Starting phenix.real_space_refine (version: dev) on Wed Feb 22 22:30:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/02_2023/3j5p_5778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/02_2023/3j5p_5778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.275 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/02_2023/3j5p_5778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/02_2023/3j5p_5778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/02_2023/3j5p_5778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/02_2023/3j5p_5778.pdb" } resolution = 3.275 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 281": "OD1" <-> "OD2" Residue "B ASP 296": "OD1" <-> "OD2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B ASP 411": "OD1" <-> "OD2" Residue "B GLU 416": "OE1" <-> "OE2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 536": "OE1" <-> "OE2" Residue "B TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 654": "OD1" <-> "OD2" Residue "B PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 281": "OD1" <-> "OD2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ASP 411": "OD1" <-> "OD2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 281": "OD1" <-> "OD2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 383": "OD1" <-> "OD2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C ASP 411": "OD1" <-> "OD2" Residue "C GLU 416": "OE1" <-> "OE2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C GLU 478": "OE1" <-> "OE2" Residue "C PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 536": "OE1" <-> "OE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "C TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 600": "OE1" <-> "OE2" Residue "C TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 654": "OD1" <-> "OD2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 692": "OE1" <-> "OE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D ASP 296": "OD1" <-> "OD2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 327": "OE1" <-> "OE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 356": "OE1" <-> "OE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D GLU 405": "OE1" <-> "OE2" Residue "D ASP 411": "OD1" <-> "OD2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "D PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 499": "NH1" <-> "NH2" Residue "D TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 536": "OE1" <-> "OE2" Residue "D TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 557": "NH1" <-> "NH2" Residue "D TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "D TYR 631": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 654": "OD1" <-> "OD2" Residue "D PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 692": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 18636 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4659 Classifications: {'peptide': 592} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 22} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 11, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 4659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4659 Classifications: {'peptide': 592} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 22} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 11, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 4659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4659 Classifications: {'peptide': 592} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 22} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 11, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 4659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4659 Classifications: {'peptide': 592} Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 22} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 572} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'UNK:plan-1': 11, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 11.39, per 1000 atoms: 0.61 Number of scatterers: 18636 At special positions: 0 Unit cell: (149.519, 149.519, 119.129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3368 8.00 N 3060 7.00 C 12108 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: 8.24 Conformation dependent library (CDL) restraints added in 3.0 seconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 70.4% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'B' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 170 through 183 removed outlier: 4.314A pdb=" N ALA B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 Processing helix chain 'B' and resid 203 through 211 Processing helix chain 'B' and resid 213 through 223 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 260 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'B' and resid 335 through 343 Processing helix chain 'B' and resid 345 through 354 Processing helix chain 'B' and resid 361 through 366 removed outlier: 4.245A pdb=" N LEU B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.844A pdb=" N ASP B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 Processing helix chain 'B' and resid 411 through 414 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.545A pdb=" N TRP B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 455 removed outlier: 3.533A pdb=" N PHE B 436 " --> pdb=" O ARG B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 498 removed outlier: 3.519A pdb=" N TYR B 487 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 533 removed outlier: 3.967A pdb=" N ILE B 514 " --> pdb=" O SER B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 552 removed outlier: 3.938A pdb=" N SER B 540 " --> pdb=" O