 2365 helix: 0.08 (0.27), residues: 365 sheet: -2.17 (0.27), residues: 358 loop : -1.83 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP G 502 HIS 0.007 0.001 HIS F1174 PHE 0.027 0.002 PHE E 70 TYR 0.017 0.002 TYR G 730 ARG 0.012 0.001 ARG E 597 *********************** 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 229 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 184 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8212 (pp) cc_final: 0.7739 (mt) REVERT: E 581 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7431 (mm-30) REVERT: G 111 MET cc_start: 0.9014 (ttt) cc_final: 0.8670 (ttt) REVERT: G 280 MET cc_start: 0.8271 (tmm) cc_final: 0.8060 (tmm) REVERT: G 333 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7216 (tp30) REVERT: G 730 TYR cc_start: 0.7094 (p90) cc_final: 0.6725 (p90) outliers start: 45 outliers final: 38 residues processed: 213 average time/residue: 0.2946 time to fit residues: 97.5780 Evaluate side-chains 214 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 175 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1027 VAL Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 374 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 466 MET Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1009 SER Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 144 optimal weight: 0.2980 chunk 154 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 901 ASN F1226 HIS ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18623 Z= 0.216 Angle : 0.630 12.574 25271 Z= 0.318 Chirality : 0.045 0.242 2757 Planarity : 0.005 0.092 3358 Dihedral : 5.261 57.127 2730 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.26 % Favored : 90.69 % Rotamer: Outliers : 2.21 % Allowed : 15.40 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.17 (0.17), residues: 2365 helix: 0.18 (0.27), residues: 365 sheet: -2.13 (0.27), residues: 374 loop : -1.75 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP G 502 HIS 0.006 0.001 HIS G 737 PHE 0.021 0.001 PHE E 70 TYR 0.013 0.001 TYR F 988 ARG 0.013 0.000 ARG E 597 *********************** 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 221 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 177 time to evaluate : 2.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8246 (pp) cc_final: 0.7940 (mt) REVERT: E 581 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7394 (mm-30) REVERT: G 111 MET cc_start: 0.8963 (ttt) cc_final: 0.8611 (ttt) REVERT: G 333 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7059 (tp30) outliers start: 44 outliers final: 33 residues processed: 208 average time/residue: 0.2968 time to fit residues: 96.0773 Evaluate side-chains 206 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 172 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 1027 VAL Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 374 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1187 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 chunk 200 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 911 ASN ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18623 Z= 0.239 Angle : 0.633 13.304 25271 Z= 0.320 Chirality : 0.045 0.240 2757 Planarity : 0.005 0.094 3358 Dihedral : 5.175 56.905 2730 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 2.01 % Allowed : 15.79 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.15 (0.17), residues: 2365 helix: 0.20 (0.27), residues: 365 sheet: -2.02 (0.27), residues: 378 loop : -1.76 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP G 502 HIS 0.004 0.001 HIS G 726 PHE 0.022 0.001 PHE E 70 TYR 0.014 0.001 TYR F 988 ARG 0.014 0.000 ARG E 597 *********************** 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 217 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8263 (pp) cc_final: 0.7837 (mt) REVERT: E 581 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7429 (mm-30) REVERT: F 768 ARG cc_start: 0.6866 (ttp-170) cc_final: 0.6638 (ttp-170) REVERT: F 947 MET cc_start: 0.8398 (mmm) cc_final: 0.8077 (mmm) REVERT: G 111 MET cc_start: 0.8948 (ttt) cc_final: 0.8597 (ttt) REVERT: G 280 MET cc_start: 0.8102 (tmm) cc_final: 0.7714 (tmm) REVERT: G 333 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7055 (tp30) REVERT: G 730 TYR cc_start: 0.7154 (p90) cc_final: 0.6379 (p90) outliers start: 40 outliers final: 37 residues processed: 204 average time/residue: 0.3614 time to fit residues: 113.0603 Evaluate side-chains 210 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 911 ASN Chi-restraints excluded: chain F residue 1027 VAL Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 374 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 235 optimal weight: 30.0000 chunk 216 optimal weight: 0.0970 chunk 187 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 144 optimal weight: 0.3980 chunk 114 optimal weight: 30.0000 chunk 148 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 overall best weight: 2.