Starting phenix.real_space_refine on Tue Apr 9 17:00:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2024/5h3o_6656_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2024/5h3o_6656.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2024/5h3o_6656_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2024/5h3o_6656_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2024/5h3o_6656_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2024/5h3o_6656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2024/5h3o_6656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2024/5h3o_6656_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h3o_6656/04_2024/5h3o_6656_updated.pdb" } resolution = 3.5 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 96 5.16 5 Na 3 4.78 5 C 11008 2.51 5 N 2852 2.21 5 O 2995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 473": "OD1" <-> "OD2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "B TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 473": "OD1" <-> "OD2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 601": "OE1" <-> "OE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 473": "OD1" <-> "OD2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 601": "OE1" <-> "OE2" Residue "D TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 473": "OD1" <-> "OD2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 518": "OD1" <-> "OD2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 601": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16958 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4215 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4216 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "C" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4216 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "D" Number of atoms: 4216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4216 Classifications: {'peptide': 510} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 494} Chain breaks: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' NA': 2, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' NA': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.30, per 1000 atoms: 0.55 Number of scatterers: 16958 At special positions: 0 Unit cell: (109.56, 109.56, 135.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 4 15.00 Na 3 11.00 O 2995 8.00 N 2852 7.00 C 11008 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: 7.02 Conformation dependent library (CDL) restraints added in 3.1 seconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 8 sheets defined 54.3% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.88 Creating SS restraints... Processing helix chain 'A' and resid 107 through 109 No H-bonds generated for 'chain 'A' and resid 107 through 109' Processing helix chain 'A' and resid 119 through 144 removed outlier: 5.415A pdb=" N ILE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 223 Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.500A pdb=" N LEU A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 277 through 298 removed outlier: 3.531A pdb=" N ILE A 285 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 286 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS A 288 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU A 295 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 298 " --> pdb=" O GLU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 333 removed outlier: 3.675A pdb=" N VAL A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 Processing helix chain 'A' and resid 386 through 416 removed outlier: 3.987A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 437 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 473 through 483 Processing helix chain 'A' and resid 485 through 490 removed outlier: 3.738A pdb=" N LYS A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 502 through 508 removed outlier: 4.733A pdb=" N LEU A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LYS A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 563 No H-bonds generated for 'chain 'A' and resid 560 through 563' Processing helix chain 'A' and resid 592 through 599 Processing helix chain 'A' and resid 603 through 618 removed outlier: 3.818A pdb=" N GLU A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 119 through 144 removed outlier: 5.404A pdb=" N ILE B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 238 through 246 Processing helix chain 'B' and resid 248 through 258 removed outlier: 4.223A pdb=" N ILE B 258 " --> pdb=" O GLY B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 277 through 298 removed outlier: 3.549A pdb=" N ILE B 285 " --> pdb=" O ASN B 282 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR B 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS B 288 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU B 295 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU B 298 " --> pdb=" O GLU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 333 removed outlier: 3.664A pdb=" N VAL B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 375 Processing helix chain 'B' and resid 386 through 416 removed outlier: 3.995A pdb=" N ALA B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B 412 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 437 Processing helix chain 'B' and resid 442 through 457 Processing helix chain 'B' and resid 465 through 470 Processing helix chain 'B' and resid 473 through 483 Processing helix chain 'B' and resid 485 through 490 removed outlier: 3.741A pdb=" N LYS B 490 " --> pdb=" O GLU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 496 Processing helix chain 'B' and resid 502 through 508 removed outlier: 4.719A pdb=" N LEU B 507 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 508 " --> pdb=" O GLU B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 563 No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing helix chain 'B' and resid 592 through 599 Processing helix chain 'B' and resid 603 through 618 removed outlier: 3.801A pdb=" N GLU B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 119 through 144 removed outlier: 5.395A pdb=" N ILE C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 223 Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 248 through 258 removed outlier: 4.221A pdb=" N ILE C 258 " --> pdb=" O GLY C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 277 through 298 removed outlier: 3.539A pdb=" N ILE C 285 " --> pdb=" O ASN C 282 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 286 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR C 287 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LYS C 288 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLU C 295 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 298 " --> pdb=" O GLU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 333 removed outlier: 3.662A pdb=" N VAL C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 375 Processing helix chain 'C' and resid 386 through 416 removed outlier: 3.999A pdb=" N ALA C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 437 Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 473 through 483 Processing helix chain 'C' and resid 485 through 490 removed outlier: 3.733A pdb=" N LYS C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 502 