Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 16:53:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/08_2023/7vqo_32091.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/08_2023/7vqo_32091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/08_2023/7vqo_32091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/08_2023/7vqo_32091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/08_2023/7vqo_32091.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/08_2023/7vqo_32091.pdb" } resolution = 2.19 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= 0.052 sd= 2.444 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 156 5.16 5 C 24156 2.51 5 N 6664 2.21 5 O 7660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ASP 127": "OD1" <-> "OD2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 191": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 470": "OD1" <-> "OD2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A GLU 506": "OE1" <-> "OE2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ASP 516": "OD1" <-> "OD2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ASP 615": "OD1" <-> "OD2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ASP 635": "OD1" <-> "OD2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "A ASP 807": "OD1" <-> "OD2" Residue "A GLU 822": "OE1" <-> "OE2" Residue "A GLU 829": "OE1" <-> "OE2" Residue "A ASP 835": "OD1" <-> "OD2" Residue "A GLU 838": "OE1" <-> "OE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 850": "OD1" <-> "OD2" Residue "A ARG 852": "NH1" <-> "NH2" Residue "A GLU 855": "OE1" <-> "OE2" Residue "A TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A ARG 886": "NH1" <-> "NH2" Residue "A TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 969": "OD1" <-> "OD2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A ASP 993": "OD1" <-> "OD2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A ASP 1001": "OD1" <-> "OD2" Residue "A ASP 1023": "OD1" <-> "OD2" Residue "A ASP 1050": "OD1" <-> "OD2" Residue "A ASP 1051": "OD1" <-> "OD2" Residue "A GLU 1053": "OE1" <-> "OE2" Residue "A GLU 1058": "OE1" <-> "OE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1065": "OE1" <-> "OE2" Residue "A TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1075": "NH1" <-> "NH2" Residue "A GLU 1123": "OE1" <-> "OE2" Residue "A ARG 1128": "NH1" <-> "NH2" Residue "A ASP 1133": "OD1" <-> "OD2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A ARG 1150": "NH1" <-> "NH2" Residue "A PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1169": "OD1" <-> "OD2" Residue "A TYR 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1203": "OE1" <-> "OE2" Residue "A ARG 1211": "NH1" <-> "NH2" Residue "A ARG 1215": "NH1" <-> "NH2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ASP 1240": "OD1" <-> "OD2" Residue "B PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ASP 127": "OD1" <-> "OD2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ASP 162": "OD1" <-> "OD2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 191": "OD1" <-> "OD2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ARG 348": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 436": "NH1" <-> "NH2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 470": "OD1" <-> "OD2" Residue "B ARG 473": "NH1" <-> "NH2" Residue "B ASP 482": "OD1" <-> "OD2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B GLU 506": "OE1" <-> "OE2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B ASP 516": "OD1" <-> "OD2" Residue "B ARG 523": "NH1" <-> "NH2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B ARG 572": "NH1" <-> "NH2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B ASP 615": "OD1" <-> "OD2" Residue "B ARG 627": "NH1" <-> "NH2" Residue "B ASP 635": "OD1" <-> "OD2" Residue "B ARG 675": "NH1" <-> "NH2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 711": "NH1" <-> "NH2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 760": "OD1" <-> "OD2" Residue "B TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 779": "NH1" <-> "NH2" Residue "B ASP 807": "OD1" <-> "OD2" Residue "B GLU 822": "OE1" <-> "OE2" Residue "B GLU 829": "OE1" <-> "OE2" Residue "B ASP 835": "OD1" <-> "OD2" Residue "B GLU 838": "OE1" <-> "OE2" Residue "B GLU 846": "OE1" <-> "OE2" Residue "B PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 850": "OD1" <-> "OD2" Residue "B ARG 852": "NH1" <-> "NH2" Residue "B GLU 855": "OE1" <-> "OE2" Residue "B TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 881": "OE1" <-> "OE2" Residue "B ARG 886": "NH1" <-> "NH2" Residue "B TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 902": "OD1" <-> "OD2" Residue "B TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 969": "OD1" <-> "OD2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B ASP 993": "OD1" <-> "OD2" Residue "B ARG 997": "NH1" <-> "NH2" Residue "B ASP 1001": "OD1" <-> "OD2" Residue "B ASP 1023": "OD1" <-> "OD2" Residue "B ASP 1050": "OD1" <-> "OD2" Residue "B ASP 1051": "OD1" <-> "OD2" Residue "B GLU 1053": "OE1" <-> "OE2" Residue "B GLU 1058": "OE1" <-> "OE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1065": "OE1" <-> "OE2" Residue "B TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1075": "NH1" <-> "NH2" Residue "B GLU 1123": "OE1" <-> "OE2" Residue "B ARG 1128": "NH1" <-> "NH2" Residue "B ASP 1133": "OD1" <-> "OD2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "B ARG 1150": "NH1" <-> "NH2" Residue "B PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1169": "OD1" <-> "OD2" Residue "B TYR 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1203": "OE1" <-> "OE2" Residue "B ARG 1211": "NH1" <-> "NH2" Residue "B ARG 1215": "NH1" <-> "NH2" Residue "B ARG 1218": "NH1" <-> "NH2" Residue "B ASP 1240": "OD1" <-> "OD2" Residue "C PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ASP 207": "OD1" <-> "OD2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C ARG 348": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 436": "NH1" <-> "NH2" Residue "C TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C ARG 473": "NH1" <-> "NH2" Residue "C ASP 482": "OD1" <-> "OD2" Residue "C ASP 484": "OD1" <-> "OD2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C ASP 516": "OD1" <-> "OD2" Residue "C ARG 523": "NH1" <-> "NH2" Residue "C ARG 539": "NH1" <-> "NH2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C ARG 572": "NH1" <-> "NH2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "C GLU 581": "OE1" <-> "OE2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C ASP 615": "OD1" <-> "OD2" Residue "C ARG 627": "NH1" <-> "NH2" Residue "C ASP 635": "OD1" <-> "OD2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C GLU 677": "OE1" <-> "OE2" Residue "C GLU 683": "OE1" <-> "OE2" Residue "C GLU 685": "OE1" <-> "OE2" Residue "C PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 711": "NH1" <-> "NH2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 760": "OD1" <-> "OD2" Residue "C TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 779": "NH1" <-> "NH2" Residue "C ASP 807": "OD1" <-> "OD2" Residue "C GLU 822": "OE1" <-> "OE2" Residue "C GLU 829": "OE1" <-> "OE2" Residue "C ASP 835": "OD1" <-> "OD2" Residue "C GLU 838": "OE1" <-> "OE2" Residue "C GLU 846": "OE1" <-> "OE2" Residue "C PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 850": "OD1" <-> "OD2" Residue "C ARG 852": "NH1" <-> "NH2" Residue "C GLU 855": "OE1" <-> "OE2" Residue "C TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 881": "OE1" <-> "OE2" Residue "C ARG 886": "NH1" <-> "NH2" Residue "C TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 902": "OD1" <-> "OD2" Residue "C TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 969": "OD1" <-> "OD2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C ASP 993": "OD1" <-> "OD2" Residue "C ARG 997": "NH1" <-> "NH2" Residue "C ASP 1001": "OD1" <-> "OD2" Residue "C ASP 1023": "OD1" <-> "OD2" Residue "C ASP 1050": "OD1" <-> "OD2" Residue "C ASP 1051": "OD1" <-> "OD2" Residue "C GLU 1053": "OE1" <-> "OE2" Residue "C GLU 1058": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1065": "OE1" <-> "OE2" Residue "C TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1075": "NH1" <-> "NH2" Residue "C GLU 1123": "OE1" <-> "OE2" Residue "C ARG 1128": "NH1" <-> "NH2" Residue "C ASP 1133": "OD1" <-> "OD2" Residue "C GLU 1144": "OE1" <-> "OE2" Residue "C ARG 1150": "NH1" <-> "NH2" Residue "C PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1169": "OD1" <-> "OD2" Residue "C TYR 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1203": "OE1" <-> "OE2" Residue "C ARG 1211": "NH1" <-> "NH2" Residue "C ARG 1215": "NH1" <-> "NH2" Residue "C ARG 1218": "NH1" <-> "NH2" Residue "C ASP 1240": "OD1" <-> "OD2" Residue "D PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 19": "NH1" <-> "NH2" Residue "D TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ASP 127": "OD1" <-> "OD2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ASP 162": "OD1" <-> "OD2" Residue "D GLU 165": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 191": "OD1" <-> "OD2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D ASP 207": "OD1" <-> "OD2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 230": "OD1" <-> "OD2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 272": "OD1" <-> "OD2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D ARG 348": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 367": "OE1" <-> "OE2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 436": "NH1" <-> "NH2" Residue "D TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D ARG 473": "NH1" <-> "NH2" Residue "D ASP 482": "OD1" <-> "OD2" Residue "D ASP 484": "OD1" <-> "OD2" Residue "D GLU 506": "OE1" <-> "OE2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "D ASP 516": "OD1" <-> "OD2" Residue "D ARG 523": "NH1" <-> "NH2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D ARG 572": "NH1" <-> "NH2" Residue "D ARG 578": "NH1" <-> "NH2" Residue "D GLU 581": "OE1" <-> "OE2" Residue "D GLU 599": "OE1" <-> "OE2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "D ASP 615": "OD1" <-> "OD2" Residue "D ARG 627": "NH1" <-> "NH2" Residue "D ASP 635": "OD1" <-> "OD2" Residue "D ARG 675": "NH1" <-> "NH2" Residue "D GLU 677": "OE1" <-> "OE2" Residue "D GLU 683": "OE1" <-> "OE2" Residue "D GLU 685": "OE1" <-> "OE2" Residue "D PHE 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 711": "NH1" <-> "NH2" Residue "D PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 760": "OD1" <-> "OD2" Residue "D TYR 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 779": "NH1" <-> "NH2" Residue "D ASP 807": "OD1" <-> "OD2" Residue "D GLU 822": "OE1" <-> "OE2" Residue "D GLU 829": "OE1" <-> "OE2" Residue "D ASP 835": "OD1" <-> "OD2" Residue "D GLU 838": "OE1" <-> "OE2" Residue "D GLU 846": "OE1" <-> "OE2" Residue "D PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 850": "OD1" <-> "OD2" Residue "D ARG 852": "NH1" <-> "NH2" Residue "D GLU 855": "OE1" <-> "OE2" Residue "D TYR 858": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 871": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 881": "OE1" <-> "OE2" Residue "D ARG 886": "NH1" <-> "NH2" Residue "D TYR 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 969": "OD1" <-> "OD2" Residue "D ASP 985": "OD1" <-> "OD2" Residue "D ASP 993": "OD1" <-> "OD2" Residue "D ARG 997": "NH1" <-> "NH2" Residue "D ASP 1001": "OD1" <-> "OD2" Residue "D ASP 1023": "OD1" <-> "OD2" Residue "D ASP 1050": "OD1" <-> "OD2" Residue "D ASP 1051": "OD1" <-> "OD2" Residue "D GLU 1053": "OE1" <-> "OE2" Residue "D GLU 1058": "OE1" <-> "OE2" Residue "D PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1065": "OE1" <-> "OE2" Residue "D TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1075": "NH1" <-> "NH2" Residue "D GLU 1123": "OE1" <-> "OE2" Residue "D ARG 1128": "NH1" <-> "NH2" Residue "D ASP 1133": "OD1" <-> "OD2" Residue "D GLU 1144": "OE1" <-> "OE2" Residue "D ARG 1150": "NH1" <-> "NH2" Residue "D PHE 1165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1169": "OD1" <-> "OD2" Residue "D TYR 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1203": "OE1" <-> "OE2" Residue "D ARG 1211": "NH1" <-> "NH2" Residue "D ARG 1215": "NH1" <-> "NH2" Residue "D ARG 1218": "NH1" <-> "NH2" Residue "D ASP 1240": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 38640 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9487 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 66, 'TRANS': 1113} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9487 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 66, 'TRANS': 1113} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9487 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 66, 'TRANS': 1113} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 9487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9487 Classifications: {'peptide': 1180} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 66, 'TRANS': 1113} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 173 Classifications: {'water': 173} Link IDs: {None: 172} Chain: "D" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Time building chain proxies: 18.55, per 1000 atoms: 0.48 Number of scatterers: 38640 At special positions: 0 Unit cell: (167.44, 142.48, 136.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 156 16.00 O 7660 8.00 N 6664 7.00 C 24156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 14.59 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 292 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 614 " pdb=" ZN B1701 " pdb="ZN ZN B1701 " - pdb=" NE2 HIS B 292 " pdb="ZN ZN B1701 " - pdb=" NE2 HIS B 614 " pdb=" ZN C1701 " pdb="ZN ZN C1701 " - pdb=" NE2 HIS C 292 " pdb="ZN ZN C1701 " - pdb=" NE2 HIS C 614 " pdb=" ZN D1701 " pdb="ZN ZN D1701 " - pdb=" NE2 HIS D 292 " pdb="ZN ZN D1701 " - pdb=" NE2 HIS D 614 " 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8800 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 56 sheets defined 28.