Starting phenix.real_space_refine on Sun Mar 17 18:58:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/03_2024/3j5p_5778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/03_2024/3j5p_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_5778/03_2024/3j5p_5778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/03_2024/3j5p_5778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/03_2024/3j5p_5778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/03_2024/3j5p_5778.pdb" } resolution = 3.275 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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. 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.61, per 1000 atoms: 0.52 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: 6.60 Conformation dependent library (CDL) restraints added in 3.6 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: 1.97 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: 5.27 Time building geometry restraints manager: 7.23 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 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.610 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 48.750 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 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 : 1.527 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 % Allowed : 16.84 % Favored : 55.38 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 697 HIS 0.007 0.002 HIS B 289 PHE 0.024 0.001 PHE C 235 TYR 0.022 0.002 TYR A 309 ARG 0.004 0.000 ARG A 181 *********************** 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 : 2.127 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: B 147 GLU cc_start: 0.1866 (OUTLIER) cc_final: 0.1429 (pt0) REVERT: B 187 LYS cc_start: -0.2051 (OUTLIER) cc_final: -0.2875 (mtpp) REVERT: B 669 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6642 (pp) REVERT: A 147 GLU cc_start: 0.1886 (OUTLIER) cc_final: 0.1420 (pt0) REVERT: A 187 LYS cc_start: -0.2484 (OUTLIER) cc_final: -0.3345 (mtpp) REVERT: A 597 THR cc_start: 0.7126 (p) cc_final: 0.6887 (p) REVERT: A 669 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6673 (pp) REVERT: C 147 GLU cc_start: 0.1888 (OUTLIER) cc_final: 0.1461 (pt0) REVERT: C 187 LYS cc_start: -0.2531 (OUTLIER) cc_final: -0.3312 (mtpp) REVERT: C 669 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6618 (pp) REVERT: D 147 GLU cc_start: 0.2002 (OUTLIER) cc_final: 0.1668 (pt0) REVERT: D 187 LYS cc_start: -0.2098 (OUTLIER) cc_final: -0.2855 (mtpp) REVERT: D 304 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5400 (p90) REVERT: D 597 THR cc_start: 0.7084 (p) cc_final: 0.6836 (p) REVERT: D 669 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6695 (pp) outliers start: 548 outliers final: 164 residues processed: 853 average time/residue: 0.3217 time to fit residues: 402.5306 Evaluate side-chains 522 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 345 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 367 ARG Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 631 TYR Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 704 THR Chi-restraints excluded: chain B residue 708 THR Chi-restraints excluded: chain B residue 710 LYS Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 242 ARG Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 631 TYR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 710 LYS Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 362 CYS Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain C residue 369 PHE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 426 TRP Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 516 PHE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 579 ARG Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 631 TYR Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 704 THR Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 LYS Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 717 ARG Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 147 GLU Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 245 PHE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 362 CYS Chi-restraints excluded: chain D residue 367 ARG Chi-restraints excluded: chain D residue 369 PHE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 473 PHE Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 516 PHE Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 631 TYR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 710 LYS Chi-restraints excluded: chain D residue 716 MET Chi-restraints excluded: chain D residue 717 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9980 chunk 178 optimal weight: 40.0000 chunk 99 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 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: 0.8782 ------------------------------------------------------------------------------- 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: 0.5714 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19032 Z= 0.289 Angle : 0.945 14.012 25760 Z= 0.474 Chirality : 0.046 0.187 2940 Planarity : 0.006 0.074 3232 Dihedral : 13.639 71.945 2960 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.73 % Favored : 95.93 % Rotamer: Outliers : 9.69 % Allowed : 21.81 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -0.03 (0.16), residues: 2308 helix: 0.76 (0.12), residues: 1504 sheet: None (None), residues: 