through 508 removed outlier: 4.694A pdb=" N LEU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 563 No H-bonds generated for 'chain 'C' and resid 560 through 563' Processing helix chain 'C' and resid 592 through 599 Processing helix chain 'C' and resid 603 through 618 removed outlier: 3.826A pdb=" N GLU C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 119 through 144 removed outlier: 5.429A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 223 Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 248 through 258 removed outlier: 4.226A pdb=" N ILE D 258 " --> pdb=" O GLY D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 277 through 298 removed outlier: 3.527A pdb=" N ILE D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG D 286 " --> pdb=" O ARG D 283 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR D 287 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS D 288 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU D 295 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 298 " --> pdb=" O GLU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 333 removed outlier: 3.674A pdb=" N VAL D 312 " --> pdb=" O ARG D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 375 Processing helix chain 'D' and resid 386 through 416 removed outlier: 4.005A pdb=" N ALA D 404 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 412 " --> pdb=" O GLY D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 437 Processing helix chain 'D' and resid 442 through 457 Processing helix chain 'D' and resid 465 through 470 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 485 through 490 removed outlier: 3.725A pdb=" N LYS D 490 " --> pdb=" O GLU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 Processing helix chain 'D' and resid 502 through 508 removed outlier: 4.730A pdb=" N LEU D 507 " --> pdb=" O ALA D 503 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS D 508 " --> pdb=" O GLU D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 563 No H-bonds generated for 'chain 'D' and resid 560 through 563' Processing helix chain 'D' and resid 592 through 599 Processing helix chain 'D' and resid 603 through 618 removed outlier: 3.794A pdb=" N GLU D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 510 through 514 removed outlier: 6.138A pdb=" N PHE A 588 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL A 533 " --> pdb=" O PHE A 588 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU A 590 " --> pdb=" O TYR A 531 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N TYR A 531 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 550 through 552 removed outlier: 4.136A pdb=" N ASN A 578 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 510 through 514 removed outlier: 6.125A pdb=" N PHE B 588 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL B 533 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 590 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N TYR B 531 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 550 through 552 removed outlier: 4.166A pdb=" N ASN B 578 " --> pdb=" O VAL B 541 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 510 through 514 removed outlier: 6.129A pdb=" N PHE C 588 " --> pdb=" O VAL C 533 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL C 533 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU C 590 " --> pdb=" O TYR C 531 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N TYR C 531 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 550 through 552 removed outlier: 4.142A pdb=" N ASN C 578 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 510 through 514 removed outlier: 6.126A pdb=" N PHE D 588 " --> pdb=" O VAL D 533 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL D 533 " --> pdb=" O PHE D 588 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU D 590 " --> pdb=" O TYR D 531 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N TYR D 531 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 550 through 552 removed outlier: 4.140A pdb=" N ASN D 578 " --> pdb=" O VAL D 541 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2157 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: 4.73 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4780 1.33 - 1.46: 3786 1.46 - 1.58: 8635 1.58 - 1.70: 18 1.70 - 1.83: 156 Bond restraints: 17375 Sorted by residual: bond pdb=" C3' PCG C 801 " pdb=" C4' PCG C 801 " ideal model delta sigma weight residual 1.808 1.499 0.309 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C3' PCG D 801 " pdb=" C4' PCG D 801 " ideal model delta sigma weight residual 1.808 1.500 0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C3' PCG A 801 " pdb=" C4' PCG A 801 " ideal model delta sigma weight residual 1.808 1.500 0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" C3' PCG B 801 " pdb=" C4' PCG B 801 " ideal model delta sigma weight residual 1.808 1.501 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C2' PCG C 801 " pdb=" C3' PCG C 801 " ideal model delta sigma weight residual 1.200 1.496 -0.296 2.00e-02 2.50e+03 2.20e+02 ... (remaining 17370 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.85: 350 105.85 - 113.51: 9469 113.51 - 121.17: 8811 121.17 - 128.83: 4777 128.83 - 136.49: 179 Bond angle restraints: 23586 Sorted by residual: angle pdb=" N SER A 155 " pdb=" CA SER A 155 " pdb=" C SER A 155 " ideal model delta sigma weight residual 111.28 121.73 -10.45 1.09e+00 8.42e-01 9.20e+01 angle pdb=" N SER C 155 " pdb=" CA SER C 155 " pdb=" C SER C 155 " ideal model delta sigma weight residual 111.28 121.69 -10.41 1.09e+00 8.42e-01 9.12e+01 angle pdb=" N SER B 155 " pdb=" CA SER B 155 " pdb=" C SER B 155 " ideal model delta sigma weight residual 111.28 121.65 -10.37 1.09e+00 8.42e-01 9.05e+01 angle pdb=" N SER D 155 " pdb=" CA SER D 155 " pdb=" C SER D 155 " ideal model delta sigma weight residual 111.28 121.61 -10.33 1.09e+00 8.42e-01 8.99e+01 angle pdb=" N ILE B 377 " pdb=" CA ILE B 377 " pdb=" C ILE B 377 " ideal model delta sigma weight residual 111.45 102.65 8.80 9.30e-01 1.16e+00 8.96e+01 ... (remaining 23581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 9012 17.73 - 35.46: 903 35.46 - 53.19: 250 53.19 - 70.92: 58 70.92 - 88.64: 20 Dihedral angle restraints: 10243 sinusoidal: 4224 harmonic: 6019 Sorted by residual: dihedral pdb=" C LEU A 346 " pdb=" N LEU A 346 " pdb=" CA LEU A 346 " pdb=" CB LEU A 346 " ideal model delta harmonic sigma weight residual -122.60 -152.85 30.25 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" N LEU A 346 " pdb=" C LEU A 346 " pdb=" CA LEU A 346 " pdb=" CB LEU A 346 " ideal model delta harmonic sigma weight residual 122.80 151.82 -29.02 0 2.50e+00 1.60e-01 1.35e+02 dihedral pdb=" C LEU D 346 " pdb=" N LEU D 346 " pdb=" CA LEU D 346 " pdb=" CB LEU D 346 " ideal model delta harmonic sigma weight residual -122.60 -151.48 28.88 0 2.50e+00 1.60e-01 1.33e+02 ... (remaining 10240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 2592 0.261 - 0.523: 16 0.523 - 0.784: 0 0.784 - 1.046: 0 1.046 - 1.307: 4 Chirality restraints: 2612 Sorted by residual: chirality pdb=" CA LEU A 346 " pdb=" N LEU A 346 " pdb=" C LEU A 346 " pdb=" CB LEU A 346 " both_signs ideal model delta sigma weight residual False 2.51 1.20 1.31 2.00e-01 2.50e+01 4.27e+01 chirality pdb=" CA LEU D 346 " pdb=" N LEU D 346 " pdb=" C LEU D 346 " pdb=" CB LEU D 346 " both_signs ideal model delta sigma weight residual False 2.51 1.26 1.25 2.00e-01 2.50e+01 3.94e+01 chirality pdb=" CA LEU B 346 " pdb=" N LEU B 346 " pdb=" C LEU B 346 " pdb=" CB LEU B 346 " both_signs ideal model delta sigma weight residual False 2.51 1.29 1.22 2.00e-01 2.50e+01 3.70e+01 ... (remaining 2609 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 347 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASN D 347 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN D 347 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS D 348 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 347 " -0.013 2.00e-02 2.50e+03 2.52e-02 6.36e+00 pdb=" C ASN A 347 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN A 347 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 348 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 347 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C ASN C 347 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN C 347 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS C 348 " -0.014 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2881 2.77 - 3.30: 18081 3.30 - 3.83: 27385 3.83 - 4.37: 33820 4.37 - 4.90: 54043 Nonbonded interactions: 136210 Sorted by model distance: nonbonded pdb=" O GLY A 572 " pdb=" N ARG A 574 " model vdw 2.235 2.520 nonbonded pdb=" O GLY B 572 " pdb=" N ARG B 574 " model vdw 2.236 2.520 nonbonded pdb=" O GLY C 572 " pdb=" N ARG C 574 " model vdw 2.239 2.520 nonbonded pdb=" O GLY D 572 " pdb=" N ARG D 574 " model vdw 2.239 2.520 nonbonded pdb=" NH2 ARG A 537 " pdb=" OE1 GLN B 230 " model vdw 2.243 2.520 ... (remaining 136205 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' and (resid 106 through 620 or resid 801)) selection = (chain 'B' and (resid 106 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 198 through 620 or resid 801)) selection = (chain 'C' and (resid 106 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 198 through 620 or resid 801)) selection = (chain 'D' and (resid 106 through 196 or (resid 197 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 198 through 620 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.940 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 47.810 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.015 0.309 17375 Z= 0.909 Angle : 1.484 11.805 23586 Z= 0.966 Chirality : 0.082 1.307 2612 Planarity : 0.006 0.051 2904 Dihedral : 15.983 88.644 6379 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.98 % Favored : 93.43 % Rotamer: Outliers : 6.55 % Allowed : 15.85 % Favored : 77.60 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 13.33 % 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: -3.19 (0.16), residues: 2024 helix: -2.41 (0.12), residues: 1072 sheet: -0.98 (0.47), residues: 120 loop : -1.63 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 266 HIS 0.009 0.002 HIS D 484 PHE 0.026 0.003 PHE B 403 TYR 0.021 0.003 TYR D 262 ARG 0.009 0.001 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 545 time to evaluate : 1.951 Fit side-chains REVERT: A 112 TYR cc_start: 0.7449 (t80) cc_final: 0.7120 (t80) REVERT: A 119 ASP cc_start: 0.7889 (t0) cc_final: 0.7275 (t0) REVERT: A 123 TYR cc_start: 0.8477 (m-80) cc_final: 0.8186 (m-80) REVERT: A 158 ARG cc_start: 0.7794 (ptp-170) cc_final: 0.7411 (ptp-110) REVERT: A 180 MET cc_start: 0.8284 (pmm) cc_final: 0.8007 (ptp) REVERT: A 238 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7303 (mp0) REVERT: A 291 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8042 (tpt170) REVERT: A 295 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8134 (mm-30) REVERT: A 303 MET cc_start: 0.8084 (ptp) cc_final: 0.7076 (mmm) REVERT: A 375 THR cc_start: 0.8784 (p) cc_final: 0.8563 (p) REVERT: A 397 MET cc_start: 0.8613 (mmm) cc_final: 0.8186 (mtm) REVERT: A 413 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8425 (mtt) REVERT: A 432 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8618 (mtmm) REVERT: A 460 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6755 (pp30) REVERT: A 467 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8767 (m) REVERT: A 535 ARG cc_start: 0.8682 (ptp90) cc_final: 0.8449 (ttp80) REVERT: A 578 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8703 (p0) REVERT: B 119 ASP cc_start: 0.7768 (t0) cc_final: 0.7152 (t0) REVERT: B 123 TYR cc_start: 0.8453 (m-80) cc_final: 0.8141 (m-80) REVERT: B 153 SER cc_start: 0.8665 (p) cc_final: 0.8345 (m) REVERT: B 180 MET cc_start: 0.8307 (pmm) cc_final: 0.8034 (ptp) REVERT: B 234 VAL cc_start: 0.8625 (t) cc_final: 0.8424 (t) REVERT: B 291 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8059 (tpt170) REVERT: B 295 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 331 SER cc_start: 0.8642 (t) cc_final: 0.8338 (p) REVERT: B 354 ASP cc_start: 0.8228 (m-30) cc_final: 0.7922 (t0) REVERT: B 397 MET cc_start: 0.8645 (mmm) cc_final: 0.8136 (mtm) REVERT: B 423 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: B 427 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8935 (mmmt) REVERT: B 432 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8613 (mtmm) REVERT: B 460 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6611 (pp30) REVERT: B 467 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8801 (m) REVERT: B 535 ARG cc_start: 0.8683 (ptp90) cc_final: 0.8288 (ptp90) REVERT: B 543 ASP cc_start: 0.6564 (m-30) cc_final: 0.6347 (m-30) REVERT: B 578 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8638 (p0) REVERT: C 119 ASP cc_start: 0.7760 (t0) cc_final: 0.7099 (t0) REVERT: C 123 TYR cc_start: 0.8426 (m-80) cc_final: 0.8094 (m-80) REVERT: C 153 SER cc_start: 0.8696 (p) cc_final: 0.8371 (m) REVERT: C 180 MET cc_start: 0.8309 (pmm) cc_final: 0.8011 (ptp) REVERT: C 218 ASP cc_start: 0.8268 (t70) cc_final: 0.7999 (t70) REVERT: C 291 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8033 (tpt170) REVERT: C 303 MET cc_start: 0.8106 (ptp) cc_final: 0.7029 (mmm) REVERT: C 331 SER cc_start: 0.8646 (t) cc_final: 0.8349 (p) REVERT: C 354 ASP cc_start: 0.8298 (m-30) cc_final: 0.7917 (t0) REVERT: C 397 MET cc_start: 0.8605 (mmm) cc_final: 0.8073 (mtp) REVERT: C 432 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8609 (mtmm) REVERT: C 460 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6576 (pp30) REVERT: C 467 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8800 (m) REVERT: C 535 ARG cc_start: 0.8679 (ptp90) cc_final: 0.8465 (ttp80) REVERT: C 543 ASP cc_start: 0.6514 (m-30) cc_final: 0.6305 (m-30) REVERT: C 578 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8701 (p0) REVERT: D 119 ASP cc_start: 0.7809 (t0) cc_final: 0.7181 (t0) REVERT: D 123 TYR cc_start: 0.8476 (m-80) cc_final: 0.8154 (m-80) REVERT: D 153 SER cc_start: 0.8725 (p) cc_final: 0.8433 (m) REVERT: D 234 VAL cc_start: 0.8652 (t) cc_final: 0.8447 (t) REVERT: D 291 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8060 (tpt170) REVERT: D 295 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8117 (mm-30) REVERT: D 303 MET cc_start: 0.8080 (ptp) cc_final: 0.7077 (mmm) REVERT: D 331 SER cc_start: 0.8639 (t) cc_final: 0.8336 (p) REVERT: D 342 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8921 (p) REVERT: D 354 ASP cc_start: 0.8273 (m-30) cc_final: 0.7892 (t0) REVERT: D 375 THR