Starting phenix.real_space_refine (version: dev) on Wed Apr 6 05:44:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/04_2022/3j5p_5778.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/04_2022/3j5p_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_5778/04_2022/3j5p_5778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/04_2022/3j5p_5778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/04_2022/3j5p_5778.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j5p_5778/04_2022/3j5p_5778.pdb" } resolution = 3.275 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-4553/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: {'PTRANS': 13, 'CIS': 4, 'TRANS': 572, 'PCIS': 2} 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: {'PTRANS': 13, 'CIS': 4, 'TRANS': 572, 'PCIS': 2} 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: {'PTRANS': 13, 'CIS': 4, 'TRANS': 572, 'PCIS': 2} 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: {'PTRANS': 13, 'CIS': 4, 'TRANS': 572, 'PCIS': 2} 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: 10.85, per 1000 atoms: 0.58 Number of scatterers: 18636 At special positions: 0 Unit cell: (149.519, 149.519, 119.129, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3368 8.00 N 3060 7.00 C 12108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.36 Conformation dependent library (CDL) restraints added in 3.1 seconds 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4432 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 70.4% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 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: 5.90 Time building geometry restraints manager: 8.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 5937 1.37 - 1.53: 10379 1.53 - 1.69: 2548 1.69 - 1.85: 144 1.85 - 2.01: 24 Bond restraints: 19032 Sorted by residual: bond pdb=" C LEU D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.331 1.406 -0.075 8.70e-03 1.32e+04 7.42e+01 bond pdb=" C LEU C 460 " pdb=" N PRO C 461 " ideal model delta sigma weight residual 1.331 1.406 -0.075 8.70e-03 1.32e+04 7.37e+01 bond pdb=" C LEU A 460 " pdb=" N PRO A 461 " ideal model delta sigma weight residual 1.331 1.406 -0.075 8.70e-03 1.32e+04 7.37e+01 bond pdb=" C LEU B 460 " pdb=" N PRO B 461 " ideal model delta sigma weight residual 1.331 1.406 -0.074 8.70e-03 1.32e+04 7.29e+01 bond pdb=" CG MET B 162 " pdb=" SD MET B 162 " ideal model delta sigma weight residual 1.803 2.008 -0.205 2.50e-02 1.60e+03 6.74e+01 ... (remaining 19027 not shown) Histogram of bond angle deviations from ideal: 97.33 - 105.95: 364 105.95 - 114.56: 10884 114.56 - 123.17: 12990 123.17 - 131.78: 1478 131.78 - 140.39: 44 Bond angle restraints: 25760 Sorted by residual: angle pdb=" N ASN B 408 " pdb=" CA ASN B 408 " pdb=" C ASN B 408 " ideal model delta sigma weight residual 112.41 126.27 -13.86 1.30e+00 5.92e-01 1.14e+02 angle pdb=" N ASN A 408 " pdb=" CA ASN A 408 " pdb=" C ASN A 408 " ideal model delta sigma weight residual 112.41 126.24 -13.83 1.30e+00 5.92e-01 1.13e+02 angle pdb=" N ASN C 408 " pdb=" CA ASN C 408 " pdb=" C ASN C 408 " ideal model delta sigma weight residual 112.41 126.24 -13.83 1.30e+00 5.92e-01 1.13e+02 angle pdb=" N ASN D 408 " pdb=" CA ASN D 408 " pdb=" C ASN D 408 " ideal model delta sigma weight residual 112.41 126.23 -13.82 1.30e+00 5.92e-01 1.13e+02 angle pdb=" N ASP C 383 " pdb=" CA ASP C 383 " pdb=" C ASP C 383 " ideal model delta sigma weight residual 111.07 121.77 -10.70 1.07e+00 8.73e-01 1.00e+02 ... (remaining 25755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 9732 24.93 - 49.85: 1244 49.85 - 74.78: 236 74.78 - 99.71: 24 99.71 - 124.63: 8 Dihedral angle restraints: 11244 sinusoidal: 4336 harmonic: 6908 Sorted by residual: dihedral pdb=" CA GLY C 244 " pdb=" C GLY C 244 " pdb=" N PHE C 245 " pdb=" CA PHE C 245 " ideal model delta harmonic sigma weight residual 180.00 55.37 124.63 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY D 244 " pdb=" C GLY D 244 " pdb=" N PHE D 245 " pdb=" CA PHE D 245 " ideal model delta harmonic sigma weight residual 180.00 55.37 124.63 0 5.00e+00 4.00e-02 6.21e+02 dihedral pdb=" CA GLY A 244 " pdb=" C GLY A 244 " pdb=" N PHE A 245 " pdb=" CA PHE A 245 " ideal model delta harmonic sigma weight residual 180.00 55.40 124.60 0 5.00e+00 4.00e-02 6.21e+02 ... (remaining 11241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2383 0.105 - 0.211: 445 0.211 - 0.316: 96 0.316 - 0.421: 8 0.421 - 0.527: 8 Chirality restraints: 2940 Sorted by residual: chirality pdb=" CA GLU A 249 " pdb=" N GLU A 249 " pdb=" C GLU A 249 " pdb=" CB GLU A 249 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CA GLU C 249 " pdb=" N GLU C 249 " pdb=" C GLU C 249 " pdb=" CB GLU C 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.88e+00 