0 loop : -1.47 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 372 HIS 0.003 0.001 HIS B 378 PHE 0.027 0.002 PHE B 245 TYR 0.015 0.002 TYR D 584 ARG 0.009 0.001 ARG B 242 *********************** 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 552 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 361 time to evaluate : 2.213 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: B 187 LYS cc_start: -0.1956 (OUTLIER) cc_final: -0.2280 (mmtt) REVERT: B 664 LEU cc_start: 0.7614 (mp) cc_final: 0.7349 (mp) REVERT: B 682 MET cc_start: 0.5616 (mtp) cc_final: 0.5370 (mtp) REVERT: A 187 LYS cc_start: -0.1916 (OUTLIER) cc_final: -0.2222 (mmtt) REVERT: A 664 LEU cc_start: 0.7603 (mp) cc_final: 0.7333 (mp) REVERT: C 187 LYS cc_start: -0.2054 (OUTLIER) cc_final: -0.2347 (mmtt) REVERT: C 664 LEU cc_start: 0.7612 (mp) cc_final: 0.7363 (mp) REVERT: D 187 LYS cc_start: -0.2279 (OUTLIER) cc_final: -0.2584 (mmtt) outliers start: 191 outliers final: 97 residues processed: 495 average time/residue: 0.2923 time to fit residues: 218.7301 Evaluate side-chains 369 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 268 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 426 TRP Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 426 TRP Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 701 ARG Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 426 TRP Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 577 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 157 CYS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 187 LYS Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 426 TRP Chi-restraints excluded: chain D residue 428 ARG Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 701 ARG 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: 10.0000 chunk 145 optimal weight: 7.9990 chunk 59 optimal weight: 50.0000 chunk 214 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5851 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 19032 Z= 0.349 Angle : 0.860 14.249 25760 Z= 0.436 Chirality : 0.045 0.196 2940 Planarity : 0.006 0.074 3232 Dihedral : 10.177 60.551 2720 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.20 % Favored : 95.62 % Rotamer: Outliers : 8.06 % Allowed : 23.33 % Favored : 68.61 % 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: 0.51 (0.17), residues: 2308 helix: 1.20 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.25 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 372 HIS 0.004 0.001 HIS C 410 PHE 0.025 0.002 PHE C 304 TYR 0.023 0.002 TYR B 555 ARG 0.007 0.001 ARG D 242 *********************** 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 446 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 287 time to evaluate : 2.315 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: B 162 MET cc_start: -0.1545 (tpt) cc_final: -0.2545 (ttt) REVERT: B 630 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7394 (tt) REVERT: A 630 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7425 (tt) REVERT: C 630 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7393 (tt) REVERT: D 630 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7397 (tt) outliers start: 159 outliers final: 107 residues processed: 395 average time/residue: 0.2991 time to fit residues: 179.1303 Evaluate side-chains 338 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 227 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 512 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 512 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 442 CYS Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 512 SER Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 674 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 9.9990 chunk 161 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 61 optimal weight: 50.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 B 676 ASN ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN C 498 GLN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19032 Z= 0.234 Angle : 0.779 14.347 25760 Z= 0.390 Chirality : 0.042 0.208 2940 Planarity : 0.006 0.112 3232 Dihedral : 8.826 56.248 2672 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.93 % Allowed : 23.12 % Favored : 70.94 % 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: 0.68 (0.17), residues: 2308 helix: 1.30 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.05 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 426 HIS 0.004 0.001 HIS A 320 PHE 0.028 0.001 PHE B 304 TYR 0.021 0.002 TYR B 198 ARG 0.015 0.001 ARG D 701 *********************** 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 400 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 283 time to evaluate : 2.097 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: B 162 MET cc_start: -0.1552 (tpt) cc_final: -0.2473 (ttt) REVERT: B 630 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7254 (tt) REVERT: A 162 MET cc_start: -0.1699 (tpt) cc_final: -0.2559 (ttt) REVERT: A 630 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7342 (tt) REVERT: C 162 MET cc_start: -0.1893 (tpt) cc_final: -0.2704 (ttt) REVERT: C 630 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7294 (tt) REVERT: D 162 MET cc_start: -0.1411 (tpt) cc_final: -0.2490 (ttm) REVERT: D 630 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7251 (tt) outliers start: 117 outliers final: 86 residues processed: 365 