Starting phenix.real_space_refine on Mon Feb 19 03:34:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/02_2024/6zlt_11273.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/02_2024/6zlt_11273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/02_2024/6zlt_11273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/02_2024/6zlt_11273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/02_2024/6zlt_11273.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zlt_11273/02_2024/6zlt_11273.pdb" } resolution = 3.9 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= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 260 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 14766 2.51 5 N 3968 2.21 5 O 4574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 3": "OD1" <-> "OD2" Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 52": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ASP 176": "OD1" <-> "OD2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 326": "OD1" <-> "OD2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A ASP 409": "OD1" <-> "OD2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A ASP 464": "OD1" <-> "OD2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ASP 160": "OD1" <-> "OD2" Residue "B TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 268": "OD1" <-> "OD2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B GLU 379": "OE1" <-> "OE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 450": "OD1" <-> "OD2" Residue "B GLU 481": "OE1" <-> "OE2" Residue "B ASP 504": "OD1" <-> "OD2" Residue "B TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 609": "OE1" <-> "OE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ASP 615": "OD1" <-> "OD2" Residue "B GLU 629": "OE1" <-> "OE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "B TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 747": "OE1" <-> "OE2" Residue "B GLU 774": "OE1" <-> "OE2" Residue "B GLU 818": "OE1" <-> "OE2" Residue "B GLU 826": "OE1" <-> "OE2" Residue "B ARG 834": "NH1" <-> "NH2" Residue "B ASP 885": "OD1" <-> "OD2" Residue "B PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3": "OD1" <-> "OD2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C ASP 52": "OD1" <-> "OD2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ASP 176": "OD1" <-> "OD2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 326": "OD1" <-> "OD2" Residue "C GLU 356": "OE1" <-> "OE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ASP 365": "OD1" <-> "OD2" Residue "C ASP 409": "OD1" <-> "OD2" Residue "C ASP 453": "OD1" <-> "OD2" Residue "C ASP 464": "OD1" <-> "OD2" Residue "C ASP 471": "OD1" <-> "OD2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "D ASP 96": "OD1" <-> "OD2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 268": "OD1" <-> "OD2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 450": "OD1" <-> "OD2" Residue "D GLU 481": "OE1" <-> "OE2" Residue "D ASP 504": "OD1" <-> "OD2" Residue "D TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 537": "OD1" <-> "OD2" Residue "D TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 568": "NH1" <-> "NH2" Residue "D TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D ASP 614": "OD1" <-> "OD2" Residue "D ASP 615": "OD1" <-> "OD2" Residue "D GLU 629": "OE1" <-> "OE2" Residue "D ASP 659": "OD1" <-> "OD2" Residue "D TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 747": "OE1" <-> "OE2" Residue "D GLU 774": "OE1" <-> "OE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D GLU 826": "OE1" <-> "OE2" Residue "D ARG 834": "NH1" <-> "NH2" Residue "D ASP 885": "OD1" <-> "OD2" Residue "D PHE 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 994": "OD1" <-> "OD2" Residue "D TYR 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23386 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4358 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7335 Classifications: {'peptide': 933} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 900} Chain: "C" Number of atoms: 4358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4358 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 1, 'PTRANS': 18, 'TRANS': 532} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 7335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 933, 7335 Classifications: {'peptide': 933} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 900} Time building chain proxies: 12.03, per 1000 atoms: 0.51 Number of scatterers: 23386 At special positions: 0 Unit cell: (155.15, 110.21, 140.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 4574 8.00 N 3968 7.00 C 14766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 299 " distance=2.05 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 389 " distance=2.05 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 299 " distance=2.05 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 389 " distance=2.05 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: 9.05 Conformation dependent library (CDL) restraints added in 4.1 seconds 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5396 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 28 sheets defined 22.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 1 through 5 Processing helix chain 'A' and resid 17 through 21 removed outlier: 3.738A pdb=" N ALA A 20 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 84 through 108 removed outlier: 4.211A pdb=" N ASN A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 111 No H-bonds generated for 'chain 'A' and resid 109 through 111' Processing helix chain 'A' and resid 118 through 141 Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.625A pdb=" N TYR A 157 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 185 removed outlier: 4.332A pdb=" N ASP A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 213 removed outlier: 3.906A pdb=" N TYR A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.886A pdb=" N MET A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.759A pdb=" N VAL A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 313 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.910A pdb=" N HIS A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 426 through 442 Processing helix chain 'A' and resid 447 through 451 removed outlier: 4.151A