cc_start: 0.8705 (p) cc_final: 0.8498 (p) REVERT: D 397 MET cc_start: 0.8598 (mmm) cc_final: 0.8232 (mtm) REVERT: D 432 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8630 (mtmm) REVERT: D 460 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6575 (pp30) REVERT: D 467 VAL cc_start: 0.9075 (OUTLIER) cc_final: 0.8842 (m) REVERT: D 535 ARG cc_start: 0.8691 (ptp90) cc_final: 0.8146 (ptp90) REVERT: D 578 ASN cc_start: 0.9028 (OUTLIER) cc_final: 0.8677 (p0) outliers start: 121 outliers final: 37 residues processed: 637 average time/residue: 0.3269 time to fit residues: 298.1090 Evaluate side-chains 447 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 391 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 273 TRP Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 273 TRP Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 413 MET Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 273 TRP Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 273 TRP Chi-restraints excluded: chain D residue 291 ARG Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 413 MET Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 578 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 0.0010 chunk 104 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 175 ASN A 272 ASN A 323 ASN A 416 ASN A 426 ASN B 143 GLN B 272 ASN B 323 ASN B 416 ASN B 426 ASN C 143 GLN C 175 ASN C 272 ASN C 323 ASN C 416 ASN C 426 ASN C 466 GLN D 143 GLN D 175 ASN D 272 ASN D 323 ASN D 416 ASN D 426 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17375 Z= 0.187 Angle : 0.634 11.254 23586 Z= 0.318 Chirality : 0.044 0.196 2612 Planarity : 0.004 0.033 2904 Dihedral : 9.106 88.080 2440 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.33 % Allowed : 23.48 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.35 (0.18), residues: 2024 helix: 0.38 (0.15), residues: 1096 sheet: -0.80 (0.47), residues: 120 loop : -0.88 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 322 HIS 0.003 0.001 HIS D 345 PHE 0.009 0.001 PHE C 206 TYR 0.016 0.001 TYR D 287 ARG 0.006 0.000 ARG C 438 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 476 time to evaluate : 2.196 Fit side-chains REVERT: A 112 TYR cc_start: 0.7312 (t80) cc_final: 0.6647 (t80) REVERT: A 180 MET cc_start: 0.7884 (pmm) cc_final: 0.7679 (ptp) REVERT: A 238 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6940 (mp0) REVERT: A 262 TYR cc_start: 0.6592 (p90) cc_final: 0.6316 (p90) REVERT: A 303 MET cc_start: 0.8049 (ptp) cc_final: 0.7061 (mmm) REVERT: A 331 SER cc_start: 0.8341 (t) cc_final: 0.8030 (p) REVERT: A 342 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8496 (p) REVERT: A 354 ASP cc_start: 0.7979 (m-30) cc_final: 0.7768 (t0) REVERT: A 397 MET cc_start: 0.8500 (mmm) cc_final: 0.7904 (mtp) REVERT: A 460 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6702 (pp30) REVERT: A 561 LEU cc_start: 0.8317 (mt) cc_final: 0.7965 (mt) REVERT: A 586 ASP cc_start: 0.8535 (m-30) cc_final: 0.8271 (m-30) REVERT: A 594 ASP cc_start: 0.8340 (m-30) cc_final: 0.7991 (m-30) REVERT: B 303 MET cc_start: 0.8047 (ptp) cc_final: 0.7024 (mmm) REVERT: B 397 MET cc_start: 0.8570 (mmm) cc_final: 0.7929 (mtp) REVERT: B 460 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.6400 (pp30) REVERT: B 561 LEU cc_start: 0.8292 (mt) cc_final: 0.7977 (mt) REVERT: B 594 ASP cc_start: 0.8347 (m-30) cc_final: 0.7983 (m-30) REVERT: C 180 MET cc_start: 0.7836 (pmm) cc_final: 0.7564 (ptp) REVERT: C 291 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8088 (tpt170) REVERT: C 303 MET cc_start: 0.8035 (ptp) cc_final: 0.7037 (mmm) REVERT: C 354 ASP cc_start: 0.8241 (m-30) cc_final: 0.8025 (t0) REVERT: C 397 MET cc_start: 0.8531 (mmm) cc_final: 0.7954 (mtp) REVERT: C 460 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6394 (pp30) REVERT: C 561 LEU cc_start: 0.8301 (mt) cc_final: 0.7985 (mt) REVERT: C 586 ASP cc_start: 0.8483 (m-30) cc_final: 0.8232 (m-30) REVERT: C 594 ASP cc_start: 0.8338 (m-30) cc_final: 0.8003 (m-30) REVERT: D 137 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9026 (mt) REVERT: D 276 LEU cc_start: 0.9109 (mm) cc_final: 0.8479 (tp) REVERT: D 303 MET cc_start: 0.8233 (ptp) cc_final: 0.7163 (mmm) REVERT: D 331 SER cc_start: 0.8360 (t) cc_final: 0.8000 (p) REVERT: D 342 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8606 (p) REVERT: D 397 MET cc_start: 0.8502 (mmm) cc_final: 0.7893 (mtp) REVERT: D 460 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6387 (pp30) REVERT: D 561 LEU cc_start: 0.8289 (mt) cc_final: 0.7978 (mt) REVERT: D 586 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8220 (m-30) REVERT: D 594 ASP cc_start: 0.8335 (m-30) cc_final: 0.7993 (m-30) outliers start: 80 outliers final: 33 residues processed: 518 average time/residue: 0.2895 time to fit residues: 224.2044 Evaluate side-chains 398 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 356 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 586 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 416 ASN B 143 GLN B 175 ASN B 539 GLN C 143 GLN C 416 ASN C 539 GLN D 143 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17375 Z= 0.341 Angle : 0.697 10.062 23586 Z= 0.350 Chirality : 0.045 0.185 2612 Planarity : 0.004 0.043 2904 Dihedral : 7.904 89.980 2373 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 7.09 % Allowed : 24.30 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.12 (0.18), residues: 2024 helix: 0.53 (0.15), residues: 1092 sheet: -0.66 (0.51), residues: 120 loop : -0.71 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 124 HIS 0.002 0.000 HIS A 484 PHE 0.013 0.002 PHE C 328 TYR 0.021 0.002 TYR A 223 ARG 0.009 0.001 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 369 time to evaluate : 2.122 Fit side-chains REVERT: A 176 MET cc_start: 0.7787 (ttp) cc_final: 0.7480 (ttp) REVERT: A 238 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7088 (mp0) REVERT: A 303 MET cc_start: 0.8441 (ptp) cc_final: 0.7361 (mmm) REVERT: A 445 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 460 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.6393 (pp30) REVERT: A 594 ASP cc_start: 0.8413 (m-30) cc_final: 0.8065 (m-30) REVERT: B 303 MET cc_start: 0.8463 (ptp) cc_final: 0.7382 (mmm) REVERT: B 460 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6437 (pp30) REVERT: B 478 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: B 594 ASP cc_start: 0.8392 (m-30) cc_final: 0.8043 (m-30) REVERT: C 176 MET cc_start: 0.7878 (ttp) cc_final: 0.7590 (ttp) REVERT: C 291 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8152 (tpt170) REVERT: C 303 MET cc_start: 0.8442 (ptp) cc_final: 0.7351 (mmm) REVERT: C 445 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8672 (tm-30) REVERT: C 460 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.6441 (pp30) REVERT: C 478 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8399 (mp0) REVERT: C 492 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7554 (mmm160) REVERT: C 594 ASP cc_start: 0.8431 (m-30) cc_final: 0.8095 (m-30) REVERT: D 176 MET cc_start: 0.8130 (ttp) cc_final: 0.7745 (ttp) REVERT: D 303 MET cc_start: 0.8433 (ptp) cc_final: 0.7348 (mmm) REVERT: D 331 SER cc_start: 0.8621 (t) cc_final: 0.8309 (p) REVERT: D 342 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8853 (p) REVERT: D 445 