Starting phenix.real_space_refine (version: dev) on Wed Dec 14 21:51:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/12_2022/5i08_8069.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/12_2022/5i08_8069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/12_2022/5i08_8069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/12_2022/5i08_8069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/12_2022/5i08_8069.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/12_2022/5i08_8069.pdb" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 374": "OD1" <-> "OD2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 374": "OD1" <-> "OD2" Residue "C PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 822": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 22683 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7561 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 31, 'TRANS': 926} Chain breaks: 7 Chain: "B" Number of atoms: 7561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7561 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 31, 'TRANS': 926} Chain breaks: 7 Chain: "C" Number of atoms: 7561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7561 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 31, 'TRANS': 926} Chain breaks: 7 Time building chain proxies: 12.90, per 1000 atoms: 0.57 Number of scatterers: 22683 At special positions: 0 Unit cell: (146.72, 141.48, 151.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4341 8.00 N 3723 7.00 C 14499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.06 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.08 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.06 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.10 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.04 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.05 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.04 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.04 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.10 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.02 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.06 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.08 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.06 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.10 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.04 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.05 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.04 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.04 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.10 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.02 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.06 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.08 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.06 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.10 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.04 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.05 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.04 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.04 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.66 Conformation dependent library (CDL) restraints added in 3.8 seconds 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5442 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 42 sheets defined 27.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.106A pdb=" N GLU A 252 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 295 removed outlier: 4.035A pdb=" N GLN A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 4.048A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.912A pdb=" N PHE A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.957A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 823 through 833 Processing helix chain 'A' and resid 835 through 863 removed outlier: 3.999A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 840 " --> pdb=" O CYS A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 914 through 924 Processing helix chain 'A' and resid 934 through 941 Processing helix chain 'A' and resid 951 through 968 Processing helix chain 'A' and resid 978 through 988 Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1002 through 1017 Processing helix chain 'A' and resid 1018 through 1021 removed outlier: 3.951A pdb=" N ALA A1021 " --> pdb=" O GLY A1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1018 through 1021' Processing helix chain 'A' and resid 1024 through 1046 Processing helix chain 'A' and resid 1047 through 1049 No H-bonds generated for 'chain 'A' and resid 1047 through 1049' Processing helix chain 'A' and resid 1058 through 1065 removed outlier: 3.741A pdb=" N LEU A1062 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A1064 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1111 Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 248 through 252 removed outlier: 4.106A pdb=" N GLU B 252 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 285 through 295 removed outlier: 4.035A pdb=" N GLN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.049A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 374 through 381 removed outlier: 3.912A pdb=" N PHE B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.957A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 823 through 833 Processing helix chain 'B' and resid 835 through 863 removed outlier: 3.999A pdb=" N ILE B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 840 " --> pdb=" O CYS