chirality pdb=" CA GLU D 249 " pdb=" N GLU D 249 " pdb=" C GLU D 249 " pdb=" CB GLU D 249 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.86e+00 ... (remaining 2937 not shown) Planarity restraints: 3232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA UNK B 753 " -0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C UNK B 753 " 0.082 2.00e-02 2.50e+03 pdb=" O UNK B 753 " -0.032 2.00e-02 2.50e+03 pdb=" N UNK B 754 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK D 753 " 0.023 2.00e-02 2.50e+03 4.72e-02 2.22e+01 pdb=" C UNK D 753 " -0.081 2.00e-02 2.50e+03 pdb=" O UNK D 753 " 0.031 2.00e-02 2.50e+03 pdb=" N UNK D 754 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK A 753 " -0.023 2.00e-02 2.50e+03 4.71e-02 2.21e+01 pdb=" C UNK A 753 " 0.081 2.00e-02 2.50e+03 pdb=" O UNK A 753 " -0.031 2.00e-02 2.50e+03 pdb=" N UNK A 754 " -0.027 2.00e-02 2.50e+03 ... (remaining 3229 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.90: 63 1.90 - 2.65: 775 2.65 - 3.40: 28302 3.40 - 4.15: 45223 4.15 - 4.90: 81021 Nonbonded interactions: 155384 Sorted by model distance: nonbonded pdb=" OE2 GLU D 326 " pdb=" NH2 ARG D 355 " model vdw 1.156 2.520 nonbonded pdb=" OE2 GLU A 326 " pdb=" NH2 ARG A 355 " model vdw 1.156 2.520 nonbonded pdb=" OE2 GLU B 326 " pdb=" NH2 ARG B 355 " model vdw 1.156 2.520 nonbonded pdb=" OE2 GLU C 326 " pdb=" NH2 ARG C 355 " model vdw 1.157 2.520 nonbonded pdb=" CG1 VAL B 686 " pdb=" OE2 GLU A 684 " model vdw 1.355 3.460 ... (remaining 155379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 12108 2.51 5 N 3060 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 0.020 Extract box with map and model: 5.350 Check model and map are aligned: 0.260 Convert atoms to be neutral: 0.170 Process input model: 49.990 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5459 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.205 19032 Z= 0.714 Angle : 1.526 19.247 25760 Z= 1.045 Chirality : 0.091 0.527 2940 Planarity : 0.007 0.096 3232 Dihedral : 21.588 124.634 6812 Min Nonbonded Distance : 1.156 Molprobity Statistics. All-atom Clashscore : 79.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 27.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 1.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.16), residues: 2308 helix: 0.48 (0.13), residues: 1436 sheet: None (None), residues: 0 loop : -1.51 (0.18), residues: 872 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 548 poor density : 494 time to evaluate : 2.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 548 outliers final: 164 residues processed: 853 average time/residue: 0.3082 time to fit residues: 388.4110 Evaluate side-chains 508 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 344 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 164 outliers final: 0 residues processed: 164 average time/residue: 0.2341 time to fit residues: 64.9895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.9990 chunk 178 optimal weight: 30.0000 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 HIS B 410 HIS B 419 ASN B 498 GLN A 289 HIS A 419 ASN A 498 GLN C 289 HIS C 410 HIS C 419 ASN C 498 GLN D 289 HIS D 410 HIS D 419 ASN D 498 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5524 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 19032 Z= 0.301 Angle : 0.960 14.400 25760 Z= 0.478 Chirality : 0.046 0.177 2940 Planarity : 0.006 0.067 3232 Dihedral : 7.444 74.550 2580 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 22.89 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.47 % Favored : 96.19 % Rotamer Outliers : 4.61 % 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: 0.08 (0.16), residues: 2308 helix: 0.82 (0.12), residues: 1508 sheet: None (None), residues: 0 loop : -1.38 (0.20), residues: 800 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 373 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 25 residues processed: 428 average time/residue: 0.2789 time to fit residues: 185.8676 Evaluate side-chains 306 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 281 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2792 time to fit residues: 13.6020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 8.9990 chunk 66 optimal weight: 30.0000 chunk 178 optimal weight: 40.0000 chunk 145 optimal weight: 6.9990 chunk 59 optimal weight: 50.0000 chunk 214 optimal weight: 0.9990 chunk 231 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 676 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 19032 Z= 0.235 Angle : 0.849 13.654 25760 Z= 0.416 Chirality : 0.044 0.302 2940 Planarity : 0.005 0.075 3232 Dihedral : 6.602 60.415 2580 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.90 % Favored : 94.93 % Rotamer Outliers : 3.35 % 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: 0.33 (0.16), residues: 2308 helix: 0.98 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.17 (0.19), residues: 804 *********************** 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 417 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 351 time to evaluate : 2.