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18623 Z= 0.226 Angle : 0.634 11.787 25271 Z= 0.320 Chirality : 0.045 0.236 2757 Planarity : 0.005 0.095 3358 Dihedral : 5.144 56.566 2730 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.31 % Favored : 90.65 % Rotamer: Outliers : 2.01 % Allowed : 15.99 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.14 (0.17), residues: 2365 helix: 0.23 (0.27), residues: 365 sheet: -1.99 (0.26), residues: 390 loop : -1.76 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP G 502 HIS 0.004 0.001 HIS G 726 PHE 0.020 0.001 PHE E 70 TYR 0.013 0.001 TYR F 988 ARG 0.014 0.000 ARG E 597 ********************** 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 216 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 249 LEU cc_start: 0.8260 (pp) cc_final: 0.7917 (mt) REVERT: E 287 ASP cc_start: 0.7408 (m-30) cc_final: 0.6965 (m-30) REVERT: E 581 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7429 (mm-30) REVERT: F 947 MET cc_start: 0.8357 (mmm) cc_final: 0.8077 (mmm) REVERT: G 111 MET cc_start: 0.8940 (ttt) cc_final: 0.8593 (ttt) REVERT: G 280 MET cc_start: 0.8082 (tmm) cc_final: 0.7699 (tmm) REVERT: G 333 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7032 (tp30) REVERT: G 730 TYR cc_start: 0.7189 (p90) cc_final: 0.6420 (p90) outliers start: 40 outliers final: 37 residues processed: 203 average time/residue: 0.3034 time to fit residues: 95.0798 Evaluate side-chains 212 residues out of total 2051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 418 CYS Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 558 ASP Chi-restraints excluded: chain E residue 570 CYS Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain E residue 707 CYS Chi-restraints excluded: chain E residue 722 PHE Chi-restraints excluded: chain E residue 736 MET Chi-restraints excluded: chain E residue 737 HIS Chi-restraints excluded: chain F residue 846 CYS Chi-restraints excluded: chain F residue 1027 VAL Chi-restraints excluded: chain F residue 1056 VAL Chi-restraints excluded: chain F residue 1090 SER Chi-restraints excluded: chain F residue 1118 VAL Chi-restraints excluded: chain F residue 1153 CYS Chi-restraints excluded: chain F residue 1229 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 329 CYS Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 374 ASN Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 558 ASP Chi-restraints excluded: chain G residue 570 CYS Chi-restraints excluded: chain G residue 661 CYS Chi-restraints excluded: chain G residue 727 THR Chi-restraints excluded: chain H residue 929 VAL Chi-restraints excluded: chain H residue 935 GLU Chi-restraints excluded: chain H residue 955 VAL Chi-restraints excluded: chain H residue 1009 SER Chi-restraints excluded: chain H residue 1075 VAL Chi-restraints excluded: chain H residue 1187 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100297 restraints weight = 30253.330| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.80 r_work: 0.2985 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18623 Z= 0.325 Angle : 0.671 10.666 25271 Z= 0.340 Chirality : 0.046 0.231 2757 Planarity : 0.005 0.095 3358 Dihedral : 5.359 58.125 2730 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.62 % Favored : 89.34 % Rotamer: Outliers : 2.06 % Allowed : 15.94 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -2.24 (0.17), residues: 2365 helix: 0.14 (0.27), residues: 365 sheet: -2.17 (0.27), residues: 364 loop : -1.81 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 502 HIS 0.005 0.001 HIS G 726 PHE 0.022 0.002 PHE E 70 TYR 0.039 0.002 TYR E 711 ARG 0.015 0.001 ARG E 597 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3780.54 seconds wall clock time: 69 minutes 20.21 seconds (4160.21 seconds total)