B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 914 through 924 Processing helix chain 'B' and resid 934 through 941 Processing helix chain 'B' and resid 951 through 968 Processing helix chain 'B' and resid 978 through 988 Processing helix chain 'B' and resid 995 through 1000 Processing helix chain 'B' and resid 1002 through 1017 Processing helix chain 'B' and resid 1018 through 1021 removed outlier: 3.951A pdb=" N ALA B1021 " --> pdb=" O GLY B1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1018 through 1021' Processing helix chain 'B' and resid 1024 through 1046 Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1058 through 1065 removed outlier: 3.741A pdb=" N LEU B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B1064 " --> pdb=" O GLU B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1111 Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 248 through 252 removed outlier: 4.105A pdb=" N GLU C 252 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 285 through 295 removed outlier: 4.035A pdb=" N GLN C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 removed outlier: 4.049A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 344 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 374 through 381 removed outlier: 3.912A pdb=" N PHE C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.957A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 703 Processing helix chain 'C' and resid 823 through 833 Processing helix chain 'C' and resid 835 through 863 removed outlier: 3.999A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN C 840 " --> pdb=" O CYS C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 914 through 924 Processing helix chain 'C' and resid 934 through 941 Processing helix chain 'C' and resid 951 through 968 Processing helix chain 'C' and resid 978 through 988 Processing helix chain 'C' and resid 995 through 1000 Processing helix chain 'C' and resid 1002 through 1017 Processing helix chain 'C' and resid 1018 through 1021 removed outlier: 3.951A pdb=" N ALA C1021 " --> pdb=" O GLY C1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1018 through 1021' Processing helix chain 'C' and resid 1024 through 1046 Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1058 through 1065 removed outlier: 3.741A pdb=" N LEU C1062 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C1064 " --> pdb=" O GLU C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1111 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.059A pdb=" N ARG A 34 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE A 74 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.377A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP C 650 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE C 655 " --> pdb=" O ASP C 650 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 67 removed outlier: 6.408A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 95 through 97 removed outlier: 3.511A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA7, first strand: chain 'A' and resid 303 through 306 Processing sheet with id=AA8, first strand: chain 'A' and resid 317 through 319 removed outlier: 5.974A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE A 655 " --> pdb=" O ASP A 650 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP A 650 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.551A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'A' and resid 456 through 458 Processing sheet with id=AB4, first strand: chain 'A' and resid 742 through 745 Processing sheet with id=AB5, first strand: chain 'A' and resid 797 through 801 Processing sheet with id=AB6, first strand: chain 'A' and resid 809 through 812 removed outlier: 3.871A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB8, first strand: chain 'B' and resid 34 through 39 removed outlier: 4.058A pdb=" N ARG B 34 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE B 74 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 59 through 67 removed outlier: 6.407A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.511A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 111 through 112 Processing sheet with id=AC3, first strand: chain 'B' and resid 303 through 306 Processing sheet with id=AC4, first strand: chain 'B' and resid 317 through 319 removed outlier: 5.974A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE B 655 " --> pdb=" O ASP B 650 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP B 650 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AC6, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.551A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AC8, first strand: chain 'B' and resid 456 through 458 Processing sheet with id=AC9, first strand: chain 'B' and resid 742 through 745 Processing sheet with id=AD1, first strand: chain 'B' and resid 797 through 801 Processing sheet with id=AD2, first strand: chain 'B' and resid 809 through 812 removed outlier: 3.871A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'C' and resid 34 through 39 removed outlier: 4.059A pdb=" N ARG C 34 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE C 74 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 59 through 67 removed outlier: 6.408A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 95 through 97 removed outlier: 3.511A pdb=" N ILE C 124 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 111 through 112 Processing sheet with id=AD8, first strand: chain 'C' and resid 303 through 306 Processing sheet with id=AD9, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AE1, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.551A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AE3, first strand: chain 'C' and resid 456 through 458 Processing sheet with id=AE4, first strand: chain 'C' and resid 742 through 745 Processing sheet with id=AE5, first strand: chain 'C' and resid 797 through 801 Processing sheet with id=AE6, first strand: chain 'C' and resid 809 through 812 removed outlier: 3.871A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2541 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: 10.31 Time building geometry restraints manager: 10.