pdb=" N LYS A 451 " --> pdb=" O PHE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.675A pdb=" N ASN A 521 " --> pdb=" O ILE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.547A pdb=" N ILE A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.635A pdb=" N ASP B 96 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 93 through 97' Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.930A pdb=" N GLY B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 249 Processing helix chain 'B' and resid 377 through 384 Processing helix chain 'B' and resid 409 through 417 Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.726A pdb=" N LYS B 608 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 729 Processing helix chain 'B' and resid 781 through 786 removed outlier: 3.814A pdb=" N GLY B 786 " --> pdb=" O VAL B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 822 Processing helix chain 'B' and resid 890 through 896 removed outlier: 3.948A pdb=" N PHE B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 914 removed outlier: 3.595A pdb=" N ASN B 913 " --> pdb=" O ARG B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 943 Processing helix chain 'B' and resid 961 through 967 Processing helix chain 'C' and resid 1 through 5 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.738A pdb=" N ALA C 20 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 69 through 77 Processing helix chain 'C' and resid 84 through 108 removed outlier: 4.211A pdb=" N ASN C 88 " --> pdb=" O ASP C 84 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 118 through 141 Processing helix chain 'C' and resid 153 through 157 removed outlier: 3.625A pdb=" N TYR C 157 " --> pdb=" O PRO C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 185 removed outlier: 4.332A pdb=" N ASP C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.906A pdb=" N TYR C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 238 through 244 removed outlier: 3.886A pdb=" N MET C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 305 through 313 removed outlier: 3.759A pdb=" N VAL C 309 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS C 313 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 344 removed outlier: 3.910A pdb=" N HIS C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 422 Processing helix chain 'C' and resid 426 through 442 Processing helix chain 'C' and resid 447 through 451 removed outlier: 4.151A pdb=" N LYS C 451 " --> pdb=" O PHE C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 485 Processing helix chain 'C' and resid 491 through 499 Processing helix chain 'C' and resid 501 through 513 Processing helix chain 'C' and resid 517 through 521 removed outlier: 3.675A pdb=" N ASN C 521 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 542 removed outlier: 3.547A pdb=" N ILE C 539 " --> pdb=" O PRO C 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 97 removed outlier: 3.635A pdb=" N ASP D 96 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU D 97 " --> pdb=" O LYS D 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 97' Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.930A pdb=" N GLY D 113 " --> pdb=" O ILE D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 377 through 384 Processing helix chain 'D' and resid 409 through 417 Processing helix chain 'D' and resid 604 through 608 removed outlier: 3.726A pdb=" N LYS D 608 " --> pdb=" O ASN D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 729 Processing helix chain 'D' and resid 781 through 786 removed outlier: 3.814A pdb=" N GLY D 786 " --> pdb=" O VAL D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 822 Processing helix chain 'D' and resid 890 through 896 removed outlier: 3.948A pdb=" N PHE D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 914 removed outlier: 3.595A pdb=" N ASN D 913 " --> pdb=" O ARG D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 943 Processing helix chain 'D' and resid 961 through 967 Processing sheet with id= 1, first strand: chain 'A' and resid 269 through 271 removed outlier: 4.076A pdb=" N TRP A 269 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 405 " --> pdb=" O TRP A 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 271 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE A 403 " --> pdb=" O ILE A 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'B' and resid 85 through 87 removed outlier: 4.019A pdb=" N THR B 90 " --> pdb=" O THR B 87 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 101 through 104 removed outlier: 4.363A pdb=" N ILE B 179 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER B 178 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 156 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE B 202 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE B 158 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 157 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 162 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 128 through 132 Processing sheet with id= 5, first strand: chain 'B' and resid 338 through 342 removed outlier: 3.671A pdb=" N TYR B 327 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL B 304 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 305 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 218 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B1012 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 220 " --> pdb=" O PHE B1010 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN B 953 " --> pdb=" O PHE B 877 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 873 " --> pdb=" O GLY B 957 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 760 " --> pdb=" O THR B 756 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 745 " --> pdb=" O TYR B 711 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 711 " --> pdb=" O GLY B 745 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 749 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 706 " --> pdb=" O PHE B 697 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 712 " --> pdb=" O THR B 691 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 627 " --> pdb=" O GLU B 686 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 617 " --> pdb=" O ASP B 696 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY B 626 " --> pdb=" O THR B 591 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR B 591 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 574 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 514 " --> pdb=" O TYR B 552 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 554 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY B 508 " --> pdb=" O PHE B 558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET B 506 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET B 509 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 490 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP B 488 " --> pdb=" O LEU B 511 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 221 through 224 Processing sheet with id= 7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.794A pdb=" N ARG B 345 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.702A pdb=" N ARG B 426 " --> pdb=" O ASN B 366 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 452 " --> pdb=" O TRP B 483 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS B 482 " --> pdb=" O SER B 517 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS B 518 " --> pdb=" O ALA B 548 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 458 through 460 removed outlier: 3.785A pdb=" N ALA B 475 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 719 through 722 removed outlier: 3.570A pdb=" N ILE B 736 " --> pdb=" O THR B 720 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 879 through 881 Processing sheet with id= 12, first strand: chain 'B' and resid 259 through 265 removed outlier: 6.802A pdb=" N GLY B 264 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU B 273 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 740 through 744 removed outlier: 3.606A pdb=" N GLU B 777 " --> pdb=" O ALA B 740 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS B 742 " --> pdb=" O ILE B 775 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE B 775 " --> pdb=" O LYS B 742 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN B 744 " --> pdb=" O ASN B 773 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN B 773 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 804 through 806 removed outlier: 3.765A pdb=" N TYR B 853 " --> pdb=" O GLN B 804 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 806 " --> pdb=" O TRP B 851 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP B 851 " --> pdb=" O GLY B 806 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 269 through 271 removed outlier: 4.076A pdb=" N TRP C 269 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE C 405 " --> pdb=" O TRP C 269 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 271 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ILE C 403 " --> pdb=" O ILE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'D' and resid 85 through 87 removed outlier: 4.019A pdb=" N THR D 90 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 101 through 104 removed outlier: 4.363A pdb=" N ILE D 179 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER D 178 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU D 156 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE D 202 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE D 158 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR D 157 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 162 " --> pdb=" O ILE D 159 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 128 through 132 Processing sheet with id= 19, first strand: chain 'D' and resid 338 through 342 removed outlier: 3.671A pdb=" N TYR D 327 " --> pdb=" O TYR D 308 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL D 304 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE D 305 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 218 " --> pdb=" O LEU D1012 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D1012 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL D 220 " --> pdb=" O PHE D1010 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN D 953 " --> pdb=" O PHE D 877 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP D 873 " --> pdb=" O GLY D 957 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 760 " --> pdb=" O THR D 756 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY D 745 " --> pdb=" O TYR D 711 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR D 711 " --> pdb=" O GLY D 745 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 749 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 706 " --> pdb=" O PHE D 697 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D 712 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN D 627 " --> pdb=" O GLU D 686 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 617 " --> pdb=" O ASP D 696 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLY D 626 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR D 591 " --> pdb=" O GLY D 626 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 574 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU D 514 " --> pdb=" O TYR D 552 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 554 " --> pdb=" O ASN D 512 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY D 508 " --> pdb=" O PHE D 558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET D 506 " --> pdb=" O LYS D 560 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N MET D 509 " --> pdb=" O ALA D 490 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 490 " --> pdb=" O MET D 509 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP D 488 " --> pdb=" O LEU D 511 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 221 through 224 Processing sheet with id= 21, first strand: chain 'D' and resid 311 through 313 removed outlier: 3.794A pdb=" N ARG D 345 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.702A pdb=" N ARG D 426 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 452 " --> pdb=" O TRP D 483 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS D 482 " --> pdb=" O SER D 517 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS D 518 " --> pdb=" O ALA D 548 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 458 through 460 removed outlier: 3.785A pdb=" N ALA D 475 " --> pdb=" O THR D 460 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 719 through 722 removed outlier: 