Starting phenix.real_space_refine (version: dev) on Tue Dec 20 11:49:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/12_2022/7vqo_32091.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/12_2022/7vqo_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_32091/12_2022/7vqo_32091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/12_2022/7vqo_32091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/12_2022/7vqo_32091.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vqo_32091/12_2022/7vqo_32091.pdb" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.052 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 Convert atoms to be neutral 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: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 21.14, per 1000 atoms: 0.55 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: 15.79 Conformation dependent library (CDL) restraints added in 5.4 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: 2.96 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: 18.58 Time building geometry restraints manager: 17.12 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 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. 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: 0.010 Normalize map: mean=0, sd=1: 1.610 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: 0.040 Extract box with map and model: 10.340 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.300 Process input model: 106.820 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 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 : 12.29 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 : 4.814 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: 1.4247 time to fit residues: 1360.2778 Evaluate side-chains 746 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 646 time to evaluate : 4.656 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 91 residues processed: 9 average time/residue: 0.4443 time to fit residues: 13.3884 ------------------------------------------------------------------------------- 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: 0.7915 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 : 10.44 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 : 4.595 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: 1.2997 time to fit residues: 1451.2859 Evaluate side-chains 775 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 662 time to evaluate : 4.641 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 77 residues processed: 36 average time/residue: 1.0102 time to fit residues: 54.0389 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.0170 chunk 382 optimal weight: 7.9990 chunk 425 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 344 optimal weight: 2.9990 overall best weight: 1.3024 ------------------------------------------------------------------------------- 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 B1222 HIS 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 39000 Z= 0.256 Angle : 0.593 9.822 52976 Z= 0.309 Chirality : 0.044 0.172 5620 Planarity : 0.004 0.051 6856 Dihedral : 5.105 24.347 5140 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 4.42 % 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: -0.90 (0.12), residues: 4696 helix: 1.67 (0.16), residues: 1116 sheet: -0.81 (0.14), residues: 1232 loop : -1.63 (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 860 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 679 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 181 outliers final: 128 residues processed: 800 average time/residue: 1.4051 time to fit residues: 1389.3102 Evaluate side-chains 786 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 658 time to evaluate : 4.549 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 85 residues processed: 43 average time/residue: 0.8028 time to fit residues: 54.2710 ------------------------------------------------------------------------------- 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: 0.0980 chunk 322 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 430 optimal weight: 2.9990 chunk 456 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 408 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 39000 Z= 0.256 Angle : 0.582 7.241 52976 Z= 0.305 Chirality : 0.044 0.168 5620 Planarity : 0.004 0.052 6856 Dihedral : 5.070 24.350 5140 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer Outliers : 4.86 % 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: -0.83 (0.12), residues: 4696 helix: 1.71 (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 884 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 685 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 199 outliers final: 126 residues processed: 825 average time/residue: 1.4509 time to fit residues: 1497.9050 Evaluate side-chains 778 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 652 time to evaluate : 4.495 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 87 residues processed: 39 average time/residue: 0.9038 time to fit residues: 55.0851 ------------------------------------------------------------------------------- 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: 5.9990 chunk 258 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 339 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 389 optimal weight: 2.9990 chunk 315 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 409 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 728 HIS A 754 ASN B 180 ASN B 290 HIS B 754 ASN C 290 HIS C 754 ASN C1222 HIS D 290 HIS D 754 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 39000 Z= 0.489 Angle : 0.670 9.961 52976 Z= 0.350 Chirality : 0.048 0.179 5620 Planarity : 0.005 0.054 6856 Dihedral : 5.399 25.598 5140 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 5.13 % 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: -0.96 (0.12), residues: 4696 helix: 1.54 (0.16), residues: 1116 sheet: -0.79 (0.14), residues: 1204 loop : -1.65 (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 874 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 664 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 210 outliers final: 140 residues processed: 814 average time/residue: 1.4264 time to fit residues: 1432.2965 Evaluate side-chains 776 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 636 time to evaluate : 4.543 Switching outliers to nearest non-outliers outliers start: 140 outliers final: 100 residues processed: 40 average time/residue: 1.0921 time to fit residues: 62.4410 ------------------------------------------------------------------------------- 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: 0.9980 chunk 410 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 456 optimal weight: 0.8980 chunk 379 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 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 754 ASN B 754 ASN B1199 GLN B1222 HIS C 754 ASN D 754 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 39000 Z= 0.199 Angle : 0.576 6.802 52976 Z= 0.304 Chirality : 0.043 0.178 5620 Planarity : 0.004 0.053 6856 Dihedral : 5.040 24.421 5140 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 4.01 % 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: -0.87 (0.12), residues: 4696 helix: 1.70 (0.16), residues: 1116 sheet: -0.79 (0.14), residues: 1212 loop : -1.61 (0.13), residues: 2368 *********************** 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 859 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 695 time to evaluate : 5.