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 35 residues processed: 393 average time/residue: 0.2667 time to fit residues: 164.2603 Evaluate side-chains 310 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 275 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1945 time to fit residues: 14.7186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 61 optimal weight: 40.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN B 676 ASN A 498 GLN C 498 GLN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5633 moved from start: 0.5933 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= 0.286 Angle : 0.795 14.439 25760 Z= 0.394 Chirality : 0.042 0.240 2940 Planarity : 0.005 0.066 3232 Dihedral : 6.305 55.967 2580 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2308 helix: 1.06 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.02 (0.20), residues: 804 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4616 Ramachandran restraints generated. 2308 Oldfield, 0 Emsley, 2308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 291 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 41 residues processed: 335 average time/residue: 0.2500 time to fit residues: 136.2600 Evaluate side-chains 278 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 237 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.1696 time to fit residues: 16.2355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.4980 chunk 129 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 194 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 116 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN A 498 GLN A 676 ASN C 498 GLN D 498 GLN ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 0.6235 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= 0.215 Angle : 0.796 14.163 25760 Z= 0.379 Chirality : 0.040 0.233 2940 Planarity : 0.005 0.065 3232 Dihedral : 6.011 52.862 2580 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 2.64 % 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: 0.46 (0.17), residues: 2308 helix: 1.03 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.02 (0.20), residues: 804 *********************** 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 355 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 303 time to evaluate : 2.384 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 outliers start: 52 outliers final: 29 residues processed: 337 average time/residue: 0.2546 time to fit residues: 138.5839 Evaluate side-chains 279 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 250 time to evaluate : 2.287 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1728 time to fit residues: 12.3250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 189 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 0.0470 chunk 119 optimal weight: 0.0370 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN A 498 GLN C 498 GLN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5567 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 19032 Z= 0.208 Angle : 0.770 13.617 25760 Z= 0.369 Chirality : 0.040 0.221 2940 Planarity : 0.005 0.060 3232 Dihedral : 5.776 49.823 2580 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer Outliers : 1.37 % 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: 0.45 (0.17), residues: 2308 helix: 1.02 (0.13), residues: 1492 sheet: None (None), residues: 0 loop : -0.99 (0.20), residues: 816 *********************** 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 310 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 283 time to evaluate : 2.239 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 outliers start: 27 outliers final: 16 residues processed: 299 average time/residue: 0.2589 time to fit residues: 126.0339 Evaluate side-chains 263 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 247 time to evaluate : 2.388 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1946 time to fit residues: 8.9323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 166 optimal weight: 0.1980 chunk 129 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 227 optimal weight: 0.4980 chunk 142 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5566 moved from start: 0.6715 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 : 0.767 13.583 25760 Z= 0.370 Chirality : 0.040 0.221 2940 Planarity : 0.005 0.065 3232 Dihedral : 5.607 46.785 2580 