Starting phenix.real_space_refine (version: dev) on Fri Feb 24 09:44:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/02_2023/5i08_8069.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/02_2023/5i08_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_8069/02_2023/5i08_8069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/02_2023/5i08_8069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/02_2023/5i08_8069.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/02_2023/5i08_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 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 12.51, per 1000 atoms: 0.55 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: 9.93 Conformation dependent library (CDL) restraints added in 3.7 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: 1.63 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: 9.52 Time building geometry restraints manager: 10.65 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: 0.970 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: 0.010 Extract box with map and model: 5.850 Check model and map are aligned: 0.350 Process input model: 61.120 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.180 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.710 ------------------------------------------------------------------------------- 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 : 3.14 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 : 2.660 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: 0.3322 time to fit residues: 317.4207 Evaluate side-chains 271 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.607 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5893 ------------------------------------------------------------------------------- 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 : 8.66 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 : 2.941 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: 0.3099 time to fit residues: 229.8921 Evaluate side-chains 270 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7947 ------------------------------------------------------------------------------- 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: 6.9990 chunk 80 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 176 optimal weight: 0.4980 chunk 71 optimal weight: 6.9990 chunk 259 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 230 optimal weight: 7.9990 chunk 257 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 ** B 859 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: 0.7233 moved from start: 0.3720 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= 0.236 Angle : 0.665 9.348 31554 Z= 0.369 Chirality : 0.042 0.156 3570 Planarity : 0.005 0.070 4047 Dihedral : 5.716 29.871 3099 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.54 % Favored : 91.83 % 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: -0.41 (0.16), residues: 2826 helix: 1.28 (0.21), residues: 681 sheet: -0.44 (0.19), residues: 621 loop : -0.90 (0.16), residues: 1524 *********************** 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 398 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 394 time to evaluate : 2.831 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: 0 residues processed: 396 average time/residue: 0.2997 time to fit residues: 195.5271 Evaluate side-chains 248 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6732 ------------------------------------------------------------------------------- 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: 0.9980 chunk 194 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 0.0870 chunk 123 optimal weight: 9.9990 chunk 174 optimal weight: 0.4980 chunk 260 optimal weight: 0.0040 chunk 275 optimal weight: 0.9990 chunk 135 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN C 175 HIS C 470 ASN C 646 ASN C 821 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4132 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= 0.169 Angle : 0.617 12.952 31554 Z= 0.336 Chirality : 0.041 0.208 3570 Planarity : 0.004 0.068 4047 Dihedral : 5.472 29.163 3099 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.01 % Favored : 92.36 % 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: -0.52 (0.15), residues: 2826 helix: 1.41 (0.21), residues: 684 sheet: -0.44 (0.20), residues: 570 loop : -1.12 (0.15), residues: 1572 *********************** 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 382 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 379 time to evaluate : 2.703 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: 3 outliers final: 0 residues processed: 381 average time/residue: 0.2942 time to fit residues: 186.2498 Evaluate side-chains 250 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 2.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4478 ------------------------------------------------------------------------------- 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: 6.9990 chunk 156 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 204 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 821 ASN A 840 ASN A1036 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN B 402 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN B 859 ASN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN C 437 ASN C 470 ASN ** C 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN C 821 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.081 23199 Z= 0.598 Angle : 0.950 12.397 31554 Z= 0.506 Chirality : 0.052 0.257 3570 Planarity : 0.006 0.054 4047 Dihedral : 6.502 36.423 3099 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.78 % Allowed : 9.48 % Favored : 89.74 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.45 (0.15), residues: 2826 helix: 0.43 (0.19), residues: 681 sheet: -0.96 (0.18), residues: 594 loop : -1.63 (0.15), residues: 1551 *********************** 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 309 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 304 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 309 average time/residue: 0.3051 time to fit residues: 156.9145 Evaluate side-chains 205 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6561 ------------------------------------------------------------------------------- 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: 3.9990 chunk 248 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1034 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 470 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 23199 Z= 0.228 Angle : 0.690 15.515 31554 Z= 0.372 Chirality : 0.043 0.353 3570 Planarity : 0.005 0.061 4047 Dihedral : 5.845 31.839 3099 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.06 % Favored : 90.30 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 2826 helix: 1.04 (0.20), residues: 684 sheet: -0.97 (0.20), residues: 540 loop : -1.76 (0.14), residues: 1602 *********************** 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 330 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 329 time to evaluate : 2.