Starting phenix.real_space_refine on Tue Mar 19 01:15:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/03_2024/5i08_8069.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/03_2024/5i08_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_8069/03_2024/5i08_8069.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/03_2024/5i08_8069.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/03_2024/5i08_8069.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5i08_8069/03_2024/5i08_8069.pdb" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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-5265/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: 11.58, per 1000 atoms: 0.51 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: 8.67 Conformation dependent library (CDL) restraints added in 3.9 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: 2.89 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: 8.96 Time building geometry restraints manager: 9.33 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 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: 0.660 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: 4.560 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 59.260 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.110 Set refine NCS operators: 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 % Allowed : 0.35 % Favored : 99.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.007 TRP C 332 HIS 0.006 0.001 HIS B1145 PHE 0.028 0.004 PHE C 98 TYR 0.043 0.007 TYR B 49 ARG 0.007 0.001 ARG C 397 *********************** 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 : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8863 (tp) cc_final: 0.8510 (tp) REVERT: A 578 ASP cc_start: 0.7728 (t0) cc_final: 0.7332 (t0) REVERT: A 593 ILE cc_start: 0.8164 (mt) cc_final: 0.7510 (mt) REVERT: A 967 MET cc_start: 0.6827 (tpp) cc_final: 0.6347 (tpp) REVERT: A 1094 SER cc_start: 0.8775 (m) cc_final: 0.8413 (p) REVERT: B 152 GLN cc_start: 0.7963 (mt0) cc_final: 0.7745 (pt0) REVERT: B 182 LEU cc_start: 0.7148 (mt) cc_final: 0.6566 (mt) REVERT: B 257 TRP cc_start: 0.6947 (m-10) cc_final: 0.6624 (m-10) REVERT: B 281 ASP cc_start: 0.7581 (t0) cc_final: 0.7134 (t0) REVERT: B 593 ILE cc_start: 0.8290 (mt) cc_final: 0.8012 (mm) REVERT: B 701 LEU cc_start: 0.8227 (tp) cc_final: 0.8006 (tt) REVERT: B 967 MET cc_start: 0.7211 (tpp) cc_final: 0.6870 (tpt) REVERT: C 135 TYR cc_start: 0.7971 (m-80) cc_final: 0.7322 (m-10) REVERT: C 137 ILE cc_start: 0.8394 (mt) cc_final: 0.8094 (mm) REVERT: C 152 GLN cc_start: 0.8069 (mt0) cc_final: 0.7682 (mt0) REVERT: C 182 LEU cc_start: 0.7501 (mt) cc_final: 0.7017 (mp) REVERT: C 203 TYR cc_start: 0.7779 (p90) cc_final: 0.7511 (p90) REVERT: C 257 TRP cc_start: 0.7399 (m-10) cc_final: 0.6700 (m-10) REVERT: C 281 ASP cc_start: 0.7796 (t0) cc_final: 0.7304 (t0) REVERT: C 425 LEU cc_start: 0.9024 (tp) cc_final: 0.8133 (tt) REVERT: C 439 PHE cc_start: 0.3510 (m-80) cc_final: 0.3208 (m-80) REVERT: C 593 ILE cc_start: 0.8479 (mt) cc_final: 0.8100 (mm) REVERT: C 770 PHE cc_start: 0.6292 (p90) cc_final: 0.6090 (p90) REVERT: C 1094 SER cc_start: 0.8704 (m) cc_final: 0.8372 (p) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.3296 time to fit residues: 315.3491 Evaluate side-chains 279 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 2.507 ------------------------------------------------------------------------------- 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: 0.9990 chunk 119 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 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: 0.9984 ------------------------------------------------------------------------------- 