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5999 1.33 - 1.45: 6525 1.45 - 1.58: 10534 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 23199 Sorted by residual: bond pdb=" CA ASP B 281 " pdb=" C ASP B 281 " ideal model delta sigma weight residual 1.526 1.469 0.058 1.21e-02 6.83e+03 2.28e+01 bond pdb=" CA ASP A 281 " pdb=" C ASP A 281 " ideal model delta sigma weight residual 1.526 1.469 0.058 1.21e-02 6.83e+03 2.26e+01 bond pdb=" CA ASP C 281 " pdb=" C ASP C 281 " ideal model delta sigma weight residual 1.526 1.469 0.057 1.21e-02 6.83e+03 2.25e+01 bond pdb=" CA LEU C 624 " pdb=" C LEU C 624 " ideal model delta sigma weight residual 1.521 1.477 0.044 1.17e-02 7.31e+03 1.44e+01 bond pdb=" CA LEU B 624 " pdb=" C LEU B 624 " ideal model delta sigma weight residual 1.521 1.477 0.044 1.17e-02 7.31e+03 1.42e+01 ... (remaining 23194 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.02: 557 106.02 - 113.01: 11569 113.01 - 120.01: 9786 120.01 - 127.01: 9453 127.01 - 134.00: 189 Bond angle restraints: 31554 Sorted by residual: angle pdb=" C LEU A 946 " pdb=" N PRO A 947 " pdb=" CA PRO A 947 " ideal model delta sigma weight residual 119.66 127.71 -8.05 7.20e-01 1.93e+00 1.25e+02 angle pdb=" C LEU B 946 " pdb=" N PRO B 947 " pdb=" CA PRO B 947 " ideal model delta sigma weight residual 119.66 127.71 -8.05 7.20e-01 1.93e+00 1.25e+02 angle pdb=" C LEU C 946 " pdb=" N PRO C 947 " pdb=" CA PRO C 947 " ideal model delta sigma weight residual 119.66 127.70 -8.04 7.20e-01 1.93e+00 1.25e+02 angle pdb=" C PRO B 947 " pdb=" N PRO B 948 " pdb=" CA PRO B 948 " ideal model delta sigma weight residual 119.85 130.45 -10.60 1.01e+00 9.80e-01 1.10e+02 angle pdb=" C PRO C 947 " pdb=" N PRO C 948 " pdb=" CA PRO C 948 " ideal model delta sigma weight residual 119.85 130.44 -10.59 1.01e+00 9.80e-01 1.10e+02 ... (remaining 31549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 13287 17.42 - 34.84: 321 34.84 - 52.26: 87 52.26 - 69.68: 24 69.68 - 87.10: 3 Dihedral angle restraints: 13722 sinusoidal: 5268 harmonic: 8454 Sorted by residual: dihedral pdb=" CB CYS B 814 " pdb=" SG CYS B 814 " pdb=" SG CYS B 836 " pdb=" CB CYS B 836 " ideal model delta sinusoidal sigma weight residual -86.00 -139.76 53.76 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CB CYS A 814 " pdb=" SG CYS A 814 " pdb=" SG CYS A 836 " pdb=" CB CYS A 836 " ideal model delta sinusoidal sigma weight residual -86.00 -139.76 53.76 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CB CYS C 814 " pdb=" SG CYS C 814 " pdb=" SG CYS C 836 " pdb=" CB CYS C 836 " ideal model delta sinusoidal sigma weight residual -86.00 -139.75 53.75 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2781 0.103 - 0.207: 690 0.207 - 0.310: 84 0.310 - 0.414: 12 0.414 - 0.517: 3 Chirality restraints: 3570 Sorted by residual: chirality pdb=" CA PHE A 802 " pdb=" N PHE A 802 " pdb=" C PHE A 802 " pdb=" CB PHE A 802 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA PHE C 802 " pdb=" N PHE C 802 " pdb=" C PHE C 802 " pdb=" CB PHE C 802 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.68e+00 chirality pdb=" CA PHE B 802 " pdb=" N PHE B 802 " pdb=" C PHE B 802 " pdb=" CB PHE B 802 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 3567 not shown) Planarity restraints: 4047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 218 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 219 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 218 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO C 219 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO C 219 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 219 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 218 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO B 219 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 219 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 219 " 0.057 5.00e-02 4.00e+02 ... (remaining 4044 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2441 2.72 - 3.26: 23866 3.26 - 3.81: 36374 3.81 - 4.35: 45822 4.35 - 4.90: 74355 Nonbonded interactions: 182858 Sorted by model distance: nonbonded pdb=" O PHE B 802 " pdb=" CD1 PHE B 802 " model vdw 2.174 3.340 nonbonded pdb=" O PHE A 802 " pdb=" CD1 PHE A 802 " model vdw 2.175 3.340 nonbonded pdb=" O PHE C 802 " pdb=" CD1 PHE C 802 " model vdw 2.175 3.340 nonbonded pdb=" OG1 THR B 123 " pdb=" O VAL B 139 " model vdw 2.282 2.440 nonbonded pdb=" OG1 THR A 123 " pdb=" O VAL A 139 " model vdw 2.283 2.440 ... (remaining 182853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 14499 2.51 5 N 3723 2.21 5 O 4341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.730 Check model and map are aligned: 0.320 Convert atoms to be neutral: 0.180 Process input model: 64.630 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 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 : 0.014 0.062 23199 Z= 0.921 Angle : 1.744 12.847 31554 Z= 1.185 Chirality : 0.090 0.517 3570 Planarity : 0.009 0.108 4047 Dihedral : 8.794 87.098 8145 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.01 % Favored : 92.