Starting phenix.real_space_refine on Sun Mar 17 08:54:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/03_2024/8wea_37476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/03_2024/8wea_37476.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/03_2024/8wea_37476_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/03_2024/8wea_37476_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/03_2024/8wea_37476_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/03_2024/8wea_37476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/03_2024/8wea_37476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/03_2024/8wea_37476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/03_2024/8wea_37476_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Br 1 7.06 5 S 92 5.16 5 C 11099 2.51 5 N 2826 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 127": "OE1" <-> "OE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 899": "OD1" <-> "OD2" Residue "A PHE 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 921": "OD1" <-> "OD2" Residue "A TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1242": "OE1" <-> "OE2" Residue "A PHE 1282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1317": "OD1" <-> "OD2" Residue "A GLU 1464": "OE1" <-> "OE2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A PHE 1499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "A PHE 1611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1627": "OE1" <-> "OE2" Residue "A GLU 1631": "OE1" <-> "OE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "D GLU 573": "OE1" <-> "OE2" Residue "D GLU 585": "OE1" <-> "OE2" Residue "D ASP 596": "OD1" <-> "OD2" Residue "D GLU 636": "OE1" <-> "OE2" Residue "D TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 655": "OE1" <-> "OE2" Residue "D ASP 665": "OD1" <-> "OD2" Residue "D TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 674": "OD1" <-> "OD2" Residue "D GLU 685": "OE1" <-> "OE2" Residue "D PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 737": "OD1" <-> "OD2" Residue "D GLU 747": "OE1" <-> "OE2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D ASP 771": "OD1" <-> "OD2" Residue "D TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 899": "OD1" <-> "OD2" Residue "D TYR 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17188 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1206, 9335 Classifications: {'peptide': 1206} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 39, 'TRANS': 1166} Chain breaks: 12 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 211 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' CA': 1, '9Z9': 1, 'WB9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.35, per 1000 atoms: 0.54 Number of scatterers: 17188 At special positions: 0 Unit cell: (137.022, 141.478, 176.012, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 1 34.99 Ca 2 19.99 S 92 16.00 O 3168 8.00 N 2826 7.00 C 11099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.02 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.02 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " distance=2.04 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG E 3 " - " NAG E 4 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG C 1 " - " ASN D 348 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 781 " " NAG E 1 " - " ASN D 468 " " NAG F 1 " - " ASN D 613 " " NAG G 1 " - " ASN D 895 " Time building additional restraints: 7.31 Conformation dependent library (CDL) restraints added in 3.3 seconds 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 11 sheets defined 50.1% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.59 Creating SS restraints... Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.513A pdb=" N ILE A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.610A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.654A pdb=" N PHE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 216 removed outlier: 3.590A pdb=" N VAL A 205 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 207 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 240 through 250 Proline residue: A 244 - end of helix removed outlier: 4.073A pdb=" N GLY A 250 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 265 removed outlier: 4.103A pdb=" N VAL A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.687A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.713A pdb=" N PHE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 418 removed outlier: 3.638A pdb=" N LEU A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 445 removed outlier: 4.033A pdb=" N TRP A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'A' and resid 524 through 543 Processing helix chain 'A' and resid 550 through 577 removed outlier: 3.962A pdb=" N VAL A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 613 through 629 removed outlier: 3.695A pdb=" N LEU A 624 " --> pdb=" O ARG A 620 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 625 " --> pdb=" O CYS A 621 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ARG A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 650 removed outlier: 4.374A pdb=" N