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8626 (tm-30) REVERT: D 460 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6399 (pp30) REVERT: D 478 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: D 492 ARG cc_start: 0.7703 (mmm160) cc_final: 0.7498 (mmm160) REVERT: D 594 ASP cc_start: 0.8402 (m-30) cc_final: 0.8055 (m-30) outliers start: 131 outliers final: 73 residues processed: 451 average time/residue: 0.2841 time to fit residues: 200.2417 Evaluate side-chains 432 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 350 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 604 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 96 optimal weight: 0.0970 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 176 optimal weight: 0.0670 chunk 53 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 416 ASN A 426 ASN B 143 GLN B 416 ASN B 426 ASN C 143 GLN C 416 ASN C 426 ASN D 143 GLN D 416 ASN D 426 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17375 Z= 0.139 Angle : 0.561 10.654 23586 Z= 0.279 Chirality : 0.042 0.178 2612 Planarity : 0.003 0.044 2904 Dihedral : 7.335 88.452 2373 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.09 % Allowed : 26.03 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.98 (0.19), residues: 2024 helix: 1.51 (0.16), residues: 1064 sheet: -0.68 (0.50), residues: 120 loop : -0.18 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 369 HIS 0.002 0.000 HIS B 345 PHE 0.012 0.001 PHE C 206 TYR 0.018 0.001 TYR A 223 ARG 0.006 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 403 time to evaluate : 2.147 Fit side-chains revert: symmetry clash REVERT: A 112 TYR cc_start: 0.7523 (t80) cc_final: 0.6843 (t80) REVERT: A 176 MET cc_start: 0.7655 (ttp) cc_final: 0.7368 (ttp) REVERT: A 238 GLU cc_start: 0.7368 (tm-30) cc_final: 0.6817 (mp0) REVERT: A 276 LEU cc_start: 0.9151 (mm) cc_final: 0.8488 (tp) REVERT: A 303 MET cc_start: 0.8077 (ptp) cc_final: 0.7206 (mmm) REVERT: A 429 ASP cc_start: 0.8217 (m-30) cc_final: 0.8007 (m-30) REVERT: A 436 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7605 (mm-30) REVERT: A 445 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8424 (tm-30) REVERT: A 460 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.5868 (pp30) REVERT: A 594 ASP cc_start: 0.8267 (m-30) cc_final: 0.7918 (m-30) REVERT: B 176 MET cc_start: 0.7743 (ttp) cc_final: 0.7306 (ttp) REVERT: B 227 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8510 (p90) REVERT: B 229 ASP cc_start: 0.8357 (m-30) cc_final: 0.8143 (m-30) REVERT: B 303 MET cc_start: 0.8053 (ptp) cc_final: 0.7215 (mmm) REVERT: B 429 ASP cc_start: 0.8179 (m-30) cc_final: 0.7963 (m-30) REVERT: B 436 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 460 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.5953 (pp30) REVERT: B 478 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: B 594 ASP cc_start: 0.8201 (m-30) cc_final: 0.7853 (m-30) REVERT: C 276 LEU cc_start: 0.9117 (mm) cc_final: 0.8484 (tp) REVERT: C 291 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7973 (tpt170) REVERT: C 303 MET cc_start: 0.8067 (ptp) cc_final: 0.7217 (mmm) REVERT: C 429 ASP cc_start: 0.8218 (m-30) cc_final: 0.7996 (m-30) REVERT: C 436 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7610 (mm-30) REVERT: C 445 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8418 (tm-30) REVERT: C 460 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.5925 (pp30) REVERT: C 478 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: C 594 ASP cc_start: 0.8221 (m-30) cc_final: 0.7877 (m-30) REVERT: D 176 MET cc_start: 0.7988 (ttp) cc_final: 0.7592 (ttp) REVERT: D 276 LEU cc_start: 0.9059 (mm) cc_final: 0.8436 (tp) REVERT: D 303 MET cc_start: 0.8034 (ptp) cc_final: 0.7208 (mmm) REVERT: D 331 SER cc_start: 0.8342 (t) cc_final: 0.8081 (p) REVERT: D 436 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7606 (mm-30) REVERT: D 445 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8457 (tm-30) REVERT: D 460 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.5913 (pp30) REVERT: D 478 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: D 594 ASP cc_start: 0.8194 (m-30) cc_final: 0.7838 (m-30) outliers start: 94 outliers final: 45 residues processed: 461 average time/residue: 0.2732 time to fit residues: 193.7029 Evaluate side-chains 416 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 362 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 227 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 578 ASN Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 578 ASN Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 604 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 169 GLN B 169 GLN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN D 143 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17375 Z= 0.390 Angle : 0.693 9.787 23586 Z= 0.348 Chirality : 0.046 0.213 2612 Planarity : 0.005 0.074 2904 Dihedral : 7.711 86.520 2372 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 6.60 % Allowed : 25.11 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.37 (0.18), residues: 2024 helix: 0.96 (0.15), residues: 1048 sheet: -0.84 (0.54), residues: 116 loop : -0.39 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 266 HIS 0.002 0.001 HIS A 484 PHE 0.016 0.002 PHE D 494 TYR 0.020 0.002 TYR A 223 ARG 0.008 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 352 time to evaluate : 2.131 Fit side-chains REVERT: A 176 MET cc_start: 0.7761 (ttp) cc_final: 0.7404 (ttp) REVERT: A 303 MET cc_start: 0.8492 (ptp) cc_final: 0.7439 (mmm) REVERT: A 436 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7728 (mm-30) REVERT: A 445 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 460 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6439 (pp30) REVERT: A 561 LEU cc_start: 0.8607 (mm) cc_final: 0.8242 (mm) REVERT: A 594 ASP cc_start: 0.8349 (m-30) cc_final: 0.8033 (m-30) REVERT: B 176 MET cc_start: 0.7828 (ttp) cc_final: 0.7622 (ttp) REVERT: B 303 MET cc_start: 0.8529 (ptp) cc_final: 0.7481 (mmm) REVERT: B 436 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 460 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.6354 (pp30) REVERT: B 478 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: B 594 ASP cc_start: 0.8288 (m-30) cc_final: 0.7972 (m-30) REVERT: C 176 MET cc_start: 0.7648 (ttp) cc_final: 0.7429 (ttp) REVERT: C 291 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8039 (tpt170) REVERT: C 303 MET cc_start: 0.8517 (ptp) cc_final: 0.7434 (mmm) REVERT: C 436 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7704 (mm-30) REVERT: C 445 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8572 (tm-30) REVERT: C 460 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6388 (pp30) REVERT: C 478 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: C 594 ASP cc_start: 0.8307 (m-30) cc_final: 0.7986 (m-30) REVERT: D 176 MET cc_start: 0.8096 (ttp) cc_final: 0.7590 (ttp) REVERT: D 227 TYR cc_start: 0.8743 (p90) cc_final: 0.8448 (p90) REVERT: D 303 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7432 (mmm) REVERT: D 436 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7650 (mm-30) REVERT: D 445 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8555 (tm-30) REVERT: D 460 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6341 (pp30) REVERT: D 478 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: D 561 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8480 (mm) REVERT: D 594 ASP cc_start: 0.8280 (m-30) cc_final: 0.7959 (m-30) outliers start: 122 outliers final: 76 residues processed: 433 average time/residue: 0.2696 time to fit residues: 178.5344 Evaluate side-chains 409 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 323 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 303 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 604 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 0.0040 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN B 143 GLN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 17375 Z= 0.231 Angle : 0.606 10.081 23586 Z= 0.299 Chirality : 0.042 0.178 2612 Planarity : 0.004 0.053 2904 Dihedral : 7.437 88.442 2364 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.90 % Allowed : 26.35 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.63 (0.19), residues: 2024 helix: 1.20 (0.16), residues: 1044 sheet: -0.85 (0.53), residues: 116 loop : -0.28 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 124 HIS 0.002 0.001 HIS A 345 PHE 0.011 0.001 PHE C 328 TYR 0.018 0.001 TYR A 223 ARG 0.007 0.000 ARG D 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 358 time to evaluate : 1.929 Fit side-chains REVERT: A 176 MET cc_start: 0.7708 (ttp) cc_final: 0.7326 (ttp) REVERT: A 227 TYR cc_start: 0.8881 (p90) cc_final: 0.8671 (p90) REVERT: A 238 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6966 (mp0) REVERT: A 303 MET cc_start: 0.8457 (ptp) cc_final: 0.7429 (mmm) REVERT: A 445 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8466 (tm-30) REVERT: A 460 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.5938 (pp30) REVERT: A 488 LEU cc_start: 0.9508 (mt) cc_final: 0.9276 (mp) REVERT: A 561 LEU cc_start: 0.8633 (mm) cc_final: 0.8269 (mm) REVERT: A 594 ASP cc_start: 0.8267 (m-30) cc_final: 0.7951 (m-30) REVERT: B 176 MET cc_start: 0.7747 (ttp) cc_final: 0.7511 (ttp) REVERT: B 250 TYR cc_start: 0.8169 (m-10) cc_final: 0.7935 (m-10) REVERT: B 303 MET cc_start: 0.8451 (ptp) cc_final: 0.7408 (mmm) REVERT: B 397 MET cc_start: 0.8439 (mmm) cc_final: 0.7983 (mtp) REVERT: B 460 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.5958 (pp30) REVERT: B 478 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: B 560 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: B 561 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8578 (mm) REVERT: B 594 ASP cc_start: 0.8267 (m-30) cc_final: 0.7952 (m-30) REVERT: C 250 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7916 (m-10) REVERT: C 291 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7941 (tpt170) REVERT: C 303 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7404 (mmm) REVERT: C 436 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7513 (mm-30) REVERT: C 445 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8551 (tm-30) REVERT: C 460 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.5928 (pp30) REVERT: C 478 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: C 561 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8498 (mm) REVERT: C 594 ASP cc_start: 0.8280 (m-30) cc_final: 0.7981 (m-30) REVERT: D 176 MET cc_start: 0.7970 (ttp) cc_final: 0.7491 (ttp) REVERT: D 227 TYR cc_start: 0.8748 (p90) cc_final: 0.8397 (p90) REVERT: D 276 LEU cc_start: 0.9165 (mm) cc_final: 0.8502 (tp) REVERT: D 303 MET cc_start: 0.8418 (ptp) cc_final: 0.7404 (mmm) REVERT: D 445 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8471 (tm-30) REVERT: D 460 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.5878 (pp30) REVERT: D 478 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: D 561 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8525 (mm) REVERT: D 594 ASP cc_start: 0.8262 (m-30) cc_final: 0.7954 (m-30) outliers start: 109 outliers final: 71 residues processed: 425 average time/residue: 0.2646 time to fit residues: 174.2035 Evaluate side-chains 426 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 341 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 604 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 144 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 169 GLN D 143 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17375 Z= 0.253 Angle : 0.619 10.315 23586 Z= 0.306 Chirality : 0.043 0.180 2612 Planarity : 0.004 0.048 2904 Dihedral : 7.428 87.675 2364 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.06 % Allowed : 26.35 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.59 (0.18), residues: 2024 helix: 1.17 (0.16), residues: 1044 sheet: -0.88 (0.52), residues: 116 loop : -0.28 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 124 HIS 0.002 0.001 HIS B 345 PHE 0.012 0.001 PHE B 328 TYR 0.018 0.001 TYR A 223 ARG 0.006 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 352 time to evaluate : 1.816 Fit side-chains REVERT: A 176 MET cc_start: 0.7717 (ttp) cc_final: 0.7364 (ttp) REVERT: A 238 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7092 (mp0) REVERT: A 246 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7657 (mm-40) REVERT: A 303 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7424 (mmm) REVERT: A 436 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 445 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8484 (tm-30) REVERT: A 460 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.5959 (pp30) REVERT: A 561 LEU cc_start: 0.8704 (mm) cc_final: 0.8339 (mm) REVERT: A 594 ASP cc_start: 0.8306 (m-30) cc_final: 0.8061 (m-30) REVERT: B 250 TYR cc_start: 0.8155 (m-10) cc_final: 0.7804 (m-10) REVERT: B 303 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7429 (mmm) REVERT: B 436 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7529 (mm-30) REVERT: B 460 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.5957 (pp30) REVERT: B 478 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: B 560 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: B 561 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8590 (mm) REVERT: B 594 ASP cc_start: 0.8310 (m-30) cc_final: 0.8063 (m-30) REVERT: C 250 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7833 (m-10) REVERT: C 303 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7492 (mmm) REVERT: C 436 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7552 (mm-30) REVERT: C 445 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 460 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.5931 (pp30) REVERT: C 478 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: C 561 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8551 (mm) REVERT: C 594 ASP cc_start: 0.8270 (m-30) cc_final: 0.8051 (m-30) REVERT: D 176 MET cc_start: 0.7848 (ttp) cc_final: 0.7395 (ttp) REVERT: D 227 TYR cc_start: 0.8739 (p90) cc_final: 0.8349 (p90) REVERT: D 303 MET cc_start: 0.8424 (ptp) cc_final: 0.7415 (mmm) REVERT: D 436 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7778 (mm-30) REVERT: D 445 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8514 (tm-30) REVERT: D 460 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.5870 (pp30) REVERT: D 478 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: D 488 LEU cc_start: 0.9499 (mt) cc_final: 0.9287 (mp) REVERT: D 561 