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 164 outliers final: 116 residues processed: 816 average time/residue: 1.3739 time to fit residues: 1392.7881 Evaluate side-chains 777 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 661 time to evaluate : 4.738 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 93 residues processed: 23 average time/residue: 0.8842 time to fit residues: 33.7453 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 5.9990 chunk 260 optimal weight: 0.7980 chunk 333 optimal weight: 0.8980 chunk 258 optimal weight: 0.2980 chunk 384 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 454 optimal weight: 3.9990 chunk 284 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 210 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN A1199 GLN B 754 ASN C 754 ASN C1199 GLN D 754 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 39000 Z= 0.270 Angle : 0.596 9.280 52976 Z= 0.312 Chirality : 0.044 0.195 5620 Planarity : 0.004 0.053 6856 Dihedral : 5.011 24.320 5140 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % 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: -0.84 (0.12), residues: 4696 helix: 1.70 (0.16), residues: 1116 sheet: -0.77 (0.14), residues: 1204 loop : -1.59 (0.13), residues: 2376 *********************** 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 831 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 666 time to evaluate : 4.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 120 residues processed: 786 average time/residue: 1.4202 time to fit residues: 1383.9467 Evaluate side-chains 769 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 649 time to evaluate : 4.656 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 94 residues processed: 26 average time/residue: 1.2399 time to fit residues: 47.1113 ------------------------------------------------------------------------------- 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: 0.7980 chunk 181 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 89 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 357 optimal weight: 0.7980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN 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: 0.7899 moved from start: 0.1566 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= 0.210 Angle : 0.583 9.587 52976 Z= 0.305 Chirality : 0.043 0.187 5620 Planarity : 0.004 0.053 6856 Dihedral : 4.911 23.752 5140 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 3.52 % 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: -0.80 (0.12), residues: 4696 helix: 1.78 (0.16), residues: 1116 sheet: -0.76 (0.14), residues: 1196 loop : -1.58 (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 838 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 694 time to evaluate : 4.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 111 residues processed: 804 average time/residue: 1.4402 time to fit residues: 1436.2646 Evaluate side-chains 769 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 658 time to evaluate : 4.588 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 93 residues processed: 18 average time/residue: 0.8704 time to fit residues: 28.0379 ------------------------------------------------------------------------------- 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: 0.9990 chunk 435 optimal weight: 2.9990 chunk 397 optimal weight: 3.9990 chunk 423 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 332 optimal weight: 0.0670 chunk 130 optimal weight: 0.9980 chunk 383 optimal weight: 0.7980 chunk 400 optimal weight: 0.0020 chunk 422 optimal weight: 0.9980 overall best weight: 0.5726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN A1199 GLN B 754 ASN B1199 GLN C 754 ASN C1199 GLN D 754 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 39000 Z= 0.177 Angle : 0.570 8.242 52976 Z= 0.299 Chirality : 0.043 0.183 5620 Planarity : 0.004 0.053 6856 Dihedral : 4.736 23.068 5140 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 3.03 % 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: -0.75 (0.12), residues: 4696 helix: 1.87 (0.16), residues: 1116 sheet: -0.74 (0.14), residues: 1196 loop : -1.56 (0.13), residues: 2384 *********************** 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 829 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 705 time to evaluate : 4.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 96 residues processed: 807 average time/residue: 1.4469 time to fit residues: 1449.0672 Evaluate side-chains 773 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 677 time to evaluate : 4.653 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 84 residues processed: 12 average time/residue: 0.6968 time to fit residues: 19.1393 ------------------------------------------------------------------------------- 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: 0.9990 chunk 273 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 470 optimal weight: 3.9990 chunk 432 optimal weight: 3.9990 chunk 374 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 229 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN 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: 0.7913 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 39000 Z= 0.292 Angle : 0.617 8.606 52976 Z= 0.324 Chirality : 0.045 0.177 5620 Planarity : 0.005 0.053 6856 Dihedral : 4.926 23.906 5140 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 4696 helix: 1.81 (0.16), residues: 1116 sheet: -0.75 (0.14), residues: 1204 loop : -1.58 (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 781 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 667 time to evaluate : 4.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 92 residues processed: 766 average time/residue: 1.4736 time to fit residues: 1400.9023 Evaluate side-chains 746 residues out of total 4100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 654 time to evaluate : 4.538 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 84 residues processed: 8 average time/residue: 0.7483 time to fit residues: 14.9684 ------------------------------------------------------------------------------- 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: 0.0060 chunk 398 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 345 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 375 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 385 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN A1199 GLN B 754 ASN C 754 ASN D 754 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.106129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.086068 restraints weight = 50416.058| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.72 r_work: 0.2807 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 39000 Z= 0.269 Angle : 0.614 8.393 52976 Z= 0.321 Chirality : 0.044 0.173 5620 Planarity : 0.004 0.053 6856 Dihedral : 4.929 24.210 5140 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 2.59 % 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: 1.79 (0.16), residues: 1116 sheet: -0.74 (0.14), residues: 1196 loop : -1.60 (0.13), residues: 2384 =============================================================================== Job complete usr+sys time: 18423.10 seconds wall clock time: 324 minutes 5.73 seconds (19445.73 seconds total)