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: 0.7111 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23199 Z= 0.226 Angle : 0.744 9.367 31554 Z= 0.421 Chirality : 0.044 0.169 3570 Planarity : 0.005 0.080 4047 Dihedral : 6.165 26.600 3099 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.11 % Favored : 92.25 % Rotamer: Outliers : 0.16 % Allowed : 1.43 % Favored : 98.41 % 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: 0.13 (0.15), residues: 2826 helix: 1.38 (0.20), residues: 681 sheet: 0.08 (0.19), residues: 612 loop : -0.46 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 257 HIS 0.012 0.002 HIS B1129 PHE 0.031 0.002 PHE C 968 TYR 0.027 0.002 TYR B 49 ARG 0.007 0.001 ARG B1120 *********************** 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 459 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 455 time to evaluate : 2.520 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: A 79 LEU cc_start: 0.7317 (tp) cc_final: 0.6972 (mt) REVERT: A 182 LEU cc_start: 0.7407 (mt) cc_final: 0.6962 (tt) REVERT: A 281 ASP cc_start: 0.6790 (t0) cc_final: 0.6215 (t0) REVERT: A 415 LYS cc_start: 0.5375 (mtmt) cc_final: 0.5147 (mttt) REVERT: A 593 ILE cc_start: 0.7869 (mt) cc_final: 0.7613 (mt) REVERT: A 831 GLU cc_start: 0.7748 (pp20) cc_final: 0.7295 (pp20) REVERT: A 967 MET cc_start: 0.7375 (tpp) cc_final: 0.7039 (tpt) REVERT: A 994 MET cc_start: 0.6049 (ttt) cc_final: 0.5700 (ttt) REVERT: A 1023 ASN cc_start: 0.6554 (p0) cc_final: 0.5915 (p0) REVERT: A 1094 SER cc_start: 0.8205 (m) cc_final: 0.7945 (p) REVERT: B 182 LEU cc_start: 0.7311 (mt) cc_final: 0.6651 (mt) REVERT: B 281 ASP cc_start: 0.7536 (t0) cc_final: 0.6861 (t0) REVERT: B 593 ILE cc_start: 0.7878 (mt) cc_final: 0.7547 (mt) REVERT: B 967 MET cc_start: 0.7515 (tpp) cc_final: 0.7255 (tpt) REVERT: B 1023 ASN cc_start: 0.6720 (p0) cc_final: 0.6212 (p0) REVERT: B 1079 ASN cc_start: 0.7785 (t0) cc_final: 0.7538 (t0) REVERT: C 137 ILE cc_start: 0.8667 (mt) cc_final: 0.8435 (mm) REVERT: C 182 LEU cc_start: 0.7803 (mt) cc_final: 0.7467 (mp) REVERT: C 281 ASP cc_start: 0.7196 (t0) cc_final: 0.6710 (t0) REVERT: C 439 PHE cc_start: 0.3690 (m-80) cc_final: 0.3225 (m-80) REVERT: C 967 MET cc_start: 0.6886 (tpt) cc_final: 0.5710 (tpp) REVERT: C 1023 ASN cc_start: 0.6330 (p0) cc_final: 0.5646 (p0) outliers start: 4 outliers final: 0 residues processed: 458 average time/residue: 0.2944 time to fit residues: 218.2496 Evaluate side-chains 272 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.712 ------------------------------------------------------------------------------- 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: 9.9990 chunk 80 optimal weight: 0.7980 chunk 215 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS 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 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: 0.7278 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23199 Z= 0.307 Angle : 0.713 9.433 31554 Z= 0.394 Chirality : 0.044 0.179 3570 Planarity : 0.005 0.069 4047 Dihedral : 5.904 31.835 3099 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.96 % Favored : 91.40 % Rotamer: Outliers : 0.16 % Allowed : 2.25 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 2826 helix: 1.03 (0.21), residues: 684 sheet: -0.69 (0.19), residues: 609 loop : -0.89 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 444 HIS 0.014 0.003 HIS B1129 PHE 0.028 0.002 PHE B 383 TYR 0.025 0.002 TYR B 49 ARG 0.028 0.001 ARG C1120 *********************** 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 383 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 379 time to evaluate : 2.606 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: A 15 ILE cc_start: 0.7668 (mm) cc_final: 0.7367 (mt) REVERT: A 578 ASP cc_start: 0.7372 (t70) cc_final: 0.7134 (t70) REVERT: A 967 MET cc_start: 0.7557 (tpp) cc_final: 0.7172 (tpp) REVERT: A 1023 ASN cc_start: 0.6543 (p0) cc_final: 0.5846 (p0) REVERT: A 1094 SER cc_start: 0.8299 (m) cc_final: 0.7946 (p) REVERT: B 15 ILE cc_start: 0.7619 (mm) cc_final: 0.7381 (mt) REVERT: B 94 PHE cc_start: 0.6806 (m-10) cc_final: 0.6518 (m-80) REVERT: B 257 TRP cc_start: 0.7363 (m-10) cc_final: 0.7133 (m-10) REVERT: B 281 ASP cc_start: 0.7763 (t0) cc_final: 0.7284 (t70) REVERT: B 415 LYS cc_start: 0.6083 (mtpt) cc_final: 0.5673 (mttt) REVERT: B 593 ILE cc_start: 0.7860 (mt) cc_final: 0.7492 (mt) REVERT: B 967 MET cc_start: 0.7476 (tpp) cc_final: 0.7237 (tpt) REVERT: B 1023 ASN cc_start: 0.6498 (p0) cc_final: 0.6024 (p0) REVERT: C 15 ILE cc_start: 0.7780 (mm) cc_final: 0.7480 (mt) REVERT: C 182 LEU cc_start: 0.7634 (mt) cc_final: 0.7408 (mt) REVERT: C 281 ASP cc_start: 0.7357 (t0) cc_final: 0.6995 (t0) REVERT: C 967 MET cc_start: 0.7310 (tpt) cc_final: 0.6002 (tpp) REVERT: C 1023 ASN cc_start: 0.6196 (p0) cc_final: 0.5569 (p0) outliers start: 4 outliers final: 0 residues processed: 381 average time/residue: 0.2998 time to fit residues: 187.7667 Evaluate side-chains 255 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.502 ------------------------------------------------------------------------------- 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: 0.4980 chunk 194 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 28 optimal weight: 0.0040 chunk 123 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 260 optimal weight: 0.4980 chunk 275 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 246 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 595 ASN A 646 ASN ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN B 175 HIS B 269 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 595 ASN C 175 HIS ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 646 ASN C 821 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.4253 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 : 0.632 12.114 31554 Z= 0.346 Chirality : 0.041 0.204 3570 Planarity : 0.005 0.061 4047 Dihedral : 5.602 30.500 3099 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.75 % Favored : 91.61 % Rotamer: Outliers : 0.16 % Allowed : 2.33 % Favored : 97.52 % 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: -0.62 (0.15), residues: 2826 helix: 1.39 (0.21), residues: 666 sheet: -0.60 (0.20), residues: 573 loop : -1.15 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 332 HIS 0.007 0.002 HIS B1129 PHE 0.020 0.001 PHE C 589 TYR 0.038 0.002 TYR B 266 ARG 0.007 0.000 ARG B 396 *********************** 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 375 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 371 time to evaluate : 2.589 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: A 15 ILE cc_start: 0.7406 (mm) cc_final: 0.7078 (mt) REVERT: A 281 ASP cc_start: 0.7078 (t0) cc_final: 0.6456 (t0) REVERT: A 415 LYS cc_start: 0.5872 (mttt) cc_final: 0.5448 (mtmt) REVERT: A 967 MET cc_start: 0.7515 (tpp) cc_final: 0.7209 (tpp) REVERT: A 1094 SER cc_start: 0.8375 (m) cc_final: 0.7921 (p) REVERT: B 15 ILE cc_start: 0.7489 (mm) cc_final: 0.7154 (mt) REVERT: B 415 LYS cc_start: 0.5826 (mtpt) cc_final: 0.5502 (mttt) REVERT: B 593 ILE cc_start: 0.7879 (mt) cc_final: 0.7616 (mt) REVERT: B 829 LEU cc_start: 0.8074 (mt) cc_final: 0.7847 (mm) REVERT: B 967 MET cc_start: 0.7848 (tpp) cc_final: 0.7502 (tpt) REVERT: B 1023 ASN cc_start: 0.6526 (p0) cc_final: 0.5899 (p0) REVERT: C 649 TYR cc_start: 0.7485 (m-80) cc_final: 0.7249 (m-10) REVERT: C 967 MET cc_start: 0.7206 (tpt) cc_final: 0.6075 (tpp) REVERT: C 1023 ASN cc_start: 0.6421 (p0) cc_final: 0.5772 (p0) outliers start: 4 outliers final: 1 residues processed: 375 average time/residue: 0.2846 time to fit residues: 176.6370 Evaluate side-chains 243 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 2.340 ------------------------------------------------------------------------------- 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: 9.9990 chunk 156 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 247 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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 437 ASN A 646 ASN A 821 ASN ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 470 ASN B 646 ASN B 821 ASN B 859 ASN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN C 424 GLN 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: 0.7257 moved from start: 0.4589 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= 0.222 Angle : 0.644 10.267 31554 Z= 0.346 Chirality : 0.042 0.177 3570 Planarity : 0.005 0.063 4047 Dihedral : 5.448 30.339 3099 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.63 % Favored : 90.73 % Rotamer: Outliers : 0.27 % Allowed : 1.67 % Favored : 98.06 % 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: -0.80 (0.16), residues: 2826 helix: 1.24 (0.21), residues: 684 sheet: -0.71 (0.20), residues: 570 loop : -1.29 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 444 HIS 0.007 0.002 HIS C1129 PHE 0.014 0.001 PHE C 270 TYR 0.036 0.002 TYR A 266 ARG 0.004 0.000 ARG B 396 *********************** 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 352 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 345 time to evaluate : 2.900 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: A 15 ILE cc_start: 0.7394 (mm) cc_final: 0.7092 (mt) REVERT: A 415 LYS cc_start: 0.6065 (mttt) cc_final: 0.5708 (mtmt) REVERT: A 967 MET cc_start: 0.7148 (tpp) cc_final: 0.6846 (tpp) REVERT: A 997 LEU cc_start: 0.7120 (tp) cc_final: 0.6816 (tp) REVERT: B 15 ILE cc_start: 0.7440 (mm) cc_final: 0.7141 (mt) REVERT: B 257 TRP cc_start: 0.6954 (m-10) cc_final: 0.6741 (m-10) REVERT: B 415 LYS cc_start: 0.6005 (mtpt) cc_final: 0.5452 (mttt) REVERT: B 593 ILE cc_start: 0.7997 (mt) cc_final: 0.7667 (mt) REVERT: B 967 MET cc_start: 0.7827 (tpp) cc_final: 0.7353 (tpp) REVERT: B 997 LEU cc_start: 0.6815 (tp) cc_final: 0.6579 (tp) REVERT: B 1023 ASN cc_start: 0.6572 (p0) cc_final: 0.5879 (p0) REVERT: B 1079 ASN cc_start: 0.7791 (t0) cc_final: 0.7573 (t0) REVERT: C 649 TYR cc_start: 0.7466 (m-80) cc_final: 0.7210 (m-10) REVERT: C 829 LEU cc_start: 0.8561 (mt) cc_final: 0.8220 (mm) REVERT: C 967 MET cc_start: 0.6888 (tpt) cc_final: 0.5836 (tpp) REVERT: C 1023 ASN cc_start: 0.6458 (p0) cc_final: 0.5771 (p0) outliers start: 7 outliers final: 0 residues processed: 351 average time/residue: 0.2806 time to fit residues: 164.1072 Evaluate side-chains 254 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.474 ------------------------------------------------------------------------------- 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: 0.1980 chunk 248 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 161 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 127 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 646 ASN A 821 ASN A 840 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 470 ASN B 646 ASN B 821 ASN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C 470 ASN C 595 ASN C 646 ASN C 821 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23199 Z= 0.160 Angle : 0.606 10.873 31554 Z= 0.324 Chirality : 0.041 0.192 3570 Planarity : 0.004 0.060 4047 