average time/residue: 0.2689 time to fit residues: 154.2498 Evaluate side-chains 321 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 231 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 717 ARG Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 704 THR Chi-restraints excluded: chain D residue 717 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 9.9990 chunk 129 optimal weight: 0.0020 chunk 3 optimal weight: 10.0000 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 194 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 116 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 overall best weight: 5.9996 ------------------------------------------------------------------------------- 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** C 676 ASN ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN D 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 19032 Z= 0.557 Angle : 0.890 15.534 25760 Z= 0.465 Chirality : 0.046 0.167 2940 Planarity : 0.006 0.081 3232 Dihedral : 8.792 59.366 2662 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 8.37 % Allowed : 22.26 % Favored : 69.37 % 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: 0.34 (0.17), residues: 2308 helix: 0.93 (0.13), residues: 1484 sheet: None (None), residues: 0 loop : -1.02 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 372 HIS 0.006 0.002 HIS C 320 PHE 0.031 0.002 PHE B 304 TYR 0.026 0.003 TYR B 555 ARG 0.009 0.001 ARG D 701 *********************** 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 385 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 220 time to evaluate : 2.057 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: B 136 LEU cc_start: -0.0680 (OUTLIER) cc_final: -0.0915 (pt) REVERT: B 162 MET cc_start: -0.1232 (tpt) cc_final: -0.2583 (ttm) REVERT: B 634 CYS cc_start: 0.6559 (OUTLIER) cc_final: 0.6257 (t) REVERT: A 136 LEU cc_start: -0.0660 (OUTLIER) cc_final: -0.0894 (pt) REVERT: A 162 MET cc_start: -0.1374 (tpt) cc_final: -0.2512 (ttm) REVERT: A 634 CYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6259 (t) REVERT: C 136 LEU cc_start: -0.0711 (OUTLIER) cc_final: -0.0951 (pt) REVERT: C 162 MET cc_start: -0.1634 (tpt) cc_final: -0.2625 (ttm) REVERT: D 136 LEU cc_start: -0.0654 (OUTLIER) cc_final: -0.0955 (pt) outliers start: 165 outliers final: 125 residues processed: 344 average time/residue: 0.2626 time to fit residues: 142.9075 Evaluate side-chains 324 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 193 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 303 LYS Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 674 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 717 ARG Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain D residue 706 LEU Chi-restraints excluded: chain D residue 717 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 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 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** ** 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: 0.5849 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19032 Z= 0.219 Angle : 0.784 15.051 25760 Z= 0.386 Chirality : 0.041 0.200 2940 Planarity : 0.005 0.076 3232 Dihedral : 8.347 58.589 2660 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.07 % Allowed : 24.70 % Favored : 70.23 % 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: 0.72 (0.17), residues: 2308 helix: 1.30 (0.13), residues: 1476 sheet: None (None), residues: 0 loop : -0.98 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 697 HIS 0.002 0.001 HIS B 289 PHE 0.036 0.001 PHE A 304 TYR 0.019 0.001 TYR D 401 ARG 0.005 0.001 ARG B 455 *********************** 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 365 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 265 time to evaluate : 2.192 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: B 136 LEU cc_start: -0.0559 (OUTLIER) cc_final: -0.0840 (pt) REVERT: B 162 MET cc_start: -0.1360 (tpt) cc_final: -0.2503 (ttm) REVERT: B 584 TYR cc_start: 0.7042 (t80) cc_final: 0.6819 (t80) REVERT: B 630 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7464 (tt) REVERT: A 162 MET cc_start: -0.1471 (tpt) cc_final: -0.2419 (ttm) REVERT: A 630 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7486 (tt) REVERT: C 162 MET cc_start: -0.1731 (tpt) cc_final: -0.2528 (ttm) REVERT: C 630 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7403 (tt) REVERT: D 136 LEU cc_start: -0.0659 (OUTLIER) cc_final: -0.0925 (pt) REVERT: D 162 MET cc_start: -0.1609 (tpt) cc_final: -0.2246 (ttm) REVERT: D 630 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7408 (tt) outliers start: 100 outliers final: 74 residues processed: 338 average time/residue: 0.2846 time to fit residues: 148.1689 Evaluate side-chains 312 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 232 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 LEU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 717 ARG Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 717 ARG Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 412 MET Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain C residue 717 ARG Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 717 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 227 optimal weight: 0.0980 chunk 142 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5815 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19032 