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.15), residues: 2826 helix: 0.03 (0.17), residues: 657 sheet: 0.75 (0.19), residues: 612 loop : 0.53 (0.16), residues: 1557 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 614 time to evaluate : 2.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.3276 time to fit residues: 313.7107 Evaluate side-chains 271 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.914 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 258 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 269 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 470 ASN A 646 ASN A 838 ASN B 269 ASN B 437 ASN B 470 ASN ** B 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 269 ASN C 437 ASN C 470 ASN ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 23199 Z= 0.231 Angle : 0.742 9.290 31554 Z= 0.418 Chirality : 0.044 0.154 3570 Planarity : 0.005 0.081 4047 Dihedral : 6.155 26.541 3099 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.18 % Favored : 92.18 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2826 helix: 1.37 (0.20), residues: 678 sheet: 0.08 (0.20), residues: 612 loop : -0.50 (0.16), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 453 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 456 average time/residue: 0.3156 time to fit residues: 232.7973 Evaluate side-chains 270 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 3.104 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 230 optimal weight: 7.9990 chunk 257 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 ASN A 595 ASN A 646 ASN B 175 HIS B 269 ASN B 470 ASN B 595 ASN B 646 ASN ** B1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN C 175 HIS C 470 ASN C 646 ASN C 821 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 23199 Z= 0.197 Angle : 0.644 9.179 31554 Z= 0.358 Chirality : 0.042 0.150 3570 Planarity : 0.005 0.071 4047 Dihedral : 5.677 28.739 3099 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.72 % Favored : 92.64 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2826 helix: 1.49 (0.21), residues: 663 sheet: -0.39 (0.19), residues: 621 loop : -0.87 (0.16), residues: 1542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 399 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 401 average time/residue: 0.3067 time to fit residues: 201.7250 Evaluate side-chains 254 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.695 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 123 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS A 595 ASN A 646 ASN A1045 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 470 ASN B 595 ASN B 646 ASN C 175 HIS C 437 ASN C 470 ASN C 646 ASN C 821 ASN ** C 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 23199 Z= 0.289 Angle : 0.685 9.616 31554 Z= 0.373 Chirality : 0.043 0.148 3570 Planarity : 0.005 0.066 4047 Dihedral : 5.738 31.259 3099 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.70 % Favored : 90.66 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 2826 helix: 0.91 (0.21), residues: 690 sheet: -0.74 (0.19), residues: 588 loop : -1.19 (0.15), residues: 1548 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 355 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 357 average time/residue: 0.2935 time to fit residues: 173.9009 Evaluate side-chains 232 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 2.725 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2509 time to fit residues: 4.1088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 205 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 235 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 0.0070 chunk 247 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 646 ASN A 821 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 269 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN B 821 ASN B 859 ASN C 175 HIS C 646 ASN C 821 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 23199 Z= 0.168 Angle : 0.631 12.014 31554 Z= 0.340 Chirality : 0.041 0.237 3570 Planarity : 0.004 0.059 4047 Dihedral : 5.438 28.844 3099 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.68 % Favored : 91.68 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 2826 helix: 1.19 (0.21), residues: 684 sheet: -0.67 (0.20), residues: 573 loop : -1.30 (0.15), residues: 1569 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 353 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 358 average time/residue: 0.2929 time to fit residues: 175.0292 Evaluate side-chains 246 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 2.718 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1961 time to fit residues: 4.0288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.8980 chunk 248 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 275 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 646 ASN A 840 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 175 HIS ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN B 821 ASN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN C 424 GLN C 595 ASN C 646 ASN C 821 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 23199 Z= 0.199 Angle : 0.635 14.284 31554 Z= 0.341 Chirality : 0.042 0.301 3570 Planarity : 0.004 0.061 4047 Dihedral : 5.320 28.599 3099 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.78 % Favored : 90.59 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2826 helix: 1.38 (0.21), residues: 684 sheet: -0.62 (0.20), residues: 573 loop : -1.38 (0.15), residues: 1569 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 329 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 332 average time/residue: 0.2999 time to fit residues: 165.5658 Evaluate side-chains 233 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 3.