Starting phenix.real_space_refine on Sun Mar 24 18:04:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sml_10243/03_2024/6sml_10243_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sml_10243/03_2024/6sml_10243.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sml_10243/03_2024/6sml_10243_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sml_10243/03_2024/6sml_10243_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sml_10243/03_2024/6sml_10243_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sml_10243/03_2024/6sml_10243.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sml_10243/03_2024/6sml_10243.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sml_10243/03_2024/6sml_10243_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sml_10243/03_2024/6sml_10243_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 21184 atoms to isotropic. 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 82 5.16 5 C 14056 2.51 5 N 3720 2.21 5 O 4294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "A ASP 30": "OD1" <-> "OD2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 94": "OD1" <-> "OD2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 218": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 461": "OE1" <-> "OE2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 355": "OD1" <-> "OD2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 400": "OD1" <-> "OD2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 551": "OD1" <-> "OD2" Residue "B ASP 563": "OD1" <-> "OD2" Residue "B TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 613": "OD1" <-> "OD2" Residue "B ASP 635": "OD1" <-> "OD2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "B ARG 715": "NH1" <-> "NH2" Residue "B PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 770": "OD1" <-> "OD2" Residue "B TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B ASP 822": "OD1" <-> "OD2" Residue "B PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 921": "OD1" <-> "OD2" Residue "B GLU 924": "OE1" <-> "OE2" Residue "B ASP 926": "OD1" <-> "OD2" Residue "B PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 21": "OE1" <-> "OE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 94": "OD1" <-> "OD2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D GLU 218": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 349": "OD1" <-> "OD2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D ASP 452": "OD1" <-> "OD2" Residue "D GLU 461": "OE1" <-> "OE2" Residue "D TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E ASP 286": "OD1" <-> "OD2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E ASP 294": "OD1" <-> "OD2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 355": "OD1" <-> "OD2" Residue "E GLU 362": "OE1" <-> "OE2" Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 400": "OD1" <-> "OD2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 429": "OD1" <-> "OD2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 551": "OD1" <-> "OD2" Residue "E ASP 563": "OD1" <-> "OD2" Residue "E TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 613": "OD1" <-> "OD2" Residue "E ASP 635": "OD1" <-> "OD2" Residue "E PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 643": "OE1" <-> "OE2" Residue "E ARG 715": "NH1" <-> "NH2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 770": "OD1" <-> "OD2" Residue "E TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 817": "OE1" <-> "OE2" Residue "E ASP 822": "OD1" <-> "OD2" Residue "E PHE 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 921": "OD1" <-> "OD2" Residue "E GLU 924": "OE1" <-> "OE2" Residue "E ASP 926": "OD1" <-> "OD2" Residue "E PHE 936": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain: "B" Number of atoms: 7134 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 911, 7126 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 911, 7126 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 7280 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 65 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, 'PLM:plan-1': 1, '5PL:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain: "E" Number of atoms: 7134 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 911, 7126 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Conformer: "B" Number of residues, atoms: 911, 7126 Classifications: {'peptide': 911} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 31, 'TRANS': 879} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 bond proxies already assigned to first conformer: 7280 Chain: "F" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 65 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, 'PLM:plan-1': 1, '5PL:plan-2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 17.76, per 1000 atoms: 0.80 Number of scatterers: 22152 At special positions: 0 Unit cell: (151.94, 127.33, 133.75, 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 82 16.00 O 4294 8.00 N 3720 7.00 C 14056 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.00 Conformation dependent library (CDL) restraints added in 6.4 seconds 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 20 sheets defined 16.9% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'A' and