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.48 Creating SS restraints... Processing helix chain 'A' and resid 28 through 37 removed outlier: 3.577A pdb=" N ILE A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.738A pdb=" N MET A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 Processing helix chain 'A' and resid 113 through 117 removed outlier: 3.816A pdb=" N GLN A 117 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 227 Processing helix chain 'A' and resid 231 through 247 removed outlier: 4.068A pdb=" N HIS A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 removed outlier: 4.062A pdb=" N LYS A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N TYR A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 removed outlier: 3.923A pdb=" N SER A 279 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 322 removed outlier: 3.823A pdb=" N VAL A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 342 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 374 through 393 Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 427 through 432 Processing helix chain 'A' and resid 467 through 477 removed outlier: 4.024A pdb=" N MET A 475 " --> pdb=" O VAL A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 518 Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.585A pdb=" N ARG A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 544 Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.549A pdb=" N TYR A 560 " --> pdb=" O ARG A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 591 removed outlier: 3.506A pdb=" N LYS A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 612 Processing helix chain 'A' and resid 622 through 651 Processing helix chain 'A' and resid 772 through 778 Processing helix chain 'A' and resid 873 through 878 Processing helix chain 'A' and resid 948 through 960 removed outlier: 3.820A pdb=" N ILE A 952 " --> pdb=" O SER A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'B' and resid 28 through 37 removed outlier: 3.579A pdb=" N ILE B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.738A pdb=" N MET B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 113 through 117 removed outlier: 3.816A pdb=" N GLN B 117 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 227 Processing helix chain 'B' and resid 231 through 247 removed outlier: 4.068A pdb=" N HIS B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 268 removed outlier: 4.062A pdb=" N LYS B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 279 removed outlier: 3.924A pdb=" N SER B 279 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 322 removed outlier: 3.824A pdb=" N VAL B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 374 through 393 Processing helix chain 'B' and resid 411 through 419 Processing helix chain 'B' and resid 427 through 432 Processing helix chain 'B' and resid 467 through 477 removed outlier: 4.024A pdb=" N MET B 475 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 518 Processing helix chain 'B' and resid 529 through 539 removed outlier: 3.586A pdb=" N ARG B 539 " --> pdb=" O ASP B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 556 through 561 removed outlier: 3.549A pdb=" N TYR B 560 " --> pdb=" O ARG B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 591 removed outlier: 3.505A pdb=" N LYS B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 612 Processing helix chain 'B' and resid 622 through 651 Processing helix chain 'B' and resid 772 through 778 Processing helix chain 'B' and resid 873 through 878 Processing helix chain 'B' and resid 948 through 960 removed outlier: 3.820A pdb=" N ILE B 952 " --> pdb=" O SER B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 976 Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.578A pdb=" N ILE C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 49 through 54 removed outlier: 3.738A pdb=" N MET C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.816A pdb=" N GLN C 117 " --> pdb=" O GLU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 227 Processing helix chain 'C' and resid 231 through 247 removed outlier: 4.068A pdb=" N HIS C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 268 removed outlier: 4.062A pdb=" N LYS C 257 " --> pdb=" O ARG C 253 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 279 removed outlier: 3.923A pdb=" N SER C 279 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 322 removed outlier: 3.823A pdb=" N VAL C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER C 314 " --> pdb=" O ARG C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 342 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 374 through 393 Processing helix chain 'C' and resid 411 through 419 Processing helix chain 'C' and resid 427 through 432 Processing helix chain 'C' and resid 467 through 477 removed outlier: 4.024A pdb=" N MET C 475 " --> pdb=" O VAL C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 518 Processing helix chain 'C' and resid 529 through 539 removed outlier: 3.585A pdb=" N ARG C 539 " --> pdb=" O ASP C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 544 Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.549A pdb=" N TYR C 560 " --> pdb=" O ARG C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 591 removed outlier: 3.505A pdb=" N LYS C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 612 Processing helix chain 'C' and resid 622 through 651 Processing helix chain 'C' and resid 772 through 778 Processing helix chain 'C' and resid 873 through 878 Processing helix chain 'C' and resid 948 through 960 removed outlier: 3.820A pdb=" N ILE C 952 " --> pdb=" O SER C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 976 Processing helix chain 'D' and resid 28 through 37 removed outlier: 3.579A pdb=" N ILE D 36 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'D' and resid 49 through 54 removed outlier: 3.738A pdb=" N MET D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 Processing helix chain 'D' and resid 113 through 117 removed outlier: 3.816A pdb=" N GLN D 117 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 227 Processing helix chain 'D' and resid 231 through 247 removed outlier: 4.069A pdb=" N HIS D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 268 removed outlier: 4.062A pdb=" N LYS D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR D 266 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 279 removed outlier: 3.924A pdb=" N SER D 279 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 322 removed outlier: 3.824A pdb=" N VAL D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER D 314 " --> pdb=" O ARG D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 342 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 374 through 393 Processing helix chain 'D' and resid 411 through 419 Processing helix chain 'D' and resid 427 through 432 Processing helix chain 'D' and resid 467 through 477 removed outlier: 4.024A pdb=" N MET D 475 " --> pdb=" O VAL D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 518 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.586A pdb=" N ARG D 539 " --> pdb=" O ASP D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 544 Processing helix chain 'D' and resid 556 through 561 removed outlier: 3.550A pdb=" N TYR D 560 " --> pdb=" O ARG D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 591 removed outlier: 3.505A pdb=" N LYS D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 622 through 651 Processing helix chain 'D' and resid 