Z= 0.217 Angle : 0.776 14.486 25760 Z= 0.381 Chirality : 0.041 0.181 2940 Planarity : 0.005 0.068 3232 Dihedral : 7.874 57.643 2654 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 5.38 % Allowed : 25.00 % Favored : 69.62 % 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: 0.71 (0.17), residues: 2308 helix: 1.34 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.09 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 697 HIS 0.001 0.001 HIS B 358 PHE 0.033 0.001 PHE A 304 TYR 0.020 0.001 TYR D 401 ARG 0.006 0.001 ARG B 575 *********************** 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 394 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 288 time to evaluate : 2.080 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: B 136 LEU cc_start: -0.0661 (OUTLIER) cc_final: -0.0899 (pt) REVERT: B 162 MET cc_start: -0.1877 (tpt) cc_final: -0.3062 (ttm) REVERT: B 716 MET cc_start: 0.5686 (tmm) cc_final: 0.4954 (tmm) REVERT: A 136 LEU cc_start: -0.0627 (OUTLIER) cc_final: -0.0850 (pt) REVERT: A 162 MET cc_start: -0.1981 (tpt) cc_final: -0.2866 (ttm) REVERT: A 716 MET cc_start: 0.5692 (tmm) cc_final: 0.4980 (tmm) REVERT: C 136 LEU cc_start: -0.0630 (OUTLIER) cc_final: -0.0924 (pt) REVERT: C 162 MET cc_start: -0.2016 (tpt) cc_final: -0.2914 (ttm) REVERT: C 630 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7350 (tt) REVERT: D 136 LEU cc_start: -0.0678 (OUTLIER) cc_final: -0.0962 (pt) REVERT: D 162 MET cc_start: -0.1729 (tpt) cc_final: -0.2028 (ttt) REVERT: D 630 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7348 (tt) outliers start: 106 outliers final: 72 residues processed: 354 average time/residue: 0.2600 time to fit residues: 145.1940 Evaluate side-chains 324 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 246 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 701 ARG Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 481 SER Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 685 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.0770 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 178 optimal weight: 0.0470 chunk 206 optimal weight: 0.8980 overall best weight: 0.5836 ------------------------------------------------------------------------------- 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: 0.5796 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19032 Z= 0.210 Angle : 0.787 14.164 25760 Z= 0.388 Chirality : 0.041 0.183 2940 Planarity : 0.006 0.068 3232 Dihedral : 7.456 56.468 2644 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.33 % Favored : 94.50 % Rotamer: Outliers : 4.21 % Allowed : 25.81 % Favored : 69.98 % 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: 0.71 (0.17), residues: 2308 helix: 1.36 (0.13), residues: 1468 sheet: None (None), residues: 0 loop : -1.11 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 549 HIS 0.006 0.001 HIS D 410 PHE 0.022 0.001 PHE D 582 TYR 0.018 0.001 TYR D 401 ARG 0.020 0.001 ARG B 717 *********************** 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 361 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 278 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.0687 (OUTLIER) cc_final: -0.0931 (pt) REVERT: B 162 MET cc_start: -0.1880 (tpt) cc_final: -0.3037 (ttm) REVERT: A 136 LEU cc_start: -0.0671 (OUTLIER) cc_final: -0.0896 (pt) REVERT: A 162 MET cc_start: -0.1979 (tpt) cc_final: -0.2808 (ttt) REVERT: C 136 LEU cc_start: -0.0717 (OUTLIER) cc_final: -0.0953 (pt) REVERT: C 162 MET cc_start: -0.1994 (tpt) cc_final: -0.2900 (ttm) REVERT: C 630 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7178 (tt) REVERT: D 136 LEU cc_start: -0.0693 (OUTLIER) cc_final: -0.0984 (pt) REVERT: D 162 MET cc_start: -0.1671 (tpt) cc_final: -0.2115 (ttm) REVERT: D 630 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7238 (tt) outliers start: 83 outliers final: 66 residues processed: 327 average time/residue: 0.2522 time to fit residues: 133.2966 Evaluate side-chains 331 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 259 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 571 LYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 603 LYS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 603 LYS Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 704 THR 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: 0.3980 chunk 211 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.5808 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19032 Z= 0.219 Angle : 0.801 15.905 25760 Z= 0.392 Chirality : 0.042 0.256 2940 Planarity : 0.005 0.063 3232 Dihedral : 7.210 53.871 2640 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.33 % Favored : 94.50 % Rotamer: Outliers : 4.11 % Allowed : 26.37 % Favored : 69.52 % 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: 0.68 (0.17), residues: 2308 helix: 1.32 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.10 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 549 HIS 0.002 0.000 HIS D 410 PHE 0.025 0.001 PHE C 304 TYR 0.018 0.001 TYR D 401 ARG 0.009 0.001 ARG C 717 *********************** 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 352 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 271 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.0736 (OUTLIER) cc_final: -0.0969 (pt) REVERT: B 162 MET cc_start: -0.1821 (tpt) cc_final: -0.2993 (ttm) REVERT: B 630 