resid 39 through 55 removed outlier: 3.696A pdb=" N ASN A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 82 through 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 106 through 132 Processing helix chain 'A' and resid 139 through 166 removed outlier: 4.042A pdb=" N SER A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 337 through 340 No H-bonds generated for 'chain 'A' and resid 337 through 340' Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 398 through 412 removed outlier: 3.655A pdb=" N ARG A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 438 through 444 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'B' and resid 139 through 142 Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.071A pdb=" N THR B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 262 through 271 removed outlier: 3.897A pdb=" N ASP B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 938 through 940 No H-bonds generated for 'chain 'B' and resid 938 through 940' Processing helix chain 'D' and resid 39 through 55 removed outlier: 3.696A pdb=" N ASN D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 66 Processing helix chain 'D' and resid 82 through 85 No H-bonds generated for 'chain 'D' and resid 82 through 85' Processing helix chain 'D' and resid 106 through 132 Processing helix chain 'D' and resid 139 through 166 removed outlier: 4.042A pdb=" N SER D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 381 through 395 Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.655A pdb=" N ARG D 412 " --> pdb=" O LEU D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'E' and resid 139 through 142 Processing helix chain 'E' and resid 189 through 194 removed outlier: 4.071A pdb=" N THR E 194 " --> pdb=" O ASP E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 262 through 271 removed outlier: 3.897A pdb=" N ASP E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 325 Processing helix chain 'E' and resid 412 through 416 Processing helix chain 'E' and resid 446 through 452 Processing helix chain 'E' and resid 738 through 740 No H-bonds generated for 'chain 'E' and resid 738 through 740' Processing helix chain 'E' and resid 895 through 897 No H-bonds generated for 'chain 'E' and resid 895 through 897' Processing helix chain 'E' and resid 912 through 914 No H-bonds generated for 'chain 'E' and resid 912 through 914' Processing helix chain 'E' and resid 938 through 940 No H-bonds generated for 'chain 'E' and resid 938 through 940' Processing sheet with id= A, first strand: chain 'A' and resid 71 through 73 Processing sheet with id= B, first strand: chain 'A' and resid 308 through 311 Processing sheet with id= C, first strand: chain 'A' and resid 342 through 346 removed outlier: 5.863A pdb=" N GLY A 351 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 122 through 125 removed outlier: 7.071A pdb=" N GLN B 227 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET B 203 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE B 225 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL B 205 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 223 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 179 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE B 226 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE B 181 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N THR B 228 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 149 through 152 Processing sheet with id= F, first strand: chain 'B' and resid 329 through 339 removed outlier: 3.610A pdb=" N GLN B 333 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP B 882 " --> pdb=" O LYS B 950 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU B 952 " --> pdb=" O ASP B 880 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 880 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU B 954 " --> pdb=" O SER B 878 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER B 878 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 864 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER B 751 " --> pdb=" O THR B 787 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR B 628 " --> pdb=" O THR B 658 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY B 507 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER B 457 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG B 396 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 380 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 385 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG B 378 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA B 387 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU B 376 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU B 389 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN B 374 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLY B 391 " --> pdb=" O ARG B 372 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG B 372 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE B 393 " --> pdb=" O SER B 370 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER B 370 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN B 395 " --> pdb=" O ARG B 368 