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 232 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 274 optimal weight: 0.9990 chunk 171 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 437 ASN A 646 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN B 821 ASN C 646 ASN C 821 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 23199 Z= 0.281 Angle : 0.692 13.800 31554 Z= 0.370 Chirality : 0.044 0.277 3570 Planarity : 0.005 0.056 4047 Dihedral : 5.477 30.678 3099 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.41 % Favored : 89.99 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 2826 helix: 1.21 (0.21), residues: 687 sheet: -0.84 (0.20), residues: 558 loop : -1.61 (0.15), residues: 1581 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 300 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 303 average time/residue: 0.3023 time to fit residues: 152.7429 Evaluate side-chains 220 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.881 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 chunk 249 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN B 821 ASN B 859 ASN C 646 ASN ** C1111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 23199 Z= 0.245 Angle : 0.682 15.224 31554 Z= 0.361 Chirality : 0.043 0.287 3570 Planarity : 0.005 0.056 4047 Dihedral : 5.417 29.313 3099 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.34 % Favored : 90.13 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.15), residues: 2826 helix: 1.27 (0.21), residues: 699 sheet: -0.91 (0.20), residues: 561 loop : -1.68 (0.15), residues: 1566 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 305 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.2939 time to fit residues: 151.4754 Evaluate side-chains 222 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.774 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 201 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 231 optimal weight: 8.9990 chunk 242 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 424 GLN A 646 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN B 821 ASN C 646 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 23199 Z= 0.184 Angle : 0.649 14.287 31554 Z= 0.342 Chirality : 0.042 0.266 3570 Planarity : 0.005 0.064 4047 Dihedral : 5.227 27.742 3099 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.24 % Favored : 90.23 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2826 helix: 1.38 (0.21), residues: 699 sheet: -0.77 (0.21), residues: 549 loop : -1.67 (0.15), residues: 1578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 304 time to evaluate : 3.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 307 average time/residue: 0.2951 time to fit residues: 151.5579 Evaluate side-chains 220 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 218 time to evaluate : 2.760 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2187 time to fit residues: 4.4410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 174 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 646 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN A1111 ASN ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 595 ASN B 646 ASN C 175 HIS C 646 ASN ** C1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 23199 Z= 0.338 Angle : 0.760 15.520 31554 Z= 0.399 Chirality : 0.045 0.292 3570 Planarity : 0.005 0.057 4047 Dihedral : 5.570 28.414 3099 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.69 % Favored : 88.78 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 2826 helix: 0.96 (0.20), residues: 711 sheet: -0.94 (0.21), residues: 528 loop : -2.07 (0.14), residues: 1587 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 280 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 282 average time/residue: 0.3004 time to fit residues: 142.0768 Evaluate side-chains 214 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.836 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 94 optimal weight: 0.0570 chunk 232 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN B 859 ASN C 646 ASN ** C1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.105851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092251 restraints weight = 56716.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094446 restraints weight = 33954.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.096005 restraints weight = 23127.821| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 23199 Z= 0.179 Angle : 0.658 14.753 31554 Z= 0.344 Chirality : 0.042 0.253 3570 Planarity : 0.005 0.059 4047 Dihedral : 5.299 28.905 3099 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.45 % Favored : 89.99 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 2826 helix: 1.21 (0.21), residues: 711 sheet: -0.54 (0.22), residues: 474 loop : -2.01 (0.14), residues: 1641 =============================================================================== Job complete usr+sys time: 4075.14 seconds wall clock time: 75 minutes 52.29 seconds (4552.29 seconds total)