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7337 (tt) REVERT: B 677 MET cc_start: 0.5968 (tpp) cc_final: 0.5458 (mmm) REVERT: A 136 LEU cc_start: -0.0909 (OUTLIER) cc_final: -0.1157 (pt) REVERT: A 162 MET cc_start: -0.1956 (tpt) cc_final: -0.2846 (ttm) REVERT: A 630 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7383 (tt) REVERT: C 136 LEU cc_start: -0.0752 (OUTLIER) cc_final: -0.0992 (pt) REVERT: C 162 MET cc_start: -0.1980 (tpt) cc_final: -0.2875 (ttm) REVERT: C 630 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7203 (tt) REVERT: D 136 LEU cc_start: -0.0743 (OUTLIER) cc_final: -0.1039 (pt) REVERT: D 162 MET cc_start: -0.1575 (tpt) cc_final: -0.2008 (ttm) REVERT: D 630 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7239 (tt) outliers start: 81 outliers final: 64 residues processed: 314 average time/residue: 0.2535 time to fit residues: 128.4820 Evaluate side-chains 323 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 251 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 571 LYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 moved from start: 0.7217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19032 Z= 0.219 Angle : 0.809 14.956 25760 Z= 0.397 Chirality : 0.043 0.227 2940 Planarity : 0.005 0.065 3232 Dihedral : 7.095 50.812 2640 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.29 % Favored : 94.54 % Rotamer: Outliers : 3.90 % Allowed : 26.22 % Favored : 69.88 % 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: 0.64 (0.17), residues: 2308 helix: 1.25 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.06 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 549 HIS 0.001 0.000 HIS C 410 PHE 0.032 0.001 PHE B 304 TYR 0.018 0.001 TYR B 584 ARG 0.005 0.001 ARG B 717 ********************** 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 344 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 267 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 LEU cc_start: -0.0760 (OUTLIER) cc_final: -0.1007 (pt) REVERT: B 162 MET cc_start: -0.1809 (tpt) cc_final: -0.2969 (ttm) REVERT: B 630 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7334 (tt) REVERT: B 677 MET cc_start: 0.5811 (tpp) cc_final: 0.5450 (mmm) REVERT: A 136 LEU cc_start: -0.0943 (OUTLIER) cc_final: -0.1202 (pt) REVERT: A 162 MET cc_start: -0.1962 (tpt) cc_final: -0.2829 (ttm) REVERT: C 136 LEU cc_start: -0.0963 (OUTLIER) cc_final: -0.1223 (pt) REVERT: C 162 MET cc_start: -0.1988 (tpt) cc_final: -0.2857 (ttm) REVERT: C 630 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7236 (tt) REVERT: D 136 LEU cc_start: -0.0771 (OUTLIER) cc_final: -0.1076 (pt) REVERT: D 162 MET cc_start: -0.1574 (tpt) cc_final: -0.1948 (ttt) REVERT: D 630 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7250 (tt) outliers start: 77 outliers final: 66 residues processed: 307 average time/residue: 0.2504 time to fit residues: 124.5646 Evaluate side-chains 326 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 253 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 442 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 599 ILE Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 634 CYS Chi-restraints excluded: chain B residue 635 LEU Chi-restraints excluded: chain B residue 647 LEU Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 442 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 138 ARG Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 442 CYS Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 571 LYS Chi-restraints excluded: chain C residue 573 ILE Chi-restraints excluded: chain C residue 599 ILE Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 138 ARG Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 236 PHE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 346 ILE Chi-restraints excluded: chain D residue 384 LEU Chi-restraints excluded: chain D residue 387 ILE Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 599 ILE Chi-restraints excluded: chain D residue 630 LEU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 647 LEU Chi-restraints excluded: chain D residue 662 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.0060 chunk 172 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 187 optimal weight: 0.0670 chunk 78 optimal weight: 9.9990 chunk 192 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 overall best weight: 0.5134 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.123029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.070791 restraints weight = 48840.257| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 6.28 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19032 Z= 0.211 Angle : 0.814 14.794 25760 Z= 0.396 Chirality : 0.042 0.246 2940 Planarity : 0.005 0.060 3232 Dihedral : 6.967 48.057 2640 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.24 % Favored : 94.58 % Rotamer: Outliers : 3.75 % Allowed : 26.52 % Favored : 69.73 % 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: 0.59 (0.17), residues: 2308 helix: 1.22 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.08 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 549 HIS 0.002 0.000 HIS B 410 PHE 0.024 0.001 PHE C 304 TYR 0.019 0.001 TYR D 401 ARG 0.005 0.001 ARG D 409 =============================================================================== Job complete usr+sys time: 4190.87 seconds wall clock time: 76 minutes 22.06 seconds (4582.06 seconds total)