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG B 368 " --> pdb=" O ASN B 395 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 673 through 675 Processing sheet with id= H, first strand: chain 'B' and resid 814 through 816 Processing sheet with id= I, first strand: chain 'B' and resid 890 through 892 Processing sheet with id= J, first strand: chain 'B' and resid 946 through 948 Processing sheet with id= K, first strand: chain 'D' and resid 71 through 73 Processing sheet with id= L, first strand: chain 'D' and resid 308 through 311 Processing sheet with id= M, first strand: chain 'D' and resid 342 through 346 removed outlier: 5.863A pdb=" N GLY D 351 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 122 through 125 removed outlier: 7.071A pdb=" N GLN E 227 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N MET E 203 " --> pdb=" O PHE E 225 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE E 225 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL E 205 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL E 223 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU E 179 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE E 226 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE E 181 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N THR E 228 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 149 through 152 Processing sheet with id= P, first strand: chain 'E' and resid 329 through 339 removed outlier: 3.610A pdb=" N GLN E 333 " --> pdb=" O SER E 244 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP E 882 " --> pdb=" O LYS E 950 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU E 952 " --> pdb=" O ASP E 880 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP E 880 " --> pdb=" O LEU E 952 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU E 954 " --> pdb=" O SER E 878 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER E 878 " --> pdb=" O LEU E 954 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 864 " --> pdb=" O VAL E 887 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER E 751 " --> pdb=" O THR E 787 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR E 628 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLY E 507 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER E 457 " --> pdb=" O ARG E 396 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG E 396 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU E 383 " --> pdb=" O ASN E 380 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN E 380 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 385 " --> pdb=" O ARG E 378 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ARG E 378 " --> pdb=" O VAL E 385 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA E 387 " --> pdb=" O GLU E 376 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLU E 376 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU E 389 " --> pdb=" O ASN E 374 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN E 374 " --> pdb=" O LEU E 389 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N GLY E 391 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ARG E 372 " --> pdb=" O GLY E 391 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE E 393 " --> pdb=" O SER E 370 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER E 370 " --> pdb=" O ILE E 393 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN E 395 " --> pdb=" O ARG E 368 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG E 368 " --> pdb=" O ASN E 395 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 673 through 675 Processing sheet with id= R, first strand: chain 'E' and resid 814 through 816 Processing sheet with id= S, first strand: chain 'E' and resid 890 through 892 Processing sheet with id= T, first strand: chain 'E' and resid 946 through 948 810 hydrogen bonds defined for protein. 2356 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: 7.18 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3744 1.30 - 1.42: 6148 1.42 - 1.55: 12564 1.55 - 1.68: 36 1.68 - 1.80: 158 Bond restraints: 22650 Sorted by residual: bond pdb=" CA SER B 591 " pdb=" CB SER B 591 " ideal model delta sigma weight residual 1.533 1.490 0.043 1.66e-02 3.63e+03 6.81e+00 bond pdb=" CA SER E 591 " pdb=" CB SER E 591 " ideal model delta sigma weight residual 1.533 1.490 0.043 1.66e-02 3.63e+03 6.81e+00 bond pdb=" CB ASP A 349 " pdb=" CG ASP A 349 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.33e+00 bond pdb=" CB ASP D 349 " pdb=" CG ASP D 349 " ideal model delta sigma weight residual 1.516 1.574 -0.058 2.50e-02 1.60e+03 5.33e+00 bond pdb=" CB ARG B 490 " pdb=" CG ARG B 490 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.73e+00 ... (remaining 22645 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.33: 406 105.33 - 112.51: 10740 112.51 - 119.69: 8008 119.69 - 126.86: 11236 126.86 - 134.04: 268 Bond angle restraints: 30658 Sorted by residual: angle pdb=" CBR 5PL D 601 " pdb=" CBS 5PL D 601 " pdb=" CBT 5PL D 601 " ideal model delta sigma weight residual 131.61 109.97 21.64 3.00e+00 1.11e-01 5.20e+01 angle pdb=" CBR 5PL A 601 " pdb=" CBS 5PL A 601 " pdb=" CBT 5PL A 601 " ideal model delta sigma weight residual 131.61 109.97 