GLU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 557 Processing helix chain 'B' and resid 559 through 599 removed outlier: 3.812A pdb=" N ARG B 575 " --> pdb=" O LYS B 571 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 643 removed outlier: 4.193A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 671 removed outlier: 3.900A pdb=" N PHE B 659 " --> pdb=" O PHE B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 711 removed outlier: 3.510A pdb=" N ALA B 690 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN B 691 " --> pdb=" O ASN B 687 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU B 692 " --> pdb=" O LYS B 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 170 through 183 removed outlier: 4.314A pdb=" N ALA A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 223 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'A' and resid 335 through 343 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.244A pdb=" N LEU A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.844A pdb=" N ASP A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 401 Processing helix chain 'A' and resid 411 through 414 Processing helix chain 'A' and resid 415 through 429 removed outlier: 3.545A pdb=" N TRP A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 455 removed outlier: 3.533A pdb=" N PHE A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 498 removed outlier: 3.519A pdb=" N TYR A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 488 " --> pdb=" O GLY A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 533 removed outlier: 3.967A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.937A pdb=" N SER A 540 " --> pdb=" O GLU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 557 Processing helix chain 'A' and resid 559 through 599 removed outlier: 3.812A pdb=" N ARG A 575 " --> pdb=" O LYS A 571 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 643 removed outlier: 4.193A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 671 removed outlier: 3.899A pdb=" N PHE A 659 " --> pdb=" O PHE A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 711 removed outlier: 3.510A pdb=" N ALA A 690 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN A 691 " --> pdb=" O ASN A 687 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU A 692 " --> pdb=" O LYS A 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.656A pdb=" N LEU C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 170 through 183 removed outlier: 4.313A pdb=" N ALA C 174 " --> pdb=" O ASN C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 191 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 213 through 223 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 260 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 345 through 354 Processing helix chain 'C' and resid 361 through 366 removed outlier: 4.244A pdb=" N LEU C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.845A pdb=" N ASP C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 411 through 414 Processing helix chain 'C' and resid 415 through 429 removed outlier: 3.544A pdb=" N TRP C 426 " --> pdb=" O LEU C 422 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 455 removed outlier: 3.533A pdb=" N PHE C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 498 removed outlier: 3.519A pdb=" N TYR C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 533 removed outlier: 3.968A pdb=" N ILE C 514 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.938A pdb=" N SER C 540 " --> pdb=" O GLU C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 559 through 599 removed outlier: 3.812A pdb=" N ARG C 575 " --> pdb=" O LYS C 571 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 643 removed outlier: 4.194A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 671 removed outlier: 3.900A pdb=" N PHE C 659 " --> pdb=" O PHE C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 711 removed outlier: 3.510A pdb=" N ALA C 690 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN C 691 " --> pdb=" O ASN C 687 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU C 692 " --> pdb=" O LYS C 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 123 removed outlier: 3.561A pdb=" N ILE D 117 " --> pdb=" O ASP D 113 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.657A pdb=" N LEU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 170 through 183 removed outlier: 4.314A pdb=" N ALA D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 191 Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 250 through 258 Processing helix chain 'D' and resid 260 through 270 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'D' and resid 345 through 354 Processing helix chain 'D' and resid 361 through 366 removed outlier: 4.244A pdb=" N LEU D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 removed outlier: 3.844A pdb=" N ASP D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 Processing helix chain 'D' and resid 411 through 414 Processing helix chain 'D' and resid 415 through 429 removed outlier: 3.544A pdb=" N TRP D 426 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 455 removed outlier: 3.533A pdb=" N PHE D 436 " --> pdb=" O ARG D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 498 removed outlier: 3.519A pdb=" N TYR D 487 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D 488 " --> pdb=" O GLY D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 533 removed outlier: 3.968A pdb=" N ILE D 514 " --> pdb=" O SER D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 552 removed outlier: 3.937A pdb=" N SER D 540 " --> pdb=" O