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8591 (mm) REVERT: D 594 ASP cc_start: 0.8284 (m-30) cc_final: 0.8044 (m-30) outliers start: 112 outliers final: 82 residues processed: 417 average time/residue: 0.2656 time to fit residues: 171.5427 Evaluate side-chains 428 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 331 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 435 MET Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 398 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 435 MET Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 478 GLU Chi-restraints excluded: chain B residue 560 GLU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 604 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 0.0370 chunk 178 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17375 Z= 0.143 Angle : 0.574 11.171 23586 Z= 0.277 Chirality : 0.040 0.173 2612 Planarity : 0.004 0.046 2904 Dihedral : 6.940 88.420 2360 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.49 % Allowed : 28.41 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.99 (0.19), residues: 2024 helix: 1.49 (0.16), residues: 1060 sheet: -0.88 (0.50), residues: 120 loop : -0.08 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 369 HIS 0.001 0.000 HIS A 321 PHE 0.009 0.001 PHE B 494 TYR 0.016 0.001 TYR A 223 ARG 0.006 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 365 time to evaluate : 2.178 Fit side-chains REVERT: A 176 MET cc_start: 0.7559 (ttp) cc_final: 0.7145 (ttp) REVERT: A 202 MET cc_start: 0.7392 (mmm) cc_final: 0.7145 (mmm) REVERT: A 238 GLU cc_start: 0.7459 (tm-30) cc_final: 0.6889 (mp0) REVERT: A 303 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7194 (mmm) REVERT: A 436 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 445 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 460 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.5793 (pp30) REVERT: A 492 ARG cc_start: 0.7377 (mmm160) cc_final: 0.6643 (mmm-85) REVERT: A 594 ASP cc_start: 0.8064 (m-30) cc_final: 0.7808 (m-30) REVERT: B 147 ASP cc_start: 0.8269 (t0) cc_final: 0.8033 (t0) REVERT: B 202 MET cc_start: 0.7417 (mmm) cc_final: 0.7169 (mmm) REVERT: B 212 ASP cc_start: 0.8562 (m-30) cc_final: 0.8269 (m-30) REVERT: B 303 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7200 (mmm) REVERT: B 436 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7599 (mm-30) REVERT: B 460 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.5724 (pp30) REVERT: B 561 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8420 (mm) REVERT: B 594 ASP cc_start: 0.8088 (m-30) cc_final: 0.7871 (m-30) REVERT: C 147 ASP cc_start: 0.8250 (t0) cc_final: 0.8015 (t0) REVERT: C 202 MET cc_start: 0.7427 (mmm) cc_final: 0.7190 (mmm) REVERT: C 250 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7773 (m-10) REVERT: C 303 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7212 (mmm) REVERT: C 354 ASP cc_start: 0.8300 (m-30) cc_final: 0.7931 (t0) REVERT: C 436 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7649 (mm-30) REVERT: C 445 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8447 (tm-30) REVERT: C 460 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.5774 (pp30) REVERT: C 478 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: C 561 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8582 (mm) REVERT: C 594 ASP cc_start: 0.8035 (m-30) cc_final: 0.7829 (m-30) REVERT: D 147 ASP cc_start: 0.8288 (t0) cc_final: 0.8058 (t0) REVERT: D 176 MET cc_start: 0.7821 (ttp) cc_final: 0.7270 (ttp) REVERT: D 202 MET cc_start: 0.7379 (mmm) cc_final: 0.7164 (mmm) REVERT: D 227 TYR cc_start: 0.8700 (p90) cc_final: 0.8378 (p90) REVERT: D 276 LEU cc_start: 0.9132 (mm) cc_final: 0.8494 (tp) REVERT: D 303 MET cc_start: 0.7961 (ptp) cc_final: 0.7181 (mmm) REVERT: D 436 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7706 (mm-30) REVERT: D 445 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8385 (tm-30) REVERT: D 460 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.5730 (pp30) REVERT: D 478 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: D 561 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8588 (mm) REVERT: D 594 ASP cc_start: 0.8071 (m-30) cc_final: 0.7842 (m-30) REVERT: D 620 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6508 (t0) outliers start: 83 outliers final: 48 residues processed: 413 average time/residue: 0.2717 time to fit residues: 173.2362 Evaluate side-chains 401 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 339 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 303 MET Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 620 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 143 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 165 optimal weight: 0.0040 chunk 173 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN D 143 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17375 Z= 0.184 Angle : 0.601 10.213 23586 Z= 0.291 Chirality : 0.042 0.174 2612 Planarity : 0.004 0.045 2904 Dihedral : 6.910 88.598 2359 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.49 % Allowed : 28.63 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 0.92 (0.19), residues: 2024 helix: 1.46 (0.16), residues: 1036 sheet: -0.81 (0.51), residues: 120 loop : -0.12 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.002 0.001 HIS A 484 PHE 0.011 0.001 PHE C 452 TYR 0.021 0.001 TYR D 262 ARG 0.005 0.000 ARG D 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 346 time to evaluate : 1.972 Fit side-chains REVERT: A 176 MET cc_start: 0.7537 (ttp) cc_final: 0.7162 (ttp) REVERT: A 202 MET cc_start: 0.7408 (mmm) cc_final: 0.7180 (mmm) REVERT: A 238 GLU cc_start: 0.7473 (tm-30) cc_final: 0.6855 (mp0) REVERT: A 303 MET cc_start: 0.8141 (ptp) cc_final: 0.7227 (mmm) REVERT: A 436 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7668 (mm-30) REVERT: A 445 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 460 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.5804 (pp30) REVERT: A 492 ARG cc_start: 0.7475 (mmm160) cc_final: 0.6673 (mmm-85) REVERT: A 594 ASP cc_start: 0.8076 (m-30) cc_final: 0.7849 (m-30) REVERT: A 620 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6531 (t0) REVERT: B 202 MET cc_start: 0.7381 (mmm) cc_final: 0.7166 (mmm) REVERT: B 212 ASP cc_start: 0.8519 (m-30) cc_final: 0.8276 (m-30) REVERT: B 303 MET cc_start: 0.8166 (ptp) cc_final: 0.7235 (mmm) REVERT: B 436 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 460 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.5773 (pp30) REVERT: B 561 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 594 ASP cc_start: 0.8097 (m-30) cc_final: 0.7851 (m-30) REVERT: B 620 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6502 (t0) REVERT: C 202 MET cc_start: 0.7390 (mmm) cc_final: 0.7183 (mmm) REVERT: C 250 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: C 276 LEU cc_start: 0.9162 (mm) cc_final: 0.8510 (tp) REVERT: C 303 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7312 (mmm) REVERT: C 354 ASP cc_start: 0.8344 (m-30) cc_final: 0.7948 (t0) REVERT: C 436 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7653 (mm-30) REVERT: C 445 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8508 (tm-30) REVERT: C 460 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.5742 (pp30) REVERT: C 478 