21.64 3.00e+00 1.11e-01 5.20e+01 angle pdb=" C GLY E 996 " pdb=" N ASN E 997 " pdb=" CA ASN E 997 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C GLY B 996 " pdb=" N ASN B 997 " pdb=" CA ASN B 997 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C LYS D 348 " pdb=" N ASP D 349 " pdb=" CA ASP D 349 " ideal model delta sigma weight residual 123.93 131.89 -7.96 1.54e+00 4.22e-01 2.67e+01 ... (remaining 30653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 12008 18.12 - 36.25: 1148 36.25 - 54.37: 200 54.37 - 72.50: 30 72.50 - 90.62: 22 Dihedral angle restraints: 13408 sinusoidal: 5286 harmonic: 8122 Sorted by residual: dihedral pdb=" CA GLY E 691 " pdb=" C GLY E 691 " pdb=" N ASN E 692 " pdb=" CA ASN E 692 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA GLY B 691 " pdb=" C GLY B 691 " pdb=" N ASN B 692 " pdb=" CA ASN B 692 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ARG B 495 " pdb=" C ARG B 495 " pdb=" N MET B 496 " pdb=" CA MET B 496 " ideal model delta harmonic sigma weight residual -180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 13405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2156 0.051 - 0.102: 820 0.102 - 0.152: 222 0.152 - 0.203: 50 0.203 - 0.254: 6 Chirality restraints: 3254 Sorted by residual: chirality pdb=" CA ASP A 349 " pdb=" N ASP A 349 " pdb=" C ASP A 349 " pdb=" CB ASP A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ASP D 349 " pdb=" N ASP D 349 " pdb=" C ASP D 349 " pdb=" CB ASP D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU D 22 " pdb=" CB LEU D 22 " pdb=" CD1 LEU D 22 " pdb=" CD2 LEU D 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3251 not shown) Planarity restraints: 4016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 82 " 0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO A 83 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 82 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO D 83 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 83 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 83 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 33 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO D 34 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 34 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 34 " -0.031 5.00e-02 4.00e+02 ... (remaining 4013 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5057 2.77 - 3.31: 17480 3.31 - 3.84: 34417 3.84 - 4.37: 40571 4.37 - 4.90: 76058 Nonbonded interactions: 173583 Sorted by model distance: nonbonded pdb=" OG SER B 171 " pdb=" OE2 GLU B 698 " model vdw 2.243 2.440 nonbonded pdb=" OG SER E 171 " pdb=" OE2 GLU E 698 " model vdw 2.243 2.440 nonbonded pdb=" O THR B 471 " pdb=" OG1 THR B 471 " model vdw 2.273 2.440 nonbonded pdb=" O THR E 471 " pdb=" OG1 THR E 471 " model vdw 2.273 2.440 nonbonded pdb=" O TYR D 249 " pdb=" OG SER D 391 " model vdw 2.293 2.440 ... (remaining 173578 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 'D' } ncs_group { reference = (chain 'B' and (resid 103 through 721 or resid 723 through 1017)) selection = (chain 'E' and (resid 103 through 721 or resid 723 through 1017)) } ncs_group { reference = chain 'C' selection = chain 'F' } 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=0.50 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.030 Extract box with map and model: 3.400 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 64.300 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.170 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: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.009 0.072 22650 Z= 0.583 Angle : 1.018 21.636 30658 Z= 0.551 Chirality : 0.059 0.254 3254 Planarity : 0.006 0.066 4016 Dihedral : 14.675 90.623 8256 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.13), residues: 2796 helix: -2.98 (0.15), residues: 584 sheet: -0.72 (0.17), residues: 808 loop : -2.96 (0.13), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 161 HIS 0.020 0.002 HIS B 582 PHE 0.027 0.003 PHE B1017 TYR 0.023 0.003 TYR E 514 ARG 0.004 0.001 ARG B 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 341 time to evaluate : 2.596 Fit side-chains REVERT: A 22 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8252 (pp) REVERT: A 278 TYR cc_start: 0.8747 (t80) cc_final: 0.8419 (t80) REVERT: A 359 GLU cc_start: 0.7459 (pt0) cc_final: 0.7193 (pt0) REVERT: B 312 PRO cc_start: 0.9108 (Cg_endo) cc_final: 0.8904 (Cg_exo) REVERT: B 774 TYR cc_start: 0.7922 (p90) cc_final: 0.7630 (p90) REVERT: B 783 ARG cc_start: 0.7640 (ptm160) cc_final: 0.7363 (ttp-170) REVERT: D 430 ARG cc_start: 0.8118 (mtm-85) cc_final: 0.7865 (mtp180) REVERT: E 227 GLN cc_start: 0.7487 (tp40) cc_final: 0.7282 (tp40) REVERT: E 279 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7490 (mm110) REVERT: E 314 ASP cc_start: 0.7666 (t0) cc_final: 0.7378 (p0) REVERT: E 370 SER cc_start: 0.8529 (p) cc_final: 0.8290 (t) REVERT: E 374 ASN cc_start: 0.8316 (m-40) cc_final: 0.8074 (m-40) REVERT: E 783 ARG cc_start: 0.7447 (ptm160) cc_final: 0.7132 (ttp-170) outliers start: 2 outliers final: 0 residues processed: 343 average time/residue: 0.3408 time to fit residues: 180.4928 Evaluate side-chains 242 