772 through 778 Processing helix chain 'D' and resid 873 through 878 Processing helix chain 'D' and resid 948 through 960 removed outlier: 3.820A pdb=" N ILE D 952 " --> pdb=" O SER D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 971 through 976 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 3.643A pdb=" N PHE A 196 " --> pdb=" O PHE A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 removed outlier: 4.161A pdb=" N LYS A 200 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.636A pdb=" N LEU A 67 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 131 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY A 132 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY A 144 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 134 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL A 328 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY A 289 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR A 286 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE A 491 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE A 288 " --> pdb=" O PHE A 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL A 328 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY A 289 " --> pdb=" O VAL A 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 399 through 401 removed outlier: 4.658A pdb=" N VAL A 545 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 675 through 679 removed outlier: 3.614A pdb=" N LYS A 697 " --> pdb=" O HIS A 690 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU A 698 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 665 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS A 963 " --> pdb=" O LEU A 668 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 708 through 711 removed outlier: 3.586A pdb=" N ARG A 744 " --> pdb=" O ASP A 739 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 780 through 781 removed outlier: 6.789A pdb=" N LYS A 841 " --> pdb=" O ARG A 920 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG A 920 " --> pdb=" O LYS A 841 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 843 " --> pdb=" O LEU A 918 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY A 906 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 788 through 793 removed outlier: 6.427A pdb=" N SER A 798 " --> pdb=" O HIS A 790 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN A 792 " --> pdb=" O ARG A 796 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER A 809 " --> pdb=" O VAL A 805 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TRP A 887 " --> pdb=" O GLU A 859 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER A 891 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 855 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 863 " --> pdb=" O THR A 860 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 980 through 982 Processing sheet with id=AB3, first strand: chain 'A' and resid 990 through 997 removed outlier: 5.177A pdb=" N LEU A 992 " --> pdb=" O TYR A1022 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR A1022 " --> pdb=" O LEU A 992 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER A1073 " --> pdb=" O LYS A1044 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS A1044 " --> pdb=" O SER A1073 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG A1075 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A1042 " --> pdb=" O ARG A1075 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1077 " --> pdb=" O LYS A1040 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL A1042 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL A1054 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYS A1044 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1125 through 1129 removed outlier: 6.896A pdb=" N VAL A1148 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A1129 " --> pdb=" O THR A1146 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR A1146 " --> pdb=" O ASP A1129 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1135 through 1137 removed outlier: 6.184A pdb=" N THR A1135 " --> pdb=" O VAL A1242 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N HIS A1235 " --> pdb=" O LEU A1225 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU A1225 " --> pdb=" O HIS A1235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 55 through 59 removed outlier: 3.642A pdb=" N PHE B 196 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 59 removed outlier: 4.160A pdb=" N LYS B 200 " --> pdb=" O ASP B 127 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.635A pdb=" N LEU B 67 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU B 131 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY B 132 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY B 144 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 134 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL B 328 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY B 289 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR B 286 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE B 491 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE B 288 " --> pdb=" O PHE B 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL B 328 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY B 289 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 399 through 401 removed outlier: 4.658A pdb=" N VAL B 545 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 675 through 679 removed outlier: 3.613A pdb=" N LYS B 697 " --> pdb=" O HIS B 690 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU B 698 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR B 665 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS B 963 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 708 through 711 removed outlier: 3.586A pdb=" N ARG B 744 " --> pdb=" O ASP B 739 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 780 through 781 removed outlier: 6.788A pdb=" N LYS B 841 " --> pdb=" O ARG B 920 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG B 920 " --> pdb=" O LYS B 841 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 843 " --> pdb=" O LEU B 918 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY B 906 " --> pdb=" O SER B 917 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 788 through 793 removed outlier: 6.428A pdb=" N SER B 798 " --> pdb=" O HIS B 790 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN B 792 " --> pdb=" O ARG B 796 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG B 796 " --> pdb=" O ASN B 792 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER B 809 " --> pdb=" O VAL B 805 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TRP B 887 " --> pdb=" O GLU B 859 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER B 891 " --> pdb=" O GLU B 855 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU B 855 " --> pdb=" O SER B 891 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 863 " --> pdb=" O THR B 860 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 980 through 982 Processing sheet with id=AC8, first strand: chain 'B' and resid 990 through 997 removed outlier: 5.177A pdb=" N LEU B 992 " --> pdb=" O TYR B1022 