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: C 561 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8516 (mm) REVERT: C 594 ASP cc_start: 0.8166 (m-30) cc_final: 0.7936 (m-30) REVERT: D 176 MET cc_start: 0.7794 (ttp) cc_final: 0.7325 (ttp) REVERT: D 202 MET cc_start: 0.7394 (mmm) cc_final: 0.7182 (mmm) REVERT: D 227 TYR cc_start: 0.8728 (p90) cc_final: 0.8302 (p90) REVERT: D 276 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8549 (tp) REVERT: D 303 MET cc_start: 0.8125 (ptp) cc_final: 0.7225 (mmm) REVERT: D 436 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7760 (mm-30) REVERT: D 445 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8430 (tm-30) REVERT: D 460 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.5710 (pp30) REVERT: D 478 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: D 561 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8582 (mm) REVERT: D 594 ASP cc_start: 0.8060 (m-30) cc_final: 0.7832 (m-30) REVERT: D 620 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6530 (t0) outliers start: 83 outliers final: 65 residues processed: 399 average time/residue: 0.2551 time to fit residues: 159.9623 Evaluate side-chains 412 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 332 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain A residue 620 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 398 CYS Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 620 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 6.9990 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 0.0980 chunk 125 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17375 Z= 0.150 Angle : 0.590 10.960 23586 Z= 0.283 Chirality : 0.041 0.171 2612 Planarity : 0.004 0.046 2904 Dihedral : 6.663 89.229 2359 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.38 % Allowed : 29.33 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: 1.05 (0.19), residues: 2024 helix: 1.47 (0.16), residues: 1064 sheet: -0.77 (0.52), residues: 120 loop : 0.02 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 369 HIS 0.001 0.000 HIS A 345 PHE 0.008 0.001 PHE A 328 TYR 0.014 0.001 TYR A 223 ARG 0.005 0.000 ARG D 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 350 time to evaluate : 2.132 Fit side-chains REVERT: A 176 MET cc_start: 0.7595 (ttp) cc_final: 0.7186 (ttp) REVERT: A 202 MET cc_start: 0.7426 (mmm) cc_final: 0.7175 (mmm) REVERT: A 238 GLU cc_start: 0.7503 (tm-30) cc_final: 0.6891 (mp0) REVERT: A 303 MET cc_start: 0.7813 (ptp) cc_final: 0.7174 (mmm) REVERT: A 436 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 445 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8369 (tm-30) REVERT: A 460 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.5896 (pp30) REVERT: A 492 ARG cc_start: 0.7369 (mmm160) cc_final: 0.6570 (mmm-85) REVERT: A 594 ASP cc_start: 0.8155 (m-30) cc_final: 0.7885 (m-30) REVERT: B 202 MET cc_start: 0.7426 (mmm) cc_final: 0.7199 (mmm) REVERT: B 303 MET cc_start: 0.7932 (ptp) cc_final: 0.7154 (mmm) REVERT: B 436 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7520 (mm-30) REVERT: B 460 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.5698 (pp30) REVERT: B 490 LYS cc_start: 0.9296 (ptpt) cc_final: 0.8842 (mtmm) REVERT: B 554 GLU cc_start: 0.8457 (pt0) cc_final: 0.8189 (tt0) REVERT: B 561 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8350 (mm) REVERT: B 594 ASP cc_start: 0.8167 (m-30) cc_final: 0.7900 (m-30) REVERT: B 620 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6406 (t0) REVERT: C 202 MET cc_start: 0.7438 (mmm) cc_final: 0.7202 (mmm) REVERT: C 212 ASP cc_start: 0.8597 (m-30) cc_final: 0.8313 (m-30) REVERT: C 250 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7609 (m-10) REVERT: C 276 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8481 (tp) REVERT: C 303 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7163 (mmm) REVERT: C 354 ASP cc_start: 0.8278 (m-30) cc_final: 0.7953 (t0) REVERT: C 436 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7619 (mm-30) REVERT: C 445 GLU cc_start: 0.8713 (tm-30) cc_final: 0.8456 (tm-30) REVERT: C 460 GLN cc_start: 0.7085 (OUTLIER) cc_final: 0.5742 (pp30) REVERT: C 478 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: C 490 LYS cc_start: 0.9060 (ptpt) cc_final: 0.8798 (ptpp) REVERT: C 561 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8589 (mm) REVERT: C 594 ASP cc_start: 0.8102 (m-30) cc_final: 0.7864 (m-30) REVERT: D 176 MET cc_start: 0.7768 (ttp) cc_final: 0.7264 (ttp) REVERT: D 202 MET cc_start: 0.7397 (mmm) cc_final: 0.7176 (mmm) REVERT: D 227 TYR cc_start: 0.8693 (p90) cc_final: 0.8364 (p90) REVERT: D 276 LEU cc_start: 0.9111 (mm) cc_final: 0.8508 (tp) REVERT: D 303 MET cc_start: 0.7902 (ptp) cc_final: 0.7148 (mmm) REVERT: D 436 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7639 (mm-30) REVERT: D 445 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8402 (tm-30) REVERT: D 460 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.5700 (pp30) REVERT: D 478 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: D 561 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8567 (mm) REVERT: D 594 ASP cc_start: 0.8142 (m-30) cc_final: 0.7902 (m-30) REVERT: D 620 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6461 (t0) outliers start: 81 outliers final: 58 residues processed: 399 average time/residue: 0.2584 time to fit residues: 160.3749 Evaluate side-chains 408 residues out of total 1848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 336 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 460 GLN Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 460 GLN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 604 ASP Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 250 TYR Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain C residue 398 CYS Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 460 GLN Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 396 LEU Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 460 GLN Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 478 GLU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 604 ASP Chi-restraints excluded: chain D residue 620 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 ASN D 416 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.160373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.120130 restraints weight = 25051.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.122217 restraints weight = 13052.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.122880 restraints weight = 9241.343| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17375 Z= 0.198 Angle : 0.623 11.263 23586 Z= 0.301 Chirality : 0.042 0.179 2612 Planarity : 0.004 0.047 2904 Dihedral : 6.780 89.730 2359 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.76 % Allowed : 29.06 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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 (0.19), residues: 2024 helix: 1.33 (0.16), residues: 1064 sheet: -0.66 (0.55), residues: 116 loop : -0.15 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 451 HIS 0.002 0.001 HIS A 484 PHE 0.013 0.001 PHE B 549 TYR 0.016 0.001 TYR A 223 ARG 0.006 0.000 ARG C 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.53 seconds wall clock time: 71 minutes 45.07 seconds (4305.07 seconds total)