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 219 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 86 ASN A 121 ASN A 125 ASN A 283 ASN A 318 ASN B 113 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 ASN B 463 ASN B 469 GLN B 621 ASN B 638 ASN B 704 ASN B 714 ASN B 748 ASN B 778 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN B 980 ASN B1002 GLN D 32 GLN D 64 GLN D 86 ASN D 121 ASN D 283 ASN D 318 ASN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 ASN E 463 ASN E 469 GLN E 582 HIS E 621 ASN E 638 ASN E 704 ASN E 713 ASN E 714 ASN E 747 GLN E 748 ASN E 778 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN E 967 ASN E 980 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22650 Z= 0.333 Angle : 0.658 17.401 30658 Z= 0.339 Chirality : 0.044 0.181 3254 Planarity : 0.005 0.069 4016 Dihedral : 6.543 61.643 3138 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.09 % Rotamer: Outliers : 1.88 % Allowed : 14.41 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.14), residues: 2796 helix: -1.53 (0.19), residues: 574 sheet: -0.64 (0.17), residues: 852 loop : -2.60 (0.14), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 697 HIS 0.011 0.002 HIS E 582 PHE 0.018 0.002 PHE E 868 TYR 0.021 0.002 TYR B1003 ARG 0.006 0.000 ARG E 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 256 time to evaluate : 2.320 Fit side-chains REVERT: A 22 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8059 (pp) REVERT: A 359 GLU cc_start: 0.7446 (pt0) cc_final: 0.7132 (pt0) REVERT: B 172 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8002 (pp) REVERT: B 227 GLN cc_start: 0.7814 (mt0) cc_final: 0.7487 (mt0) REVERT: B 367 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8201 (ttmm) REVERT: B 547 GLU cc_start: 0.8079 (tt0) cc_final: 0.7794 (tt0) REVERT: B 778 ASN cc_start: 0.8711 (p0) cc_final: 0.8447 (p0) REVERT: B 993 GLU cc_start: 0.8402 (tt0) cc_final: 0.8201 (tt0) REVERT: D 22 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8101 (pp) REVERT: D 164 MET cc_start: 0.8693 (mmm) cc_final: 0.8012 (mmt) REVERT: D 430 ARG cc_start: 0.8287 (mtm-85) cc_final: 0.8075 (mtm-85) REVERT: E 172 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8154 (pp) REVERT: E 185 MET cc_start: 0.8881 (ptm) cc_final: 0.8622 (ptm) REVERT: E 446 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7303 (mm-30) REVERT: E 783 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7562 (ttp-170) outliers start: 44 outliers final: 22 residues processed: 288 average time/residue: 0.3084 time to fit residues: 143.2371 Evaluate side-chains 250 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 607 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain B residue 894 ASN Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 757 VAL Chi-restraints excluded: chain E residue 894 ASN Chi-restraints excluded: chain E residue 926 ASP Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 0.0170 chunk 78 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 254 optimal weight: 0.3980 chunk 275 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 252 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 198 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 ASN B 543 HIS B 638 ASN B 714 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN D 449 ASN E 282 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 523 ASN E 677 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN E1005 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22650 Z= 0.139 Angle : 0.529 12.513 30658 Z= 0.274 Chirality : 0.041 0.179 3254 Planarity : 0.004 0.044 4016 Dihedral : 5.396 56.786 3138 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.63 % Allowed : 16.17 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.15), residues: 2796 helix: -0.66 (0.21), residues: 570 sheet: -0.26 (0.17), residues: 840 loop : -2.24 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 697 HIS 0.005 0.001 HIS B 582 PHE 0.012 0.001 PHE E 868 TYR 0.014 0.001 TYR D 109 ARG 0.003 0.000 ARG B 783 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 274 time to evaluate : 2.597 Fit side-chains REVERT: A 22 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8209 (pp) REVERT: A 60 MET cc_start: 0.8586 (mmp) cc_final: 0.8295 (mmt) REVERT: A 359 GLU cc_start: 0.7340 (pt0) cc_final: 0.7084 (pt0) REVERT: B 172 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7921 (pp) REVERT: B 367 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8078 (ttmm) REVERT: B 446 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7303 (mm-30) REVERT: B 537 LEU cc_start: 0.8373 (mp) cc_final: 0.8159 (mp) REVERT: B 547 GLU cc_start: 0.7965 (tt0) cc_final: 0.7664 (tt0) REVERT: B 598 TYR cc_start: 0.8386 (t80) cc_final: 0.7940 (t80) REVERT: B 783 ARG cc_start: 0.7984 (ttt90) cc_final: 0.7336 (ttp-170) REVERT: B 993 GLU cc_start: 0.8371 (tt0) cc_final: 0.8143 (tt0) REVERT: D 60 MET cc_start: 0.8539 (mmp) cc_final: 0.8189 (mmt) REVERT: D 212 ARG cc_start: 0.7776 (mmp-170) cc_final: 0.7547 (mmp-170) REVERT: E 172 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8021 (pp) REVERT: E 446 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7251 (mm-30) REVERT: E 547 