3.570A pdb=" N ILE D 736 " --> pdb=" O THR D 720 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 879 through 881 Processing sheet with id= 26, first strand: chain 'D' and resid 259 through 265 removed outlier: 6.802A pdb=" N GLY D 264 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LEU D 273 " --> pdb=" O GLY D 264 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'D' and resid 740 through 744 removed outlier: 3.606A pdb=" N GLU D 777 " --> pdb=" O ALA D 740 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS D 742 " --> pdb=" O ILE D 775 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE D 775 " --> pdb=" O LYS D 742 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLN D 744 " --> pdb=" O ASN D 773 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASN D 773 " --> pdb=" O GLN D 744 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 804 through 806 removed outlier: 3.765A pdb=" N TYR D 853 " --> pdb=" O GLN D 804 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY D 806 " --> pdb=" O TRP D 851 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP D 851 " --> pdb=" O GLY D 806 " (cutoff:3.500A) 758 hydrogen bonds defined for protein. 2064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.60 Time building geometry restraints manager: 9.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7760 1.34 - 1.47: 6076 1.47 - 1.59: 9968 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 23942 Sorted by residual: bond pdb=" N ASP C 300 " pdb=" CA ASP C 300 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.06e+00 bond pdb=" N ASP A 300 " pdb=" CA ASP A 300 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.06e+00 bond pdb=" C CYS C 298 " pdb=" N CYS C 299 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.47e+00 bond pdb=" C CYS A 298 " pdb=" N CYS A 299 " ideal model delta sigma weight residual 1.329 1.351 -0.022 1.40e-02 5.10e+03 2.47e+00 bond pdb=" CA LYS B 701 " pdb=" CB LYS B 701 " ideal model delta sigma weight residual 1.530 1.554 -0.023 1.51e-02 4.39e+03 2.41e+00 ... (remaining 23937 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.34: 516 106.34 - 113.29: 12204 113.29 - 120.25: 9120 120.25 - 127.20: 10422 127.20 - 134.15: 248 Bond angle restraints: 32510 Sorted by residual: angle pdb=" C CYS C 298 " pdb=" N CYS C 299 " pdb=" CA CYS C 299 " ideal model delta sigma weight residual 121.70 129.32 -7.62 1.80e+00 3.09e-01 1.79e+01 angle pdb=" C CYS A 298 " pdb=" N CYS A 299 " pdb=" CA CYS A 299 " ideal model delta sigma weight residual 121.70 129.32 -7.62 1.80e+00 3.09e-01 1.79e+01 angle pdb=" C GLY D 167 " pdb=" N MET D 168 " pdb=" CA MET D 168 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C GLY B 167 " pdb=" N MET B 168 " pdb=" CA MET B 168 " ideal model delta sigma weight residual 121.54 129.51 -7.97 1.91e+00 2.74e-01 1.74e+01 angle pdb=" C ASP C 388 " pdb=" N CYS C 389 " pdb=" CA CYS C 389 " ideal model delta sigma weight residual 120.28 126.22 -5.94 1.44e+00 4.82e-01 1.70e+01 ... (remaining 32505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 12448 17.84 - 35.68: 1190 35.68 - 53.52: 270 53.52 - 71.36: 52 71.36 - 89.20: 32 Dihedral angle restraints: 13992 sinusoidal: 5446 harmonic: 8546 Sorted by residual: dihedral pdb=" CA CYS A 387 " pdb=" C CYS A 387 " pdb=" N ASP A 388 " pdb=" CA ASP A 388 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA CYS C 387 " pdb=" C CYS C 387 " pdb=" N ASP C 388 " pdb=" CA ASP C 388 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ALA D 566 " pdb=" C ALA D 566 " pdb=" N ASP D 567 " pdb=" CA ASP D 567 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 13989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2726 0.063 - 0.126: 570 0.126 - 0.189: 104 0.189 - 0.252: 10 0.252 - 0.315: 4 Chirality restraints: 3414 Sorted by residual: chirality pdb=" CB ILE D 212 " pdb=" CA ILE D 212 " pdb=" CG1 ILE D 212 " pdb=" CG2 ILE D 212 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB ILE B 212 " pdb=" CA ILE B 212 " pdb=" CG1 ILE B 212 " pdb=" CG2 ILE B 212 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB VAL B 668 " pdb=" CA VAL B 668 " pdb=" CG1 VAL B 668 " pdb=" CG2 VAL B 668 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 3411 not shown) Planarity restraints: 4290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 436 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 437 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 437 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 437 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 436 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO D 437 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 437 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 437 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 826 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" CD GLU B 826 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 826 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 826 " -0.013 2.00e-02 2.50e+03 ... (remaining 4287 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2136 2.74 - 3.28: 21776 3.28 - 3.82: 37984 3.82 - 4.36: 43678 4.36 - 4.90: 77374 Nonbonded interactions: 182948 Sorted by model distance: nonbonded pdb=" O THR A 324 " pdb=" OG1 THR A 324 " model vdw 2.198 2.440 nonbonded pdb=" O THR C 324 " pdb=" OG1 THR C 324 " model vdw 2.198 2.440 nonbonded pdb=" O SER A 55 " pdb=" OG SER A 55 " model vdw 2.215 2.440 nonbonded pdb=" O SER C 55 " pdb=" OG SER C 55 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR C 38 " pdb=" O SER D 653 " model vdw 2.252 2.440 ... (remaining 182943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.020 Extract box with map and model: 5.190 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 59.590 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 : 0.005 0.048 23942 Z= 0.340 Angle : 0.817 9.596 32510 Z= 0.458 Chirality : 0.055 0.315 3414 Planarity : 0.006 0.056 4290 Dihedral : 15.478 89.199 8584 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.98 % Allowed : 10.99 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % 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: -4.15 (0.13), residues: 2962 helix: -2.67 (0.14), residues: 634 sheet: -2.81 (0.17), residues: 760 loop : -2.74 (0.13), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 599 HIS 0.007 0.001 HIS D 482 PHE 0.025 0.002 PHE B 438 TYR 0.028 0.002 TYR B 191 ARG 0.004 0.000 ARG D 588 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 295 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 MET cc_start: 0.8174 (mmm) cc_final: 0.7895 (mmm) REVERT: B 176 ILE cc_start: 0.8706 (mm) cc_final: 0.8203 (tp) REVERT: B 308 TYR cc_start: 0.8389 (m-80) cc_final: 0.8182 (m-80) REVERT: B 450 ASP cc_start: 0.7839 (t70) cc_final: 0.7509 (t0) REVERT: B 607 MET cc_start: 0.6665 (mmm) cc_final: 0.6375 (tpp) REVERT: B 1010 PHE cc_start: 0.7214 (m-80) cc_final: 0.6994 (t80) REVERT: D 168 MET cc_start: 0.8383 (mmm) cc_final: 0.8168 (mmm) REVERT: D 408 ARG cc_start: 0.8475 (ttt90) cc_final: 0.8261 (ttt90) REVERT: D 419 ASP cc_start: 0.7216 (m-30) cc_final: 0.7014 (m-30) REVERT: D 607 MET cc_start: 0.6620 (mmm) cc_final: 0.5662 (tpp) REVERT: D 695 ILE cc_start: 0.9156 (mp) cc_final: 0.8903 (mt) REVERT: D 859 PHE cc_start: 0.7352 (t80) cc_final: 0.6978 (t80) outliers start: 24 outliers final: 5 residues processed: 315 average time/residue: 0.3926 time to fit residues: 187.0617 Evaluate side-chains 183 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 178 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 608 LYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 608 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 232 optimal weight: 0.0000 chunk 89 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 134 HIS ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN A 422 ASN A 506 ASN B 112 GLN B 115 ASN B 174 ASN B 233 ASN B 266 ASN B 347 ASN B 603 GLN B 628 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 ASN B 765 ASN B 816 GLN C 121 GLN C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN C 422 ASN C 506 ASN D 112 GLN D 115 ASN D 174 ASN ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN D 347 ASN D 603 GLN D 628 GLN ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 754 ASN D 765 ASN D 816 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23942 Z= 0.225 Angle : 0.568 12.305 32510 Z= 0.305 Chirality : 0.043 0.150 3414 Planarity : 0.004 0.046 4290 Dihedral : 5.314 59.217 3291 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.61 % Allowed : 16.08 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.14), residues: 2962 helix: -0.93 (0.19), residues: 652 sheet: -2.17 (0.18), residues: 770 loop : -2.29 (0.14), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 599 HIS 0.005 0.001 HIS A 343 PHE 0.018 0.001 PHE C 135 TYR 0.019 0.001 TYR D 191 ARG 0.005 0.000 ARG D 421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 202 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 488 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6214 (tm-30) REVERT: B 168 MET cc_start: 0.8468 (mmm) cc_final: 0.8220 (mmm) REVERT: D 408 ARG cc_start: 0.8446 (ttt90) cc_final: 0.8112 (ttt90) REVERT: D 607 MET cc_start: 0.6856 (mmm) cc_final: 0.5829 (tpp) outliers start: 64 outliers final: 40 residues processed: 255 average time/residue: 0.3563 time to fit residues: 144.4067 Evaluate side-chains 216 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 176 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.0670 chunk 83 optimal weight: 4.9990 chunk 223 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 269 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 267 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 139 GLN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN B 628 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 GLN ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 23942 Z= 0.396 Angle : 0.623 11.347 32510 Z= 0.337 Chirality : 0.044 0.166 3414 Planarity : 0.004 0.043 4290 Dihedral : 5.298 56.891 3283 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 4.44 % Allowed : 17.14 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.15), residues: 2962 helix: -0.27 (0.21), residues: 652 sheet: -2.01 (0.18), residues: 762 loop : -2.20 (0.14), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 599 HIS 0.018 0.003 HIS A 134 PHE 0.024 0.002 PHE A 312 TYR 0.027 0.002 TYR D 191 ARG 0.004 0.001 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 183 time to evaluate : 2.575 Fit side-chains REVERT: A 488 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6272 (tm-30) REVERT: B 191 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.6953 (t80) REVERT: B 298 GLU cc_start: 0.6535 (mm-30) cc_final: 0.6219 (mm-30) REVERT: D 109 ILE cc_start: 0.8860 (mm) cc_final: 0.8627 (mm) REVERT: D 191 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7029 (t80) REVERT: D 203 THR cc_start: 0.8913 (t) cc_final: 0.8712 (p) REVERT: D 241 MET cc_start: 0.7654 (tpp) cc_final: 0.7430 (ttt) REVERT: D 408 ARG cc_start: 0.8495 (ttt90) cc_final: 0.8151 (ttt90) REVERT: D 607 MET cc_start: 0.6885 (mmm) cc_final: 0.5994 (tpp) outliers start: 109 outliers final: 77 residues processed: 266 average time/residue: 0.3268 time to fit residues: 140.9706 Evaluate side-chains 251 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 172 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 213 LYS Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 628 GLN Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 822 HIS Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 6.9990 chunk 202 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 270 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 215 GLN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 GLN ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.126 23942 Z= 0.581 Angle : 0.726 16.471 32510 Z= 0.392 Chirality : 0.047 0.193 3414 Planarity : 0.005 0.047 4290 Dihedral : 5.633 56.906 3283 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.40 % Favored : 89.60 % Rotamer: Outliers : 5.90 % Allowed : 18.93 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.15), residues: 2962 helix: 0.03 (0.21), residues: 618 sheet: -2.11 (0.18), residues: 742 loop : -2.17 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 599 HIS 0.010 0.002 HIS D 518 PHE 0.025 0.002 PHE D 428 TYR 0.033 0.002 TYR D 191 ARG 0.005 0.001 ARG B 588 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 179 time to evaluate : 2.730 Fit side-chains revert: symmetry clash REVERT: A 288 MET cc_start: 0.9057 (mmt) cc_final: 0.8542 (mpp) REVERT: A 488 GLU cc_start: 0.7331 (mt-10) cc_final: 0.5945 (tm-30) REVERT: B 109 ILE cc_start: 0.8879 (mm) cc_final: 0.8620 (mm) REVERT: B 191 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7367 (t80) REVERT: B 298 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6527 (mm-30) REVERT: B 383 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8011 (t0) REVERT: B 905 LEU cc_start: 0.8642 (mt) cc_final: 0.8350 (mt) REVERT: D 110 GLN cc_start: 0.8469 (pp30) cc_final: 0.7407 (pp30) REVERT: D 191 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7461 (t80) REVERT: D 241 MET cc_start: 0.7654 (tpp) cc_final: 0.7337 (ttt) REVERT: D 607 MET cc_start: 0.7076 (mmm) cc_final: 0.6761 (tpp) outliers start: 145 outliers final: 107 residues processed: 292 average time/residue: 0.3058 time to fit residues: 147.8302 Evaluate side-chains 282 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 172 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 840 HIS Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 865 ILE Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 618 LEU Chi-restraints excluded: chain D residue 628 GLN Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 691 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 822 HIS Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 884 VAL Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 991 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 2.9990 chunk 162 optimal weight: 0.2980 chunk 4 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 256 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23942 Z= 0.204 Angle : 0.551 15.089 32510 Z= 0.294 Chirality : 0.043 0.141 3414 Planarity : 0.003 0.041 4290 Dihedral : 5.014 58.840 3283 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.36 % Allowed : 21.62 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 2962 helix: 0.19 (0.22), residues: 642 sheet: -1.73 (0.19), residues: 746 loop : -1.99 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 599 HIS 0.006 0.001 HIS C 134 PHE 0.019 0.001 PHE A 312 TYR 0.020 0.001 TYR D 191 ARG 0.003 0.000 ARG A 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 192 time to evaluate : 2.827 Fit side-chains revert: symmetry clash REVERT: A 488 GLU cc_start: 0.7155 (mt-10) cc_final: 0.5875 (tm-30) REVERT: B 109 ILE cc_start: 0.8825 (mm) cc_final: 0.8565 (mm) REVERT: B 191 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.6761 (t80) REVERT: B 203 THR cc_start: 0.8789 (t) cc_final: 0.8565 (p) REVERT: B 383 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8079 (t0) REVERT: B 449 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8885 (tp) REVERT: C 488 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6439 (tm-30) REVERT: D 110 GLN cc_start: 0.8355 (pp30) cc_final: 0.7280 (pp30) REVERT: D 191 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6741 (t80) REVERT: D 241 MET cc_start: 0.7702 (tpp) cc_final: 0.7412 (ttt) REVERT: D 408 ARG cc_start: 0.8454 (ttt90) cc_final: 0.8075 (ttt90) REVERT: D 607 MET cc_start: 0.7068 (mmm) cc_final: 0.6765 (tpp) REVERT: D 820 ASP cc_start: 0.6687 (OUTLIER) cc_final: 0.6455 (p0) outliers start: 107 outliers final: 79 residues processed: 282 average time/residue: 0.3237 time to fit residues: 147.7877 Evaluate side-chains 258 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 174 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 370 GLU Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 628 GLN Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 991 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.5980 chunk 257 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 286 optimal weight: 7.9990 chunk 237 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23942 Z= 0.207 Angle : 0.531 11.541 32510 Z= 0.284 Chirality : 0.042 0.138 3414 Planarity : 0.003 0.042 4290 Dihedral : 4.840 58.913 3283 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.48 % Allowed : 21.99 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.97 (0.15), residues: 2962 helix: 0.27 (0.22), residues: 642 sheet: -1.60 (0.19), residues: 752 loop : -1.84 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 599 HIS 0.005 0.001 HIS C 134 PHE 0.014 0.001 PHE A 312 TYR 0.020 0.001 TYR D 191 ARG 0.004 0.000 ARG D 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 190 time to evaluate : 2.646 Fit side-chains revert: symmetry clash REVERT: A 284 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8829 (mm) REVERT: A 347 MET cc_start: 0.5379 (mmm) cc_final: 0.5105 (mmm) REVERT: A 488 GLU cc_start: 0.7169 (mt-10) cc_final: 0.5825 (tm-30) REVERT: B 109 ILE cc_start: 0.8800 (mm) cc_final: 0.8540 (mm) REVERT: B 191 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6856 (t80) REVERT: B 383 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8056 (t0) REVERT: B 449 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8776 (tp) REVERT: B 849 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: C 488 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6361 (tm-30) REVERT: D 110 GLN cc_start: 0.8378 (pp30) cc_final: 0.7330 (pp30) REVERT: D 191 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6650 (t80) REVERT: D 241 MET cc_start: 0.7695 (tpp) cc_final: 0.7422 (ttt) REVERT: D 408 ARG cc_start: 0.8483 (ttt90) cc_final: 0.8223 (ttt90) REVERT: D 607 MET cc_start: 0.6992 (mmm) cc_final: 0.6754 (tpp) REVERT: D 820 ASP cc_start: 0.6632 (OUTLIER) cc_final: 0.6359 (p0) REVERT: D 849 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7714 (mt0) outliers start: 110 outliers final: 86 residues processed: 279 average time/residue: 0.3224 time to fit residues: 146.8159 Evaluate side-chains 271 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 177 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 984 THR Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 849 GLN Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain D residue 989 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 9.9990 chunk 32 optimal weight: 0.0670 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 241 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 178 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN B 628 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 