GLU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 557 Processing helix chain 'D' and resid 559 through 599 removed outlier: 3.812A pdb=" N ARG D 575 " --> pdb=" O LYS D 571 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 643 removed outlier: 4.193A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 671 removed outlier: 3.900A pdb=" N PHE D 659 " --> pdb=" O PHE D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 711 removed outlier: 3.510A pdb=" N ALA D 690 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN D 691 " --> pdb=" O ASN D 687 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU D 692 " --> pdb=" O LYS D 688 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 368 through 369 Processing sheet with id= B, first strand: chain 'A' and resid 368 through 369 Processing sheet with id= C, first strand: chain 'C' and resid 368 through 369 Processing sheet with id= D, first strand: chain 'D' and resid 368 through 369 1136 hydrogen bonds defined for protein. 3300 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: 5.47 Time building geometry restraints manager: 8.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 5937 1.37 - 1.53: 10379 1.53 - 1.69: 2548 1.69 - 1.85: 144 1.85 - 2.01: 24 Bond restraints: 19032 Sorted by residual: bond pdb=" C LEU D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.331 1.406 -0.075 8.70e-03 1.32e+04 7.42e+01 bond pdb=" C LEU C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.331 1.406 -0.075 8.70e-03 1.32e+04 7.37e+01 bond pdb=" C LEU A 460 " pdb=" N PRO A 461 " ideal model delta sigma weight residual 1.331 1.406 -0.075 8.70e-03 1.32e+04 7.37e+01 bond pdb=" C LEU B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.331 1.406 -0.074 8.70e-03 1.32e+04 7.29e+01 bond pdb=" CG MET B 162 " pdb=" SD MET B 162 " ideal model delta sigma weight residual 1.803 2.008 -0.205 2.50e-02 1.60e+03 6.74e+01 ... (remaining 19027 not shown) Histogram of bond angle deviations from ideal: 97.33 - 105.95: 364 105.95 - 114.56: 10884 114.56 - 123.17: 12990 123.17 - 131.78: 1478 131.78 - 140.39: 44 Bond angle restraints: 25760 Sorted by residual: angle pdb=" N ASN B 408 " pdb=" CA ASN B 408 " pdb=" C ASN B 408 " ideal model delta sigma weight residual 112.41 126.27 -13.86 1.30e+00 5.92e-01 1.14e+02 angle pdb=" N ASN A 408 " pdb=" CA ASN A 408 " pdb=" C ASN A 408 " ideal model delta sigma weight residual 112.41 126.24 -13.83 1.30e+00 5.92e-01 1.13e+02 angle pdb=" N ASN C 408 " pdb=" CA ASN C 408 " pdb=" C ASN C 408 " ideal model delta sigma weight residual 112.41 126.24 -13.83 1.30e+00 5.92e-01 1.13e+02 angle pdb=" N ASN D 408 " pdb=" CA ASN D 408 " pdb=" C ASN D 408 " ideal model delta sigma weight residual 112.41 126.23 -13.82 1.30e+00 5.92e-01 1.13e+02 angle pdb=" N ASP C 383 " pdb=" CA ASP C 383 " pdb=" C ASP C 383 " ideal model delta sigma weight residual 111.07 121.77 -10.70 1.07e+00 8.73e-01 1.00e+02 ... (remaining 25755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 9732 24.93 - 49.85: 1244 49.85 - 74.78: 236 74.78 - 99.71: 24 99.71 - 124.63: 8 Dihedral angle restraints: 11244 sinusoidal: 4336 harmonic: 6908 Sorted by residual: dihedral pdb=" CA GLY C 244 " pdb=" C GLY C 244 " pdb=" N PHE C 245 " pdb=" CA PHE C 245 " ideal model delta harmonic sigma weight residual 180.00 55.37 124.63 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY D 244 " pdb=" C GLY D 244 " pdb=" N PHE D 245 " pdb=" CA PHE D 245 " ideal model delta harmonic sigma weight residual 180.00 55.37 124.63 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY A 244 " pdb=" C GLY A 244 " pdb=" N PHE A 245 " pdb=" CA PHE A 245 " ideal model delta harmonic sigma weight residual 180.00 55.40 124.60 0 5.00e+00 4.00e-02 6.21e+02 ... (remaining 11241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2383 0.105 - 0.211: 445 0.211 - 0.316: 96 0.316 - 0.421: 8 0.421 - 0.527: 8 Chirality restraints: 2940 Sorted by residual: chirality pdb=" CA GLU A 249 " pdb=" N GLU A 249 " pdb=" C GLU A 249 " pdb=" CB GLU A 249 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CA GLU C 249 " pdb=" N GLU C 249 " pdb=" C GLU C 249 " pdb=" CB GLU C 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" CA GLU D 249 " pdb=" N GLU D 249 " pdb=" C GLU D 249 " pdb=" CB GLU D 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.86e+00 ... (remaining 2937 not shown) Planarity restraints: 3232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK B 753 " -0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C UNK B 753 " 0.082 2.00e-02 2.50e+03 pdb=" O UNK B 753 " -0.032 2.00e-02 2.50e+03 pdb=" N UNK B 754 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK D 753 " 0.023 2.00e-02 2.50e+03 4.72e-02 2.22e+01 pdb=" C UNK D 753 " -0.081 2.00e-02 2.50e+03 pdb=" O UNK D 753 " 0.031 2.00e-02 2.50e+03 pdb=" N UNK D 754 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK A 753 " -0.023 2.00e-02 2.50e+03 4.71e-02 2.21e+01 pdb=" C UNK A 753 " 0.081 2.00e-02 2.50e+03 pdb=" O UNK A 753 " -0.031 2.00e-02 2.50e+03 pdb=" N UNK A 754 " -0.027 2.00e-02 2.50e+03 ... (remaining 3229 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.90: 63 1.90 - 2.65: 775 2.65 - 3.40: 28302 3.40 - 4.15: 45223 4.15 - 4.90: 81021 Nonbonded interactions: 155384 Sorted by model distance: nonbonded pdb=" OE2 GLU D 326 " pdb=" NH2 ARG D 355 " model vdw 1.156 2.520 nonbonded pdb=" OE2 GLU A 326 " pdb=" NH2 ARG A 355 " model vdw 1.156 2.520 nonbonded pdb=" OE2 GLU B 326 " pdb=" NH2 ARG B 355 " model vdw 1.156 2.520 nonbonded pdb=" OE2 GLU C 326 " pdb=" NH2 ARG C 355 " model vdw 1.157 2.520 nonbonded pdb=" CG1 VAL B 686 " pdb=" OE2 GLU A 684 " model vdw 1.355 3.460 ... (remaining 155379 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 12108 2.51 5 N 3060 2.21 5 O 3368 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: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.350 Check model and map are aligned: 0.300 Process input model: 49.840 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5459 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 : 0.011 0.205 19032 Z= 0.714 Angle : 1.526 19.247 25760 Z= 1.045 Chirality : 0.091 0.527 2940 Planarity : 0.007 0.096 3232 Dihedral : 21.588 124.634 6812 Min Nonbonded Distance : 1.156 Molprobity Statistics. All-atom Clashscore : 79.