GLU cc_start: 0.7879 (tt0) cc_final: 0.7503 (tt0) outliers start: 38 outliers final: 22 residues processed: 298 average time/residue: 0.3183 time to fit residues: 150.6648 Evaluate side-chains 256 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 231 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 607 ASP Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 0.0980 chunk 191 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 242 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN B 481 GLN B 638 ASN B 714 ASN B 778 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 ASN E 481 GLN E 778 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22650 Z= 0.158 Angle : 0.528 12.018 30658 Z= 0.272 Chirality : 0.041 0.179 3254 Planarity : 0.003 0.037 4016 Dihedral : 5.122 52.890 3138 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.35 % Allowed : 16.51 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.15), residues: 2796 helix: -0.03 (0.23), residues: 558 sheet: -0.09 (0.17), residues: 842 loop : -2.03 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 161 HIS 0.004 0.001 HIS B 582 PHE 0.012 0.001 PHE E 990 TYR 0.014 0.001 TYR D 109 ARG 0.002 0.000 ARG D 224 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 247 time to evaluate : 2.692 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8125 (pp) REVERT: A 60 MET cc_start: 0.8599 (mmp) cc_final: 0.8274 (mmt) REVERT: A 164 MET cc_start: 0.8926 (tpt) cc_final: 0.8636 (tpt) REVERT: B 172 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7953 (pp) REVERT: B 258 ASN cc_start: 0.8674 (m-40) cc_final: 0.8406 (m110) REVERT: B 367 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8111 (ttmm) REVERT: B 547 GLU cc_start: 0.7983 (tt0) cc_final: 0.7668 (tt0) REVERT: B 598 TYR cc_start: 0.8394 (t80) cc_final: 0.7949 (t80) REVERT: B 774 TYR cc_start: 0.7810 (p90) cc_final: 0.7591 (p90) REVERT: B 783 ARG cc_start: 0.7999 (ttt90) cc_final: 0.7365 (ttp-170) REVERT: E 172 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7982 (pp) REVERT: E 446 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7301 (mm-30) REVERT: E 541 MET cc_start: 0.6725 (ptp) cc_final: 0.6414 (ptt) REVERT: E 547 GLU cc_start: 0.7967 (tt0) cc_final: 0.7609 (tt0) outliers start: 55 outliers final: 40 residues processed: 281 average time/residue: 0.2863 time to fit residues: 133.0854 Evaluate side-chains 274 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 231 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 607 ASP Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 165 ASP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 757 VAL Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 926 ASP Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 0.6980 chunk 153 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 chunk 230 optimal weight: 5.9990 chunk 187 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 68 optimal weight: 0.0770 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 ASN B 714 ASN B 778 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 ASN E 778 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22650 Z= 0.121 Angle : 0.497 9.882 30658 Z= 0.255 Chirality : 0.040 0.179 3254 Planarity : 0.003 0.037 4016 Dihedral : 4.612 50.553 3138 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.27 % Allowed : 17.19 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 2796 helix: 0.45 (0.23), residues: 546 sheet: 0.04 (0.17), residues: 842 loop : -1.81 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 161 HIS 0.004 0.001 HIS E 582 PHE 0.011 0.001 PHE E 868 TYR 0.016 0.001 TYR E 296 ARG 0.002 0.000 ARG B 515 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 276 time to evaluate : 2.277 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8178 (pp) REVERT: A 60 MET cc_start: 0.8581 (mmp) cc_final: 0.8195 (mmt) REVERT: A 164 MET cc_start: 0.8885 (tpt) cc_final: 0.8626 (tpt) REVERT: B 172 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7887 (pp) REVERT: B 258 ASN cc_start: 0.8584 (m-40) cc_final: 0.8358 (m110) REVERT: B 367 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8108 (ttmm) REVERT: B 426 VAL cc_start: 0.9128 (m) cc_final: 0.8873 (t) REVERT: B 547 GLU cc_start: 0.7927 (tt0) cc_final: 0.7618 (tt0) REVERT: B 598 TYR cc_start: 0.8319 (t80) cc_final: 0.7946 (t80) REVERT: B 774 TYR cc_start: 0.7873 (p90) cc_final: 0.7617 (p90) REVERT: B 783 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7336 (ttp-170) REVERT: D 454 PHE cc_start: 0.8602 (m-10) cc_final: 0.8195 (m-80) REVERT: E 172 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7903 (pp) REVERT: E 446 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7302 (mm-30) REVERT: E 541 MET cc_start: 0.6682 (ptp) cc_final: 0.6375 (ptt) REVERT: E 547 GLU cc_start: 0.7847 (tt0) cc_final: 0.7458 (tt0) REVERT: E 993 GLU cc_start: 0.8337 (tt0) cc_final: 0.8129 (tt0) outliers start: 53 outliers final: 32 residues processed: 309 average time/residue: 0.2989 time to fit residues: 151.2778 Evaluate side-chains 278 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 243 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 607 ASP Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 