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR B1022 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER B1073 " --> pdb=" O LYS B1044 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS B1044 " --> pdb=" O SER B1073 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARG B1075 " --> pdb=" O VAL B1042 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL B1042 " --> pdb=" O ARG B1075 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B1077 " --> pdb=" O LYS B1040 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL B1042 " --> pdb=" O VAL B1054 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL B1054 " --> pdb=" O VAL B1042 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS B1044 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1125 through 1129 removed outlier: 6.894A pdb=" N VAL B1148 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP B1129 " --> pdb=" O THR B1146 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR B1146 " --> pdb=" O ASP B1129 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1135 through 1137 removed outlier: 6.184A pdb=" N THR B1135 " --> pdb=" O VAL B1242 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N HIS B1235 " --> pdb=" O LEU B1225 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU B1225 " --> pdb=" O HIS B1235 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 55 through 59 removed outlier: 3.642A pdb=" N PHE C 196 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 55 through 59 removed outlier: 4.161A pdb=" N LYS C 200 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.635A pdb=" N LEU C 67 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU C 131 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY C 132 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY C 144 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 134 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL C 328 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY C 289 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N TYR C 286 " --> pdb=" O LEU C 489 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N PHE C 491 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE C 288 " --> pdb=" O PHE C 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL C 328 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY C 289 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 399 through 401 removed outlier: 4.658A pdb=" N VAL C 545 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 675 through 679 removed outlier: 3.613A pdb=" N LYS C 697 " --> pdb=" O HIS C 690 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU C 698 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR C 665 " --> pdb=" O LEU C 698 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS C 963 " --> pdb=" O LEU C 668 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 708 through 711 removed outlier: 3.586A pdb=" N ARG C 744 " --> pdb=" O ASP C 739 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 780 through 781 removed outlier: 6.788A pdb=" N LYS C 841 " --> pdb=" O ARG C 920 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG C 920 " --> pdb=" O LYS C 841 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 843 " --> pdb=" O LEU C 918 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY C 906 " --> pdb=" O SER C 917 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 788 through 793 removed outlier: 6.427A pdb=" N SER C 798 " --> pdb=" O HIS C 790 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN C 792 " --> pdb=" O ARG C 796 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG C 796 " --> pdb=" O ASN C 792 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER C 809 " --> pdb=" O VAL C 805 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TRP C 887 " --> pdb=" O GLU C 859 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER C 891 " --> pdb=" O GLU C 855 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU C 855 " --> pdb=" O SER C 891 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY C 863 " --> pdb=" O THR C 860 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 980 through 982 Processing sheet with id=AE4, first strand: chain 'C' and resid 990 through 997 removed outlier: 5.177A pdb=" N LEU C 992 " --> pdb=" O TYR C1022 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N TYR C1022 " --> pdb=" O LEU C 992 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER C1073 " --> pdb=" O LYS C1044 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS C1044 " --> pdb=" O SER C1073 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG C1075 " --> pdb=" O VAL C1042 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL C1042 " --> pdb=" O ARG C1075 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C1077 " --> pdb=" O LYS C1040 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL C1042 " --> pdb=" O VAL C1054 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL C1054 " --> pdb=" O VAL C1042 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS C1044 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1125 through 1129 removed outlier: 6.895A pdb=" N VAL C1148 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP C1129 " --> pdb=" O THR C1146 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR C1146 " --> pdb=" O ASP C1129 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1135 through 1137 removed outlier: 6.184A pdb=" N THR C1135 " --> pdb=" O VAL C1242 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N HIS C1235 " --> pdb=" O LEU C1225 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU C1225 " --> pdb=" O HIS C1235 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 55 through 59 removed outlier: 3.642A pdb=" N PHE D 196 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 55 through 59 removed outlier: 4.160A pdb=" N LYS D 200 " --> pdb=" O ASP D 127 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.635A pdb=" N LEU D 67 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU D 131 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY D 132 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY D 144 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 134 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL D 328 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY D 289 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TYR D 286 " --> pdb=" O LEU D 489 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N PHE D 491 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE D 288 " --> pdb=" O PHE D 491 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 327 through 328 removed outlier: 8.697A pdb=" N VAL D 328 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLY D 289 " --> pdb=" O VAL D 328 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 399 through 401 removed outlier: 4.658A pdb=" N VAL D 545 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 675 through 679 removed outlier: 3.613A pdb=" N LYS D 697 " --> pdb=" O HIS D 690 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU D 698 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR D 665 " --> pdb=" O LEU D 698 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS D 963 " --> pdb=" O LEU D 668 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 708 through 711 removed outlier: 3.587A pdb=" N ARG D 744 " --> pdb=" O ASP D 739 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 780 through 781 removed outlier: 6.789A pdb=" N LYS D 841 " --> pdb=" O ARG D 920 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG D 920 " --> pdb=" O LYS D 841 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 843 " --> pdb=" O LEU D 918 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLY D 906 " --> pdb=" O SER D 917 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 788 through 793 removed outlier: 6.427A pdb=" N SER D 798 " --> pdb=" O HIS D 790 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN D 792 " --> pdb=" O ARG D 796 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG D 796 " --> pdb=" O ASN D 792 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER D 809 " --> pdb=" O VAL D 805 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TRP D 887 " --> pdb=" O GLU D 859 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER D 891 " --> pdb=" O GLU D 855 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU D 855 " --> pdb=" O SER D 891 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 863 " --> pdb=" O THR D 860 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 980 through 982 Processing sheet with id=AF9, first strand: chain 'D' and resid 990 through 997 removed outlier: 5.177A pdb=" N LEU D 992 " --> pdb=" O TYR D1022 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR D1022 " --> pdb=" O LEU D 992 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER D1073 " --> pdb=" O LYS D1044 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS D1044 " --> pdb=" O SER D1073 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG D1075 " --> pdb=" O VAL D1042 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL D1042 " --> pdb=" O ARG D1075 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D1077 " --> pdb=" O LYS D1040 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL D1042 " --> pdb=" O VAL D1054 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL D1054 " --> pdb=" O VAL D1042 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS D1044 " --> pdb=" O LEU D1052 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 1125 through 1129 removed outlier: 6.894A pdb=" N VAL D1148 " --> pdb=" O VAL D1127 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP D1129 " --> pdb=" O THR D1146 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR D1146 " --> pdb=" O ASP D1129 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 1135 through 1137 removed outlier: 6.184A pdb=" N THR D1135 " --> pdb=" O VAL D1242 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N HIS D1235 " --> pdb=" O LEU D1225 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU D1225 " --> pdb=" O HIS D1235 " (cutoff:3.500A) 1576 hydrogen bonds defined for protein. 4368 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: 19.53 Time building geometry restraints manager: 15.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12472 1.34 - 1.46: 8737 1.46 - 1.58: 17551 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 39000 Sorted by residual: bond pdb=" CB LYS A 9 " pdb=" CG LYS A 9 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CB LYS C 9 " pdb=" CG LYS C 9 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" CB LYS D 9 " pdb=" CG LYS D 9 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" CB LYS B 9 " pdb=" CG LYS B 9 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" CB ASN B 722 " pdb=" CG ASN B 722 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.85e+00 ... (remaining 38995 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.14: 980 106.14 - 113.11: 21110 113.11 - 120.09: 13821 120.09 - 127.07: 16347 127.07 - 134.05: 718 Bond angle restraints: 52976 Sorted by residual: angle pdb=" N VAL D1004 " pdb=" CA VAL D1004 " pdb=" C VAL D1004 " ideal model delta sigma weight residual 113.20 105.94 7.26 9.60e-01 1.09e+00 5.72e+01 angle pdb=" N VAL C1004 " pdb=" CA VAL C1004 " pdb=" C VAL C1004 " ideal model delta sigma weight residual 113.20 105.96 7.24 9.60e-01 1.09e+00 5.68e+01 angle pdb=" N VAL B1004 " pdb=" CA VAL B1004 " pdb=" C VAL B1004 " ideal model delta sigma weight residual 113.20 105.97 7.23 9.60e-01 1.09e+00 5.67e+01 angle pdb=" N VAL A1004 " pdb=" CA VAL A1004 " pdb=" C VAL A1004 " ideal model delta sigma weight residual 113.20 105.98 7.22 9.60e-01 1.09e+00 5.65e+01 angle pdb=" CA LYS A 9 " pdb=" CB LYS A 9 " pdb=" CG LYS A 9 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 ... (remaining 52971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 19658 17.66 - 35.31: 2583 35.31 - 52.96: 630 52.96 - 70.62: 153 70.62 - 88.27: 64 Dihedral angle restraints: 23088 sinusoidal: 9428 harmonic: 13660 Sorted by residual: dihedral pdb=" CA SER A 682 " pdb=" C SER A 682 " pdb=" N GLU A 683 " pdb=" CA GLU A 683 " ideal model delta harmonic sigma weight residual 180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA SER D 682 " pdb=" C SER D 682 " pdb=" N GLU D 683 " pdb=" CA GLU D 683 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA SER B 682 " pdb=" C SER B 682 " pdb=" N GLU B 683 " pdb=" CA GLU B 683 " ideal model delta harmonic sigma weight residual -180.00 -152.80 -27.20 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 23085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3043 0.035 - 0.070: 1692 0.070 - 0.105: 665 0.105 - 0.140: 196 0.140 - 0.176: 24 Chirality restraints: 5620 Sorted by residual: chirality pdb=" CA THR A 662 " pdb=" N THR A 662 " pdb=" C THR A 662 " pdb=" CB THR A 662 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CA THR C 662 " pdb=" N THR C 662 " pdb=" C THR C 662 " pdb=" CB THR C 662 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.45e-01 chirality pdb=" CA THR D 662 " pdb=" N THR D 662 " pdb=" C THR D 662 " pdb=" CB THR D 662 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 5617 not shown) Planarity restraints: 6856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B1157 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO B1158 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B1158 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B1158 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A1157 " -0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO A1158 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C1157 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO C1158 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO C1158 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C1158 " 0.035 5.00e-02 4.00e+02 ... (remaining 6853 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 466 2.47 - 3.08: 26966 3.08 - 3.69: 59778 3.69 - 4.29: 93094 4.29 - 4.90: 156663 Nonbonded interactions: 336967 Sorted by model distance: nonbonded pdb=" OD2 ASP A 404 " pdb="ZN ZN A1701 " model vdw 1.865 2.230 nonbonded pdb=" OD2 ASP C 404 " pdb="ZN ZN C1701 " model vdw 1.865 2.230 nonbonded pdb=" OD2 ASP B 404 " pdb="ZN ZN B1701 " model vdw 1.866 2.230 nonbonded pdb=" OD2 ASP D 404 " pdb="ZN ZN D1701 " model vdw 1.866 2.230 nonbonded pdb=" OD1 ASP D 294 " pdb="ZN ZN D1701 " model vdw 1.867 2.230 ... (remaining 336962 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' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 10.230 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 104.190 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.008 0.049 39000 Z= 0.550 Angle : 0.749 8.288 52976 Z= 0.411 Chirality : 0.049 0.176 5620 Planarity : 0.004 0.064 6856 Dihedral : 17.417 88.275 14288 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer Outliers : 3.25 % 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: -1.44 (0.12), residues: 4696 helix: 0.91 (0.15), residues: 1176 sheet: -1.05 (0.15), residues: 1244 loop : -1.93 (0.12), residues: 2276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 675 time to evaluate : 4.