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 330 average time/residue: 0.2967 time to fit residues: 163.9277 Evaluate side-chains 222 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.900 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9206 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 153 optimal weight: 0.2980 chunk 274 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 595 ASN A 646 ASN B 470 ASN B 646 ASN B1086 ASN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.105 23199 Z= 0.326 Angle : 0.734 14.254 31554 Z= 0.393 Chirality : 0.045 0.327 3570 Planarity : 0.005 0.060 4047 Dihedral : 5.851 32.012 3099 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.58 % Favored : 88.78 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.15), residues: 2826 helix: 1.02 (0.20), residues: 684 sheet: -1.09 (0.21), residues: 531 loop : -1.85 (0.14), residues: 1611 *********************** 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 299 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 298 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 0.3011 time to fit residues: 150.4395 Evaluate side-chains 206 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 2.703 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7150 ------------------------------------------------------------------------------- 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: 1.9990 chunk 109 optimal weight: 10.0000 chunk 164 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 595 ASN A 646 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN B 470 ASN B 646 ASN B 859 ASN B1086 ASN C 175 HIS C 424 GLN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 23199 Z= 0.261 Angle : 0.707 16.169 31554 Z= 0.376 Chirality : 0.044 0.310 3570 Planarity : 0.005 0.061 4047 Dihedral : 5.711 29.466 3099 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.77 % Favored : 89.60 % 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: -1.41 (0.15), residues: 2826 helix: 1.13 (0.21), residues: 687 sheet: -1.13 (0.21), residues: 549 loop : -1.87 (0.15), residues: 1590 *********************** 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 306 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 303 time to evaluate : 2.763 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: 1 residues processed: 306 average time/residue: 0.2978 time to fit residues: 152.7752 Evaluate side-chains 209 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 2.944 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2741 time to fit residues: 5.2833 ------------------------------------------------------------------------------- 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: 6.9990 chunk 240 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 595 ASN A 646 ASN B 152 GLN B 470 ASN B 595 ASN B 646 ASN ** B1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 595 ASN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.108 23199 Z= 0.604 Angle : 0.960 15.347 31554 Z= 0.505 Chirality : 0.052 0.314 3570 Planarity : 0.006 0.109 4047 Dihedral : 6.512 33.049 3099 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.64 % Allowed : 13.02 % Favored : 86.34 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.07 (0.15), residues: 2826 helix: 0.38 (0.19), residues: 684 sheet: -1.17 (0.21), residues: 543 loop : -2.34 (0.14), residues: 1599 *********************** 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 257 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.3051 time to fit residues: 130.3127 Evaluate side-chains 179 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 2.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4270 ------------------------------------------------------------------------------- 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: 1.9990 chunk 128 optimal weight: 4.9990 chunk 188 optimal weight: 0.0970 chunk 283 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 226 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 138 optimal weight: 0.4980 chunk 179 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 595 ASN A 646 ASN B 470 ASN B 859 ASN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 23199 Z= 0.193 Angle : 0.704 15.450 31554 Z= 0.372 Chirality : 0.044 0.267 3570 Planarity : 0.005 0.098 4047 Dihedral : 5.785 31.017 3099 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.78 % Favored : 90.62 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.63 (0.15), residues: 2826 helix: 1.08 (0.21), residues: 684 sheet: -0.85 (0.22), residues: 483 loop : -2.22 (0.14), residues: 1659 ********************** 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 295 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 293 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 295 average time/residue: 0.3014 time to fit residues: 149.1579 Evaluate side-chains 207 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.743 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6224 ------------------------------------------------------------------------------- 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: 3.9990 chunk 208 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 232 optimal weight: 0.0770 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 175 HIS A 591 ASN A 595 ASN A 646 ASN B 152 GLN B 470 ASN B 646 ASN ** B1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089686 restraints weight = 57261.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091823 restraints weight = 34460.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093351 restraints weight = 23596.412| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 23199 Z= 0.223 Angle : 0.708 15.172 31554 Z= 0.369 Chirality : 0.044 0.262 3570 Planarity : 0.006 0.098 4047 Dihedral : 5.590 28.223 3099 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.60 % Allowed : 10.54 % Favored : 88.85 % 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: -1.62 (0.15), residues: 2826 helix: 1.10 (0.21), residues: 717 sheet: -0.92 (0.21), residues: 519 loop : -2.28 (0.14), residues: 1590 =============================================================================== Job complete usr+sys time: 4050.43 seconds wall clock time: 75 minutes 10.82 seconds (4510.82 seconds total)