757 VAL Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 882 ASP Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 882 ASP Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 158 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 270 optimal weight: 0.3980 chunk 224 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 575 ASN B 597 ASN B 714 ASN B 778 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 748 ASN E 778 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22650 Z= 0.155 Angle : 0.513 10.657 30658 Z= 0.263 Chirality : 0.041 0.178 3254 Planarity : 0.003 0.035 4016 Dihedral : 4.709 49.183 3138 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.27 % Allowed : 17.84 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2796 helix: 0.81 (0.23), residues: 532 sheet: 0.12 (0.17), residues: 842 loop : -1.70 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 161 HIS 0.004 0.001 HIS B 582 PHE 0.011 0.001 PHE E 868 TYR 0.014 0.001 TYR B 514 ARG 0.002 0.000 ARG E 948 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 2.433 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8126 (pp) REVERT: A 60 MET cc_start: 0.8597 (mmp) cc_final: 0.8276 (mmt) REVERT: A 164 MET cc_start: 0.8938 (tpt) cc_final: 0.8708 (tpt) REVERT: B 172 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7903 (pp) REVERT: B 258 ASN cc_start: 0.8674 (m-40) cc_final: 0.8407 (m110) REVERT: B 367 LYS cc_start: 0.8324 (ttpt) cc_final: 0.8109 (ttmm) REVERT: B 426 VAL cc_start: 0.9131 (m) cc_final: 0.8893 (t) REVERT: B 547 GLU cc_start: 0.7943 (tt0) cc_final: 0.7632 (tt0) REVERT: B 598 TYR cc_start: 0.8302 (t80) cc_final: 0.7993 (t80) REVERT: B 774 TYR cc_start: 0.7802 (p90) cc_final: 0.7578 (p90) REVERT: B 783 ARG cc_start: 0.7963 (ttt90) cc_final: 0.7324 (ttp-170) REVERT: D 348 LYS cc_start: 0.8896 (mmmm) cc_final: 0.8679 (mmmm) REVERT: E 172 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7913 (pp) REVERT: E 446 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7296 (mm-30) REVERT: E 541 MET cc_start: 0.6809 (ptp) cc_final: 0.6486 (ptt) REVERT: E 547 GLU cc_start: 0.7940 (tt0) cc_final: 0.7572 (tt0) REVERT: E 774 TYR cc_start: 0.7790 (p90) cc_final: 0.7538 (p90) REVERT: E 809 TYR cc_start: 0.8222 (m-10) cc_final: 0.7933 (m-80) outliers start: 53 outliers final: 34 residues processed: 286 average time/residue: 0.2884 time to fit residues: 136.0499 Evaluate side-chains 279 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 242 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 607 ASP Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 228 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 chunk 269 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 121 ASN B 282 GLN B 575 ASN B 582 HIS B 778 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN E 258 ASN E 575 ASN E 778 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22650 Z= 0.338 Angle : 0.631 14.496 30658 Z= 0.323 Chirality : 0.045 0.178 3254 Planarity : 0.004 0.032 4016 Dihedral : 5.625 56.181 3138 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.57 % Allowed : 18.35 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 2796 helix: 0.52 (0.23), residues: 544 sheet: 0.01 (0.17), residues: 842 loop : -1.80 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 697 HIS 0.008 0.001 HIS B 582 PHE 0.017 0.001 PHE B1017 TYR 0.022 0.002 TYR E1003 ARG 0.004 0.000 ARG E 948 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 226 time to evaluate : 2.429 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8093 (pp) REVERT: B 172 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7956 (pp) REVERT: B 547 GLU cc_start: 0.8080 (tt0) cc_final: 0.7745 (tt0) REVERT: B 598 TYR cc_start: 0.8440 (t80) cc_final: 0.8012 (t80) REVERT: B 774 TYR cc_start: 0.7774 (p90) cc_final: 0.7538 (p90) REVERT: D 22 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8123 (pp) REVERT: D 60 MET cc_start: 0.8708 (mmp) cc_final: 0.8400 (mmt) REVERT: E 172 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7969 (pp) REVERT: E 547 GLU cc_start: 0.8047 (tt0) cc_final: 0.7663 (tt0) REVERT: E 774 TYR cc_start: 0.7847 (p90) cc_final: 0.7591 (p90) outliers start: 60 outliers final: 43 residues processed: 268 average time/residue: 0.2872 time to fit residues: 127.3754 Evaluate side-chains 269 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 607 ASP Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 730 MET Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 905 LEU Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 778 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 161 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 chunk 53 optimal weight: 0.0030 chunk 52 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 183 optimal weight: 0.0870 chunk 133 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 overall best weight: 0.4768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 GLN B 343 GLN B 714 ASN B 778 ASN ** B 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 894 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 ASN ** E 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN ** E 782 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 894 ASN ** E 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22650 Z= 0.125 Angle : 0.518 10.417 30658 Z= 0.265 Chirality : 0.040 0.177 3254 Planarity : 0.003 0.036 4016 Dihedral : 4.686 49.122 3138 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.75 % Allowed : 19.29 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2796 helix: 0.72 (0.23), residues: 554 sheet: 0.14 (0.17), residues: 840 loop : -1.55 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 161 HIS 0.004 0.000 HIS E 582 PHE 0.017 0.001 PHE B 779 TYR 0.013 0.001 TYR D 109 ARG 0.002 0.000 ARG B 783 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5592 Ramachandran restraints generated. 