GLN ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23942 Z= 0.210 Angle : 0.543 20.651 32510 Z= 0.288 Chirality : 0.042 0.139 3414 Planarity : 0.003 0.043 4290 Dihedral : 4.796 59.271 3283 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.76 % Allowed : 22.23 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.83 (0.15), residues: 2962 helix: 0.37 (0.22), residues: 642 sheet: -1.48 (0.19), residues: 750 loop : -1.76 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 599 HIS 0.006 0.001 HIS C 134 PHE 0.022 0.001 PHE B 606 TYR 0.020 0.001 TYR D 191 ARG 0.011 0.000 ARG D 832 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 194 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8846 (mm) REVERT: A 488 GLU cc_start: 0.7165 (mt-10) cc_final: 0.5857 (tm-30) REVERT: B 109 ILE cc_start: 0.8815 (mm) cc_final: 0.8575 (mm) REVERT: B 383 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7975 (t0) REVERT: B 449 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8776 (tp) REVERT: B 849 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7869 (mt0) REVERT: B 905 LEU cc_start: 0.8612 (mt) cc_final: 0.8309 (mt) REVERT: C 296 LEU cc_start: 0.8018 (mm) cc_final: 0.7769 (mm) REVERT: C 488 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6761 (tm-30) REVERT: D 110 GLN cc_start: 0.8238 (pp30) cc_final: 0.7265 (pp30) REVERT: D 191 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6817 (t80) REVERT: D 241 MET cc_start: 0.7726 (tpp) cc_final: 0.7447 (ttt) REVERT: D 408 ARG cc_start: 0.8547 (ttt90) cc_final: 0.8282 (ttt90) REVERT: D 607 MET cc_start: 0.7046 (mmm) cc_final: 0.6807 (tpp) REVERT: D 820 ASP cc_start: 0.6600 (OUTLIER) cc_final: 0.6297 (p0) REVERT: D 849 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7727 (mt0) outliers start: 117 outliers final: 90 residues processed: 288 average time/residue: 0.3432 time to fit residues: 160.5132 Evaluate side-chains 280 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 183 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 638 ILE Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 991 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 628 GLN Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 849 GLN Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 991 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 10.0000 chunk 113 optimal weight: 0.0370 chunk 170 optimal weight: 0.0570 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 overall best weight: 1.0978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN B 628 GLN C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 ASN D 628 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.101 23942 Z= 0.158 Angle : 0.532 19.627 32510 Z= 0.280 Chirality : 0.042 0.158 3414 Planarity : 0.003 0.044 4290 Dihedral : 4.660 59.589 3283 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.03 % Allowed : 23.53 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.65 (0.16), residues: 2962 helix: 0.38 (0.22), residues: 654 sheet: -1.29 (0.19), residues: 750 loop : -1.63 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 599 HIS 0.009 0.001 HIS C 134 PHE 0.012 0.001 PHE C 135 TYR 0.017 0.001 TYR D 422 ARG 0.006 0.000 ARG D 832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 193 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8809 (mm) REVERT: A 488 GLU cc_start: 0.7145 (mt-10) cc_final: 0.5847 (tm-30) REVERT: B 109 ILE cc_start: 0.8849 (mm) cc_final: 0.8571 (mm) REVERT: B 383 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.8067 (t0) REVERT: B 427 MET cc_start: 0.8309 (mtm) cc_final: 0.8064 (mtt) REVERT: B 449 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8724 (tp) REVERT: B 849 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7850 (mt0) REVERT: C 284 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8752 (mm) REVERT: C 296 LEU cc_start: 0.7959 (mm) cc_final: 0.7718 (mm) REVERT: D 110 GLN cc_start: 0.8203 (pp30) cc_final: 0.7289 (pp30) REVERT: D 191 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.6950 (t80) REVERT: D 241 MET cc_start: 0.7707 (tpp) cc_final: 0.7429 (ttt) REVERT: D 408 ARG cc_start: 0.8530 (ttt90) cc_final: 0.8117 (ttt90) REVERT: D 607 MET cc_start: 0.7032 (mmm) cc_final: 0.6798 (tpp) REVERT: D 820 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6432 (p0) outliers start: 99 outliers final: 82 residues processed: 276 average time/residue: 0.3257 time to fit residues: 146.7414 Evaluate side-chains 267 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 178 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 973 LEU Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 512 ASN Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 628 GLN Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 973 LEU Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 991 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 8.9990 chunk 273 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 240 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 23942 Z= 0.364 Angle : 0.604 11.119 32510 Z= 0.323 Chirality : 0.044 0.152 3414 Planarity : 0.004 0.045 4290 Dihedral : 5.041 59.671 3283 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.48 % Allowed : 23.66 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.75 (0.16), residues: 2962 helix: 0.42 (0.22), residues: 640 sheet: -1.44 (0.19), residues: 742 loop : -1.69 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 599 HIS 0.007 0.002 HIS B 518 PHE 0.034 0.001 PHE B 606 TYR 0.027 0.001 TYR D 191 ARG 0.009 0.001 ARG B 832 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 186 time to evaluate : 2.