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 100 residues processed: 783 average time/residue: 1.5500 time to fit residues: 1467.7840 Evaluate side-chains 746 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 646 time to evaluate : 4.492 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 91 residues processed: 9 average time/residue: 0.4704 time to fit residues: 13.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 0.6980 chunk 357 optimal weight: 0.5980 chunk 198 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 241 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 369 optimal weight: 0.9980 chunk 143 optimal weight: 0.3980 chunk 224 optimal weight: 0.7980 chunk 275 optimal weight: 1.9990 chunk 428 optimal weight: 0.9990 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN B1059 ASN C 754 ASN C 944 GLN D 754 ASN D1059 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 39000 Z= 0.181 Angle : 0.582 6.642 52976 Z= 0.307 Chirality : 0.043 0.162 5620 Planarity : 0.004 0.055 6856 Dihedral : 5.214 26.245 5140 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 5.55 % 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: -1.00 (0.12), residues: 4696 helix: 1.50 (0.16), residues: 1144 sheet: -0.85 (0.14), residues: 1232 loop : -1.70 (0.13), residues: 2320 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 738 time to evaluate : 3.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 227 outliers final: 113 residues processed: 894 average time/residue: 1.3622 time to fit residues: 1512.0673 Evaluate side-chains 775 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 662 time to evaluate : 4.772 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 77 residues processed: 36 average time/residue: 1.0289 time to fit residues: 55.3514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 0.1980 chunk 133 optimal weight: 0.9990 chunk 356 optimal weight: 4.9990 chunk 291 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 429 optimal weight: 4.9990 chunk 463 optimal weight: 0.0060 chunk 382 optimal weight: 5.9990 chunk 425 optimal weight: 0.1980 chunk 146 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 HIS A 754 ASN A1222 HIS ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 HIS B 754 ASN C 439 HIS C 669 ASN C 754 ASN D 439 HIS D 669 ASN D 754 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 39000 Z= 0.200 Angle : 0.572 9.222 52976 Z= 0.298 Chirality : 0.044 0.176 5620 Planarity : 0.004 0.050 6856 Dihedral : 5.004 24.008 5140 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer Outliers : 4.33 % 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: -0.86 (0.12), residues: 4696 helix: 1.73 (0.16), residues: 1116 sheet: -0.81 (0.14), residues: 1232 loop : -1.62 (0.13), residues: 2348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 702 time to evaluate : 4.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 177 outliers final: 121 residues processed: 824 average time/residue: 1.5023 time to fit residues: 1517.0558 Evaluate side-chains 778 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 657 time to evaluate : 4.379 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 80 residues processed: 41 average time/residue: 0.7842 time to fit residues: 51.3495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 0.6980 chunk 322 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 chunk 430 optimal weight: 2.9990 chunk 456 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 408 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 728 HIS A 754 ASN A1222 HIS ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 39000 Z= 0.302 Angle : 0.600 7.767 52976 Z= 0.314 Chirality : 0.045 0.165 5620 Planarity : 0.004 0.052 6856 Dihedral : 5.095 24.464 5140 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 4.74 % 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: -0.84 (0.12), residues: 4696 helix: 1.70 (0.16), residues: 1116 sheet: -0.72 (0.14), residues: 1204 loop : -1.60 (0.13), residues: 2376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 665 time to evaluate : 4.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 123 residues processed: 795 average time/residue: 1.4816 time to fit residues: 1441.9893 Evaluate side-chains 772 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 649 time to evaluate : 4.454 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 83 residues processed: 40 average time/residue: 0.9822 time to fit residues: 58.2825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 339 optimal weight: 0.9990 chunk 188 optimal weight: 0.0030 chunk 389 optimal weight: 0.9980 chunk 315 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 409 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 39000 Z= 0.240 Angle : 0.582 8.468 52976 Z= 0.304 Chirality : 0.044 0.172 5620 Planarity : 0.004 0.052 6856 Dihedral : 5.004 24.204 5140 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 4.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4696 helix: 1.74 (0.16), residues: 1116 sheet: -0.74 (0.14), residues: 1204 loop : -1.58 (0.13), residues: 2376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 678 time to evaluate : 4.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 187 outliers final: 142 residues processed: 815 average time/residue: 1.5031 time to fit residues: 1504.1661 Evaluate side-chains 792 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 650 time to evaluate : 4.685 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 98 residues processed: 44 average time/residue: 1.0430 time to fit residues: 66.5115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 1.9990 chunk 410 optimal weight: 0.0030 chunk 90 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 456 optimal weight: 5.9990 chunk 379 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 239 optimal weight: 0.6980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 728 HIS A 754 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN B1199 GLN C 754 ASN D 754 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 39000 Z= 0.178 Angle : 0.561 7.124 52976 Z= 0.294 Chirality : 0.043 0.179 5620 Planarity : 0.004 0.051 6856 Dihedral : 4.811 23.547 5140 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 4.03 % 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: -0.74 (0.12), residues: 4696 helix: 1.83 (0.16), residues: 1116 sheet: -0.67 (0.14), residues: 1196 loop : -1.56 (0.13), residues: 2384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 714 time to evaluate : 5.