Dihedral : 5.230 27.805 3099 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.68 % Favored : 91.68 % Rotamer: Outliers : 0.19 % Allowed : 1.09 % Favored : 98.72 % 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: -0.75 (0.16), residues: 2826 helix: 1.52 (0.21), residues: 663 sheet: -0.59 (0.20), residues: 573 loop : -1.39 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 444 HIS 0.006 0.001 HIS C1129 PHE 0.022 0.001 PHE C 589 TYR 0.030 0.001 TYR A 266 ARG 0.004 0.000 ARG C 396 *********************** 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 356 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 351 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.7374 (mm) cc_final: 0.7079 (mt) REVERT: A 18 PHE cc_start: 0.3408 (t80) cc_final: 0.2883 (t80) REVERT: A 415 LYS cc_start: 0.5979 (mttt) cc_final: 0.5639 (mtmt) REVERT: A 439 PHE cc_start: 0.3924 (m-80) cc_final: 0.3610 (m-80) REVERT: A 649 TYR cc_start: 0.7871 (m-80) cc_final: 0.7619 (m-80) REVERT: B 15 ILE cc_start: 0.7329 (mm) cc_final: 0.7087 (mt) REVERT: B 289 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7610 (mm-30) REVERT: B 415 LYS cc_start: 0.5822 (mtpt) cc_final: 0.5551 (mttt) REVERT: B 1023 ASN cc_start: 0.6638 (p0) cc_final: 0.5907 (p0) REVERT: B 1079 ASN cc_start: 0.7937 (t0) cc_final: 0.7565 (t0) REVERT: C 77 LEU cc_start: 0.8892 (tp) cc_final: 0.8669 (tt) REVERT: C 829 LEU cc_start: 0.8469 (mt) cc_final: 0.8095 (mm) REVERT: C 1023 ASN cc_start: 0.6474 (p0) cc_final: 0.5800 (p0) REVERT: C 1111 ASN cc_start: 0.8715 (m-40) cc_final: 0.8493 (m110) outliers start: 5 outliers final: 0 residues processed: 356 average time/residue: 0.2828 time to fit residues: 168.1099 Evaluate side-chains 252 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.532 ------------------------------------------------------------------------------- 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: 4.9990 chunk 157 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 232 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 274 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 646 ASN A 821 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 269 ASN B 402 GLN B 470 ASN B 646 ASN B 821 ASN C 470 ASN C 646 ASN C 821 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 23199 Z= 0.358 Angle : 0.733 14.546 31554 Z= 0.391 Chirality : 0.045 0.263 3570 Planarity : 0.005 0.060 4047 Dihedral : 5.551 31.779 3099 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.60 % Allowed : 9.62 % Favored : 89.77 % Rotamer: Outliers : 0.19 % Allowed : 1.47 % Favored : 98.33 % 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: -1.09 (0.15), residues: 2826 helix: 1.06 (0.21), residues: 681 sheet: -0.67 (0.21), residues: 513 loop : -1.58 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 444 HIS 0.008 0.002 HIS C1145 PHE 0.019 0.002 PHE B 270 TYR 0.035 0.002 TYR C 649 ARG 0.004 0.001 ARG B 932 *********************** 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 314 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 309 time to evaluate : 2.626 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: B 415 LYS cc_start: 0.6203 (mtpt) cc_final: 0.5769 (mttt) REVERT: B 1023 ASN cc_start: 0.6619 (p0) cc_final: 0.5891 (p0) REVERT: B 1079 ASN cc_start: 0.7920 (t0) cc_final: 0.7591 (t0) REVERT: C 649 TYR cc_start: 0.7803 (m-80) cc_final: 0.7433 (m-10) REVERT: C 1023 ASN cc_start: 0.6478 (p0) cc_final: 0.5994 (p0) outliers start: 5 outliers final: 0 residues processed: 314 average time/residue: 0.2973 time to fit residues: 153.3275 Evaluate side-chains 224 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.595 ------------------------------------------------------------------------------- 