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8823 (mm) REVERT: A 488 GLU cc_start: 0.7236 (mt-10) cc_final: 0.5859 (tm-30) REVERT: B 109 ILE cc_start: 0.8734 (mm) cc_final: 0.8504 (mm) REVERT: B 383 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8036 (t0) REVERT: B 427 MET cc_start: 0.8409 (mtm) cc_final: 0.8125 (mtt) REVERT: B 449 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8835 (tp) REVERT: B 849 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: B 905 LEU cc_start: 0.8646 (mt) cc_final: 0.8331 (mt) REVERT: C 284 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8739 (mm) REVERT: C 296 LEU cc_start: 0.8041 (mm) cc_final: 0.7778 (mm) REVERT: D 110 GLN cc_start: 0.8349 (pp30) cc_final: 0.7412 (pp30) REVERT: D 191 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7294 (t80) REVERT: D 241 MET cc_start: 0.7683 (tpp) cc_final: 0.7346 (ttt) REVERT: D 820 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6518 (p0) REVERT: D 849 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7798 (mt0) outliers start: 110 outliers final: 92 residues processed: 274 average time/residue: 0.3182 time to fit residues: 144.1206 Evaluate side-chains 281 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 181 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 134 HIS Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 512 ASN Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 599 TRP Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 822 HIS Chi-restraints excluded: chain D residue 849 GLN Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 932 THR Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1004 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 9.9990 chunk 281 optimal weight: 0.0970 chunk 171 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 195 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 chunk 271 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 181 optimal weight: 30.0000 chunk 143 optimal weight: 2.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 23942 Z= 0.240 Angle : 0.588 19.352 32510 Z= 0.307 Chirality : 0.043 0.189 3414 Planarity : 0.003 0.046 4290 Dihedral : 4.950 59.974 3283 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.95 % Allowed : 24.10 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.63 (0.16), residues: 2962 helix: 0.45 (0.22), residues: 642 sheet: -1.28 (0.20), residues: 736 loop : -1.63 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 599 HIS 0.008 0.002 HIS C 134 PHE 0.015 0.001 PHE B 342 TYR 0.020 0.001 TYR D 191 ARG 0.005 0.000 ARG D 832 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5924 Ramachandran restraints generated. 2962 Oldfield, 0 Emsley, 2962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 181 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 284 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8854 (mm) REVERT: A 488 GLU cc_start: 0.7217 (mt-10) cc_final: 0.5878 (tm-30) REVERT: B 109 ILE cc_start: 0.8665 (mm) cc_final: 0.8462 (mm) REVERT: B 383 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7969 (t0) REVERT: B 427 MET cc_start: 0.8369 (mtm) cc_final: 0.8101 (mtt) REVERT: B 449 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8786 (tp) REVERT: B 607 MET cc_start: 0.6607 (tpp) cc_final: 0.6350 (mpp) REVERT: B 849 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7794 (mt0) REVERT: B 905 LEU cc_start: 0.8640 (mt) cc_final: 0.8331 (mt) REVERT: C 284 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8753 (mm) REVERT: C 296 LEU cc_start: 0.7977 (mm) cc_final: 0.7762 (mm) REVERT: D 110 GLN cc_start: 0.8335 (pp30) cc_final: 0.7440 (pp30) REVERT: D 191 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.6892 (t80) REVERT: D 241 MET cc_start: 0.7702 (tpp) cc_final: 0.7395 (ttt) REVERT: D 408 ARG cc_start: 0.8570 (ttt90) cc_final: 0.8289 (ttt90) REVERT: D 820 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6451 (p0) REVERT: D 849 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7785 (mt0) outliers start: 97 outliers final: 86 residues processed: 263 average time/residue: 0.3204 time to fit residues: 138.1563 Evaluate side-chains 273 residues out of total 2498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 179 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 49 TRP Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 153 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 599 TRP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 LEU Chi-restraints excluded: chain B residue 849 GLN Chi-restraints excluded: chain B residue 859 PHE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 932 THR Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 989 ASN Chi-restraints excluded: chain B residue 1004 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 TRP Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 151 ASN Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 154 ASP Chi-restraints excluded: chain D residue 191 TYR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 350 TYR Chi-restraints excluded: chain D residue 446 THR Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 516 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 628 GLN Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 678 ILE Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 716 THR Chi-restraints excluded: chain D residue 725 VAL Chi-restraints excluded: chain D residue 727 VAL Chi-restraints excluded: chain D residue 728 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 849 GLN Chi-restraints excluded: chain D residue 859 PHE Chi-restraints excluded: chain D residue 876 MET Chi-restraints excluded: chain D residue 900 SER Chi-restraints excluded: chain D residue 909 THR Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1004 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 6.9990 chunk 250 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.155452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.127472 restraints weight = 35493.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126195 restraints weight = 47518.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.124775 restraints weight = 40323.014| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.137 23942 Z= 0.301 Angle : 0.889 59.176 32510 Z= 0.525 Chirality : 0.046 0.654 3414 Planarity : 0.005 0.207 4290 Dihedral : 4.942 59.343 3283 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.19 % Allowed : 23.94 % Favored : 71.86 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.63 (0.16), residues: 2962 helix: 0.44 (0.22), residues: 642 sheet: -1.28 (0.20), residues: 736 loop : -1.63 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 599 HIS 0.267 0.007 HIS C 134 PHE 0.015 0.001 PHE B 342 TYR 0.020 0.001 TYR D 191 ARG 0.004 0.000 ARG D 832 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.24 seconds wall clock time: 75 minutes 52.91 seconds (4552.91 seconds total)