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 27.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 1.06 % 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: -0.42 (0.16), residues: 2308 helix: 0.48 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -1.51 (0.18), residues: 872 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 548 poor density : 494 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 548 outliers final: 164 residues processed: 853 average time/residue: 0.3218 time to fit residues: 402.7076 Evaluate side-chains 508 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 344 time to evaluate : 2.215 Switching outliers to nearest non-outliers outliers start: 164 outliers final: 0 residues processed: 164 average time/residue: 0.2363 time to fit residues: 65.7994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9990 chunk 178 optimal weight: 30.0000 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 HIS B 410 HIS B 419 ASN B 498 GLN A 289 HIS A 419 ASN A 498 GLN C 289 HIS C 410 HIS C 419 ASN C 498 GLN D 289 HIS D 410 HIS D 419 ASN D 498 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5524 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 19032 Z= 0.301 Angle : 0.961 14.409 25760 Z= 0.479 Chirality : 0.046 0.179 2940 Planarity : 0.006 0.068 3232 Dihedral : 7.439 74.474 2580 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.47 % Favored : 96.19 % Rotamer Outliers : 4.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: 0.07 (0.16), residues: 2308 helix: 0.81 (0.12), residues: 1508 sheet: None (None), residues: 0 loop : -1.39 (0.20), residues: 800 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 375 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 25 residues processed: 431 average time/residue: 0.2903 time to fit residues: 194.1246 Evaluate side-chains 306 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 281 time to evaluate : 2.258 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3030 time to fit residues: 14.7964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 178 optimal weight: 30.0000 chunk 145 optimal weight: 8.9990 chunk 59 optimal weight: 50.0000 chunk 214 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 212 optimal weight: 0.0060 chunk 73 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5546 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 19032 Z= 0.240 Angle : 0.855 13.735 25760 Z= 0.419 Chirality : 0.044 0.272 2940 Planarity : 0.005 0.073 3232 Dihedral : 6.748 61.698 2580 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer Outliers : 2.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.71 % 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: 0.28 (0.16), residues: 2308 helix: 0.93 (0.13), residues: 1508 sheet: None (None), residues: 0 loop : -1.19 (0.19), residues: 800 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 349 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 27 residues processed: 380 average time/residue: 0.2948 time to fit residues: 175.3327 Evaluate side-chains 306 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 279 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2214 time to fit residues: 13.2690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 228 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 676 ASN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 19032 Z= 0.223 Angle : 0.786 13.942 25760 Z= 0.384 Chirality : 0.041 0.247 2940 Planarity : 0.005 0.067 3232 Dihedral : 6.289 57.713 2580 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 2.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.71 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.16), residues: 2308 helix: 1.00 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.06 (0.20), residues: 804 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 335 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 25 residues processed: 369 average time/residue: 0.2687 time to fit residues: 161.0491 Evaluate side-chains 285 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 260 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1712 time to fit residues: 11.1705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 94 optimal weight: 0.0040 chunk 194 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 116 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 overall best weight: 3.