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 112 residues processed: 835 average time/residue: 1.4691 time to fit residues: 1513.8315 Evaluate side-chains 785 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 673 time to evaluate : 4.280 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 90 residues processed: 22 average time/residue: 0.8224 time to fit residues: 31.4364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 333 optimal weight: 0.9980 chunk 258 optimal weight: 6.9990 chunk 384 optimal weight: 0.6980 chunk 255 optimal weight: 4.9990 chunk 454 optimal weight: 0.0040 chunk 284 optimal weight: 0.0010 chunk 277 optimal weight: 0.7980 chunk 210 optimal weight: 8.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A1199 GLN B 180 ASN B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 39000 Z= 0.166 Angle : 0.556 6.932 52976 Z= 0.290 Chirality : 0.042 0.198 5620 Planarity : 0.004 0.051 6856 Dihedral : 4.672 23.098 5140 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer Outliers : 4.03 % 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: -0.69 (0.12), residues: 4696 helix: 1.90 (0.16), residues: 1116 sheet: -0.71 (0.14), residues: 1216 loop : -1.51 (0.13), residues: 2364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 715 time to evaluate : 4.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 109 residues processed: 830 average time/residue: 1.4700 time to fit residues: 1508.0264 Evaluate side-chains 790 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 681 time to evaluate : 4.308 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 81 residues processed: 28 average time/residue: 0.8359 time to fit residues: 38.7368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 137 optimal weight: 0.0370 chunk 89 optimal weight: 0.0980 chunk 88 optimal weight: 0.8980 chunk 289 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN B 754 ASN B1199 GLN C 754 ASN C1199 GLN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 39000 Z= 0.220 Angle : 0.576 8.601 52976 Z= 0.302 Chirality : 0.043 0.185 5620 Planarity : 0.004 0.051 6856 Dihedral : 4.726 23.472 5140 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 3.27 % 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: -0.69 (0.12), residues: 4696 helix: 1.89 (0.16), residues: 1116 sheet: -0.64 (0.14), residues: 1196 loop : -1.54 (0.13), residues: 2384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 694 time to evaluate : 4.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 97 residues processed: 795 average time/residue: 1.4691 time to fit residues: 1440.9974 Evaluate side-chains 775 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 678 time to evaluate : 4.506 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 79 residues processed: 18 average time/residue: 1.1082 time to fit residues: 32.1110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 1.9990 chunk 435 optimal weight: 2.9990 chunk 397 optimal weight: 0.9980 chunk 423 optimal weight: 6.9990 chunk 255 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 332 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 383 optimal weight: 1.9990 chunk 400 optimal weight: 0.7980 chunk 422 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN A1199 GLN B 754 ASN C 754 ASN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 39000 Z= 0.204 Angle : 0.579 8.457 52976 Z= 0.303 Chirality : 0.043 0.180 5620 Planarity : 0.004 0.052 6856 Dihedral : 4.708 23.147 5140 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 2.88 % 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: -0.72 (0.12), residues: 4696 helix: 1.88 (0.16), residues: 1116 sheet: -0.67 (0.14), residues: 1204 loop : -1.57 (0.13), residues: 2376 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 687 time to evaluate : 4.629 Fit side-chains revert: symmetry clash outliers start: 118 outliers final: 95 residues processed: 778 average time/residue: 1.5082 time to fit residues: 1440.7154 Evaluate side-chains 765 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 670 time to evaluate : 4.448 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 78 residues processed: 17 average time/residue: 0.8633 time to fit residues: 26.5944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 2.9990 chunk 448 optimal weight: 0.7980 chunk 273 optimal weight: 0.6980 chunk 212 optimal weight: 0.0870 chunk 311 optimal weight: 4.9990 chunk 470 optimal weight: 0.9990 chunk 432 optimal weight: 3.9990 chunk 374 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 289 optimal weight: 0.8980 chunk 229 optimal weight: 8.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 ASN B 754 ASN B1199 GLN C 754 ASN C1199 GLN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 39000 Z= 0.183 Angle : 0.573 7.954 52976 Z= 0.301 Chirality : 0.042 0.183 5620 Planarity : 0.004 0.052 6856 Dihedral : 4.647 23.646 5140 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 2.42 % 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: -0.71 (0.12), residues: 4696 helix: 1.91 (0.16), residues: 1116 sheet: -0.67 (0.14), residues: 1204 loop : -1.57 (0.13), residues: 2376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9392 Ramachandran restraints generated. 4696 Oldfield, 0 Emsley, 4696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 705 time to evaluate : 4.585 Fit side-chains outliers start: 99 outliers final: 86 residues processed: 790 average time/residue: 1.5281 time to fit residues: 1484.2194 Evaluate side-chains 767 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 681 time to evaluate : 4.373 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 77 residues processed: 9 average time/residue: 0.5976 time to fit residues: 14.3363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 2.9990 chunk 398 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 345 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 375 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 385 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 754 ASN ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 GLN B 754 ASN ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 ASN ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.081991 restraints weight = 51028.075| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.72 r_work: 0.2744 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.087 39000 Z= 0.494 Angle : 0.705 7.975 52976 Z= 0.370 Chirality : 0.049 0.189 5620 Planarity : 0.005 0.055 6856 Dihedral : 5.317 25.738 5140 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer Outliers : 2.61 % 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: -0.90 (0.12), residues: 4696 helix: 1.59 (0.16), residues: 1116 sheet: -0.68 (0.14), residues: 1204 loop : -1.67 (0.13), residues: 2376 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19720.51 seconds wall clock time: 348 minutes 37.20 seconds (20917.20 seconds total)