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2308 helix: 1.04 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -0.97 (0.20), residues: 836 *********************** 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 288 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 273 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 279 average time/residue: 0.2571 time to fit residues: 117.8363 Evaluate side-chains 255 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 2.256 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1676 time to fit residues: 5.6647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 178 optimal weight: 0.0770 chunk 206 optimal weight: 0.4980 overall best weight: 0.8540 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.6846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 19032 Z= 0.216 Angle : 0.772 15.663 25760 Z= 0.371 Chirality : 0.040 0.244 2940 Planarity : 0.005 0.066 3232 Dihedral : 5.497 45.439 2580 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.81 % 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: 0.50 (0.17), residues: 2308 helix: 1.10 (0.13), residues: 1472 sheet: None (None), residues: 0 loop : -1.02 (0.20), residues: 836 *********************** 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 286 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 270 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 274 average time/residue: 0.2643 time to fit residues: 118.1879 Evaluate side-chains 262 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 253 time to evaluate : 2.332 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1666 time to fit residues: 6.0109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 3.9990 chunk 198 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 65 optimal weight: 30.0000 chunk 191 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 224 optimal weight: 0.5980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.6949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 19032 Z= 0.236 Angle : 0.785 15.763 25760 Z= 0.378 Chirality : 0.041 0.227 2940 Planarity : 0.005 0.065 3232 Dihedral : 5.434 43.574 2580 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 1.06 % 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: 0.56 (0.17), residues: 2308 helix: 1.16 (0.14), residues: 1472 sheet: None (None), residues: 0 loop : -1.01 (0.20), residues: 836 *********************** 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 287 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 266 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 3 residues processed: 277 average time/residue: 0.2532 time to fit residues: 114.8875 Evaluate side-chains 255 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1788 time to fit residues: 4.1705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 chunk 216 optimal weight: 0.2980 chunk 187 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 19032 Z= 0.288 Angle : 0.822 15.223 25760 Z= 0.399 Chirality : 0.042 0.215 2940 Planarity : 0.005 0.066 3232 Dihedral : 5.453 40.854 2580 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2308 helix: 1.05 (0.13), residues: 1504 sheet: None (None), residues: 0 loop : -1.26 (0.19), residues: 804 ********************** 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 259 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 255 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 257 average time/residue: 0.2619 time to fit residues: 109.2007 Evaluate side-chains 245 residues out of total 2056 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 2.128 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1710 time to fit residues: 4.3938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.123110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.069194 restraints weight = 50955.563| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 6.43 r_work: 0.3210 rms_B_bonded: 6.29 restraints_weight: 2.0000 r_work: 0.3206 rms_B_bonded: 6.02 restraints_weight: 4.0000 r_work: 0.3206 rms_B_bonded: 5.59 restraints_weight: 8.0000 r_work: 0.3215 rms_B_bonded: 5.04 restraints_weight: 16.0000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 19032 Z= 0.218 Angle : 0.816 15.855 25760 Z= 0.390 Chirality : 0.042 0.235 2940 Planarity : 0.005 0.067 3232 Dihedral : 5.349 40.209 2580 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 0.30 % 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: 0.56 (0.17), residues: 2308 helix: 1.16 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.03 (0.19), residues: 832 =============================================================================== Job complete usr+sys time: 3681.29 seconds wall clock time: 68 minutes 9.10 seconds (4089.10 seconds total)