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: 2.9990 chunk 109 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 269 ASN B 470 ASN B 646 ASN B 821 ASN B 859 ASN C 152 GLN C 470 ASN C 646 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5296 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= 0.212 Angle : 0.650 13.164 31554 Z= 0.345 Chirality : 0.042 0.278 3570 Planarity : 0.005 0.064 4047 Dihedral : 5.368 28.862 3099 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.60 % Favored : 90.80 % Rotamer: Outliers : 0.16 % Allowed : 0.62 % Favored : 99.22 % 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: -1.06 (0.15), residues: 2826 helix: 1.28 (0.21), residues: 681 sheet: -0.90 (0.20), residues: 561 loop : -1.58 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 444 HIS 0.005 0.001 HIS C1145 PHE 0.022 0.001 PHE C 589 TYR 0.026 0.002 TYR A 266 ARG 0.010 0.001 ARG A 75 *********************** 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 315 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 311 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 PHE cc_start: 0.4240 (m-80) cc_final: 0.4016 (m-80) REVERT: B 415 LYS cc_start: 0.6002 (mtpt) cc_final: 0.5628 (mttt) REVERT: B 1023 ASN cc_start: 0.6669 (p0) cc_final: 0.5907 (p0) REVERT: B 1079 ASN cc_start: 0.7900 (t0) cc_final: 0.7591 (t0) REVERT: C 576 SER cc_start: 0.7655 (t) cc_final: 0.7403 (m) REVERT: C 649 TYR cc_start: 0.7658 (m-80) cc_final: 0.7313 (m-10) REVERT: C 1023 ASN cc_start: 0.6429 (p0) cc_final: 0.6017 (p0) outliers start: 4 outliers final: 1 residues processed: 315 average time/residue: 0.2818 time to fit residues: 147.2541 Evaluate side-chains 230 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 2.329 ------------------------------------------------------------------------------- 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: 1.9990 chunk 240 optimal weight: 7.9990 chunk 255 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN B 821 ASN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 646 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 23199 Z= 0.324 Angle : 0.721 16.065 31554 Z= 0.382 Chirality : 0.045 0.384 3570 Planarity : 0.005 0.059 4047 Dihedral : 5.491 29.264 3099 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.60 % Allowed : 10.23 % Favored : 89.17 % Rotamer: Outliers : 0.12 % Allowed : 0.50 % Favored : 99.38 % 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: -1.24 (0.15), residues: 2826 helix: 1.15 (0.21), residues: 681 sheet: -0.87 (0.21), residues: 549 loop : -1.77 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 444 HIS 0.008 0.002 HIS C1145 PHE 0.030 0.002 PHE B 18 TYR 0.023 0.002 TYR A 266 ARG 0.013 0.001 ARG A 396 *********************** 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 304 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 301 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 PHE cc_start: 0.4386 (m-80) cc_final: 0.4119 (m-80) REVERT: B 415 LYS cc_start: 0.6186 (mtpt) cc_final: 0.5900 (mttt) REVERT: B 1023 ASN cc_start: 0.6686 (p0) cc_final: 0.5919 (p0) REVERT: B 1079 ASN cc_start: 0.7915 (t0) cc_final: 0.7646 (t0) REVERT: C 576 SER cc_start: 0.7787 (t) cc_final: 0.7478 (m) REVERT: C 649 TYR cc_start: 0.7813 (m-80) cc_final: 0.7403 (m-10) outliers start: 3 outliers final: 1 residues processed: 304 average time/residue: 0.2872 time to fit residues: 144.7331 Evaluate side-chains 221 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 2.449 ------------------------------------------------------------------------------- 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: 8.9990 chunk 128 