ASN A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 672 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 708 through 718 Processing helix chain 'A' and resid 730 through 754 removed outlier: 3.750A pdb=" N ILE A 735 " --> pdb=" O ILE A 731 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 737 " --> pdb=" O PHE A 733 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 741 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 914 through 918 Processing helix chain 'A' and resid 928 through 969 removed outlier: 3.866A pdb=" N LEU A 953 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 954 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN A 955 " --> pdb=" O HIS A 931 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 956 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1007 removed outlier: 4.846A pdb=" N GLN A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1016 No H-bonds generated for 'chain 'A' and resid 1013 through 1016' Processing helix chain 'A' and resid 1019 through 1032 Proline residue: A1025 - end of helix Processing helix chain 'A' and resid 1039 through 1071 removed outlier: 3.509A pdb=" N THR A1056 " --> pdb=" O ILE A1052 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A1069 " --> pdb=" O CYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1121 through 1132 removed outlier: 3.637A pdb=" N SER A1132 " --> pdb=" O LEU A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1191 removed outlier: 3.781A pdb=" N TYR A1169 " --> pdb=" O PHE A1165 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE A1170 " --> pdb=" O PHE A1166 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A1187 " --> pdb=" O GLY A1183 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR A1188 " --> pdb=" O PHE A1184 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A1189 " --> pdb=" O VAL A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1213 Processing helix chain 'A' and resid 1227 through 1237 removed outlier: 3.556A pdb=" N VAL A1232 " --> pdb=" O HIS A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 Processing helix chain 'A' and resid 1265 through 1292 Processing helix chain 'A' and resid 1295 through 1299 Processing helix chain 'A' and resid 1302 through 1322 Processing helix chain 'A' and resid 1375 through 1387 removed outlier: 3.798A pdb=" N PHE A1379 " --> pdb=" O PHE A1375 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG A1380 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL A1381 " --> pdb=" O ARG A1377 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A1382 " --> pdb=" O LEU A1378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A1383 " --> pdb=" O PHE A1379 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A1384 " --> pdb=" O ARG A1380 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS A1386 " --> pdb=" O MET A1382 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A1387 " --> pdb=" O ARG A1383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1375 through 1387' Processing helix chain 'A' and resid 1392 through 1404 removed outlier: 3.526A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1429 Processing helix chain 'A' and resid 1450 through 1461 Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1498 through 1525 removed outlier: 3.622A pdb=" N ILE A1505 " --> pdb=" O PHE A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1543 through 1551 removed outlier: 3.526A pdb=" N GLU A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1567 removed outlier: 3.629A pdb=" N VAL A1566 " --> pdb=" O LEU A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1591 Processing helix chain 'A' and resid 1606 through 1617 Processing helix chain 'A' and resid 1625 through 1635 Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.739A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.686A pdb=" N VAL D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 58' Processing helix chain 'D' and resid 60 through 63 No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 75 through 110 removed outlier: 3.507A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.693A pdb=" N ASN D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 199 removed outlier: 3.569A pdb=" N ARG D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.690A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 4.094A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.529A pdb=" N LYS D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.551A pdb=" N LEU D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.696A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 423 removed outlier: 3.526A pdb=" N THR D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 419 through 423' Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.717A pdb=" N ASP D 428 " --> pdb=" O GLU D 425 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 429 " --> pdb=" O TYR D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 441 removed outlier: 4.134A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LYS D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.777A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 