2796 Oldfield, 0 Emsley, 2796 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 262 time to evaluate : 2.419 Fit side-chains revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8161 (pp) REVERT: A 60 MET cc_start: 0.8623 (mmp) cc_final: 0.8281 (mmt) REVERT: B 172 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7883 (pp) REVERT: B 426 VAL cc_start: 0.9122 (m) cc_final: 0.8879 (t) REVERT: B 547 GLU cc_start: 0.7910 (tt0) cc_final: 0.7613 (tt0) REVERT: B 598 TYR cc_start: 0.8309 (t80) cc_final: 0.8006 (t80) REVERT: B 640 PHE cc_start: 0.7108 (m-10) cc_final: 0.6888 (m-10) REVERT: B 774 TYR cc_start: 0.7833 (p90) cc_final: 0.7595 (p90) REVERT: D 60 MET cc_start: 0.8661 (mmp) cc_final: 0.8289 (mmt) REVERT: D 276 ASN cc_start: 0.8617 (t0) cc_final: 0.8336 (t0) REVERT: E 446 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7111 (mm-30) REVERT: E 541 MET cc_start: 0.6783 (ptp) cc_final: 0.6468 (ptt) REVERT: E 547 GLU cc_start: 0.7885 (tt0) cc_final: 0.7522 (tt0) REVERT: E 774 TYR cc_start: 0.7810 (p90) cc_final: 0.7573 (p90) REVERT: E 809 TYR cc_start: 0.8182 (m-10) cc_final: 0.7886 (m-80) outliers start: 41 outliers final: 32 residues processed: 286 average time/residue: 0.2882 time to fit residues: 137.0409 Evaluate side-chains 282 residues out of total 2336 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 248 time to evaluate : 2.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 607 ASP Chi-restraints excluded: chain B residue 613 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 778 ASN Chi-restraints excluded: chain B residue 791 PHE Chi-restraints excluded: chain B residue 925 THR Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 471 THR Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 730 MET Chi-restraints excluded: chain E residue 739 ILE Chi-restraints excluded: chain E residue 778 ASN Chi-restraints excluded: chain E residue 791 PHE Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 925 THR Chi-restraints excluded: chain E residue 957 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9602 > 50: distance: 69 - 90: 26.690 distance: 72 - 87: 29.180 distance: 82 - 87: 28.008 distance: 87 - 88: 35.989 distance: 88 - 89: 6.444 distance: 88 - 91: 9.096 distance: 89 - 90: 12.092 distance: 89 - 93: 42.694 distance: 93 - 94: 21.522 distance: 93 - 220: 29.883 distance: 94 - 95: 7.795 distance: 94 - 97: 20.714 distance: 95 - 96: 4.431 distance: 95 - 99: 34.771 distance: 96 - 217: 25.555 distance: 97 - 98: 9.716 distance: 99 - 100: 37.116 distance: 100 - 101: 16.028 distance: 100 - 103: 12.316 distance: 101 - 102: 19.485 distance: 101 - 108: 11.019 distance: 103 - 104: 11.773 distance: 104 - 105: 26.965 distance: 105 - 106: 41.865 distance: 106 - 107: 39.055 distance: 108 - 109: 40.770 distance: 108 - 200: 27.796 distance: 109 - 110: 23.099 distance: 109 - 112: 5.176 distance: 110 - 119: 29.097 distance: 111 - 197: 36.803 distance: 112 - 113: 27.273 distance: 113 - 114: 27.542 distance: 114 - 115: 23.500 distance: 115 - 116: 10.913 distance: 116 - 117: 24.298 distance: 116 - 118: 28.525 distance: 119 - 120: 19.602 distance: 120 - 121: 21.654 distance: 120 - 123: 21.813 distance: 121 - 127: 42.067 distance: 123 - 124: 39.419 distance: 124 - 125: 19.458 distance: 125 - 126: 20.070 distance: 127 - 128: 51.976 distance: 127 - 133: 44.567 distance: 128 - 129: 50.422 distance: 128 - 131: 45.010 distance: 129 - 130: 41.108 distance: 129 - 134: 49.028 distance: 131 - 132: 19.386 distance: 132 - 133: 19.625 distance: 134 - 135: 42.185 distance: 135 - 136: 20.133 distance: 135 - 138: 27.847 distance: 136 - 142: 7.893 distance: 138 - 139: 36.848 distance: 139 - 140: 42.729 distance: 139 - 141: 23.328 distance: 142 - 143: 55.153 distance: 143 - 144: 35.502 distance: 143 - 146: 20.644 distance: 144 - 145: 11.830 distance: 144 - 150: 45.682 distance: 146 - 147: 13.493 distance: 147 - 148: 27.097 distance: 147 - 149: 12.074 distance: 150 - 151: 27.104 distance: 150 - 156: 11.588 distance: 151 - 152: 19.180 distance: 151 - 154: 32.482 distance: 152 - 153: 25.503 distance: 152 - 157: 10.678 distance: 154 - 155: 12.736 distance: 157 - 158: 5.602 distance: 158 - 159: 48.353 distance: 158 - 161: 25.173 distance: 159 - 160: 29.204 distance: 159 - 169: 30.731 distance: 161 - 162: 5.609 distance: 162 - 163: 7.721 distance: 162 - 164: 4.676 distance: 163 - 165: 26.008 distance: 164 - 166: 23.934 distance: 165 - 167: 10.811 distance: 166 - 167: 21.709 distance: 167 - 168: 54.813