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 chunk 283 optimal weight: 3.9990 chunk 261 optimal weight: 0.0870 chunk 226 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 591 ASN A 646 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1045 GLN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN C 470 ASN C 646 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23199 Z= 0.179 Angle : 0.662 16.935 31554 Z= 0.346 Chirality : 0.042 0.311 3570 Planarity : 0.005 0.063 4047 Dihedral : 5.249 27.738 3099 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.85 % Favored : 90.59 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % 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: -1.08 (0.16), residues: 2826 helix: 1.38 (0.21), residues: 693 sheet: -0.79 (0.21), residues: 549 loop : -1.72 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 257 HIS 0.004 0.001 HIS C1129 PHE 0.022 0.001 PHE B 589 TYR 0.024 0.002 TYR A 266 ARG 0.009 0.001 ARG A 396 ********************** 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 308 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 306 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ARG cc_start: 0.7715 (ttm110) cc_final: 0.7496 (ttm110) REVERT: A 415 LYS cc_start: 0.5948 (mtmt) cc_final: 0.5728 (mtmt) REVERT: A 439 PHE cc_start: 0.4234 (m-80) cc_final: 0.3975 (m-80) REVERT: A 649 TYR cc_start: 0.8009 (m-80) cc_final: 0.7734 (m-80) REVERT: B 15 ILE cc_start: 0.7889 (mm) cc_final: 0.7616 (mt) REVERT: B 415 LYS cc_start: 0.6084 (mtpt) cc_final: 0.5768 (mttt) REVERT: B 1023 ASN cc_start: 0.6731 (p0) cc_final: 0.5906 (p0) REVERT: B 1079 ASN cc_start: 0.7951 (t0) cc_final: 0.7612 (t0) REVERT: C 176 ILE cc_start: 0.7135 (tp) cc_final: 0.6927 (tp) REVERT: C 576 SER cc_start: 0.7676 (t) cc_final: 0.7397 (m) REVERT: C 971 TRP cc_start: 0.2379 (m100) cc_final: 0.1117 (m100) outliers start: 2 outliers final: 0 residues processed: 308 average time/residue: 0.2906 time to fit residues: 148.4248 Evaluate side-chains 228 residues out of total 2580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.513 ------------------------------------------------------------------------------- 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: 2.9990 chunk 208 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 94 optimal weight: 0.0000 chunk 232 optimal weight: 6.9990 chunk 28 optimal weight: 0.0980 chunk 41 optimal weight: 0.4980 chunk 198 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 591 ASN 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 859 ASN C 160 HIS C 470 ASN C 646 ASN C1036 ASN ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.108372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.094682 restraints weight = 56477.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.096901 restraints weight = 33834.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098491 restraints weight = 23011.555| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23199 Z= 0.166 Angle : 0.656 15.530 31554 Z= 0.341 Chirality : 0.042 0.264 3570 Planarity : 0.005 0.064 4047 Dihedral : 5.071 28.613 3099 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.67 % Favored : 90.76 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % 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: -1.15 (0.16), residues: 2826 helix: 1.29 (0.21), residues: 714 sheet: -0.73 (0.21), residues: 549 loop : -1.83 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 174 HIS 0.010 0.001 HIS B 175 PHE 0.024 0.001 PHE C 589 TYR 0.034 0.001 TYR C 649 ARG 0.008 0.001 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4185.16 seconds wall clock time: 77 minutes 17.23 seconds (4637.23 seconds total)