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 19032 Z= 0.341 Angle : 0.815 14.640 25760 Z= 0.403 Chirality : 0.042 0.231 2940 Planarity : 0.005 0.059 3232 Dihedral : 6.137 54.076 2580 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: 0.50 (0.17), residues: 2308 helix: 1.06 (0.13), residues: 1500 sheet: None (None), residues: 0 loop : -1.01 (0.20), residues: 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 274 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 49 residues processed: 313 average time/residue: 0.2624 time to fit residues: 133.0888 Evaluate side-chains 284 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 235 time to evaluate : 2.178 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.1723 time to fit residues: 18.6887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 133 optimal weight: 0.0050 chunk 56 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.6435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 19032 Z= 0.217 Angle : 0.775 14.073 25760 Z= 0.374 Chirality : 0.040 0.223 2940 Planarity : 0.005 0.060 3232 Dihedral : 5.915 50.809 2580 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2308 helix: 1.05 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -0.92 (0.20), residues: 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 278 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 302 average time/residue: 0.2550 time to fit residues: 125.3025 Evaluate side-chains 252 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 237 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1905 time to fit residues: 8.1469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5637 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 19032 Z= 0.259 Angle : 0.775 14.431 25760 Z= 0.378 Chirality : 0.040 0.170 2940 Planarity : 0.005 0.059 3232 Dihedral : 5.725 47.252 2580 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.55 (0.17), residues: 2308 helix: 1.10 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.97 (0.20), residues: 812 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 257 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 23 residues processed: 275 average time/residue: 0.2575 time to fit residues: 117.0006 Evaluate side-chains 261 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 238 time to evaluate : 2.190 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1711 time to fit residues: 10.1980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 0.0050 chunk 178 optimal weight: 0.0570 chunk 206 optimal weight: 1.9990 overall best weight: 0.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5584 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 19032 Z= 0.220 Angle : 0.781 13.904 25760 Z= 0.376 Chirality : 0.040 0.190 2940 Planarity : 0.005 0.067 3232 Dihedral : 5.582 44.935 2580 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.48 (0.17), residues: 2308 helix: 1.03 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.94 (0.20), residues: 812 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 280 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 288 average time/residue: 0.2584 time to fit residues: 122.4568 Evaluate side-chains 266 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 252 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1832 time to fit residues: 7.9869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 191 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 224 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 19032 Z= 0.309 Angle : 0.800 14.408 25760 Z= 0.393 Chirality : 0.041 0.214 2940 Planarity : 0.005 0.063 3232 Dihedral : 5.558 43.688 2580 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.57 (0.17), residues: 2308 helix: 1.11 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : -0.93 (0.20), residues: 816 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 257 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 266 average time/residue: 0.2583 time to fit residues: 112.5996 Evaluate side-chains 245 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 239 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1680 time to fit residues: 4.9452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 199 optimal weight: 0.5980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.7163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 19032 Z= 0.224 Angle : 0.798 13.793 25760 Z= 0.384 Chirality : 0.041 0.217 2940 Planarity : 0.005 0.070 3232 Dihedral : 5.450 41.317 2580 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.55 (0.17), residues: 2308 helix: 1.10 (0.13), residues: 1496 sheet: None (None), residues: 0 loop : -0.96 (0.20), residues: 812 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 269 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 269 average time/residue: 0.2695 time to fit residues: 118.4217 Evaluate side-chains 253 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 2.174 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1755 time to fit residues: 3.9766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.0050 chunk 172 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 187 optimal weight: 0.0870 chunk 78 optimal weight: 4.9990 chunk 192 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 164 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 overall best weight: 0.4572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.123319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.069545 restraints weight = 51182.889| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 6.30 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 19032 Z= 0.211 Angle : 0.803 13.502 25760 Z= 0.385 Chirality : 0.041 0.209 2940 Planarity : 0.005 0.062 3232 Dihedral : 5.334 41.226 2580 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.80 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: 0.55 (0.17), residues: 2308 helix: 1.17 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.06 (0.19), residues: 840 =============================================================================== Job complete usr+sys time: 4039.73 seconds wall clock time: 74 minutes 29.19 seconds (4469.19 seconds total)