564 No H-bonds generated for 'chain 'D' and resid 561 through 564' Processing helix chain 'D' and resid 570 through 579 Processing helix chain 'D' and resid 640 through 648 removed outlier: 4.082A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 removed outlier: 4.724A pdb=" N GLU D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 684 Processing helix chain 'D' and resid 700 through 718 removed outlier: 3.987A pdb=" N GLY D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU D 715 " --> pdb=" O PHE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 750 removed outlier: 3.757A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 747 through 750' Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.601A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 826 removed outlier: 3.591A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 870 Processing helix chain 'D' and resid 875 through 878 No H-bonds generated for 'chain 'D' and resid 875 through 878' Processing helix chain 'D' and resid 880 through 888 Processing helix chain 'D' and resid 1021 through 1023 No H-bonds generated for 'chain 'D' and resid 1021 through 1023' Processing helix chain 'D' and resid 1043 through 1046 No H-bonds generated for 'chain 'D' and resid 1043 through 1046' Processing sheet with id= A, first strand: chain 'A' and resid 296 through 298 removed outlier: 3.761A pdb=" N THR A 297 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 333 " --> pdb=" O THR A 297 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 1092 through 1096 Processing sheet with id= C, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= D, first strand: chain 'D' and resid 122 through 124 Processing sheet with id= E, first strand: chain 'D' and resid 165 through 167 removed outlier: 7.099A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 410 through 413 removed outlier: 8.271A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU D 255 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE D 361 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU D 257 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN D 290 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 258 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA D 292 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 511 through 515 removed outlier: 3.548A pdb=" N ILE D 515 " --> pdb=" O SER D 618 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER D 618 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 732 through 736 removed outlier: 3.940A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 848 through 853 removed outlier: 3.692A pdb=" N MET D1017 " --> pdb=" O HIS D1004 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 892 through 899 removed outlier: 3.606A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 976 " --> pdb=" O ASP D 899 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 902 through 904 removed outlier: 3.812A pdb=" N SER D 902 " --> pdb=" O CYS D 974 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 7.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 4326 1.33 - 1.48: 5584 1.48 - 1.63: 7502 1.63 - 1.78: 2 1.78 - 1.92: 138 Bond restraints: 17552 Sorted by residual: bond pdb=" C03 WB9 A2303 " pdb=" C08 WB9 A2303 " ideal model delta sigma weight residual 1.226 1.501 -0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" CA ASP A 311 " pdb=" C ASP A 311 " ideal model delta sigma weight residual 1.524 1.467 0.057 7.00e-03 2.04e+04 6.68e+01 bond pdb=" C07 WB9 A2303 " pdb=" C08 WB9 A2303 " ideal model delta sigma weight residual 1.348 1.510 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" CA PRO A 146 " pdb=" CB PRO A 146 " ideal model delta sigma weight residual 1.535 1.447 0.088 1.12e-02 7.97e+03 6.13e+01 bond pdb=" CA CYS A 316 " pdb=" C CYS A 316 " ideal model delta sigma weight residual 1.524 1.438 0.086 1.24e-02 6.50e+03 4.81e+01 ... (remaining 17547 not shown) Histogram of bond angle deviations from ideal: 66.33 - 80.79: 5 80.79 - 95.25: 4 95.25 - 109.70: 2410 109.70 - 124.16: 21083 124.16 - 138.62: 320 Bond angle restraints: 23822 Sorted by residual: angle pdb=" C01 WB9 A2303 " pdb=" C02 WB9 A2303 " pdb=" C32 WB9 A2303 " ideal model delta sigma weight residual 115.48 74.81 40.67 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C02 WB9 A2303 " pdb=" C03 WB9 A2303 " pdb=" C04 WB9 A2303 " ideal model delta sigma weight residual 105.14 66.33 38.81 3.00e+00 1.11e-01 1.67e+02 angle pdb=" C02 WB9 A2303 " pdb=" C07 WB9 A2303 " pdb=" C06 WB9 A2303 " ideal model delta sigma weight residual 105.92 67.13 38.79 3.00e+00 1.11e-01 1.67e+02 angle pdb=" N ALA A1032 " pdb=" CA ALA A1032 " pdb=" C ALA A1032 " ideal model delta sigma weight residual 113.21 99.40 13.81 1.15e+00 7.56e-01 1.44e+02 angle pdb=" C01 WB9 A2303 " pdb=" C02 WB9 A2303 " pdb=" C03 WB9 A2303 " ideal model delta sigma weight residual 113.78 78.74 35.04 3.00e+00 1.11e-01 1.36e+02 ... (remaining 23817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.72: 9890 27.72 - 55.43: 673 55.43 - 83.15: 103 83.15 - 110.87: 44 110.87 - 138.59: 6 Dihedral angle restraints: 10716 sinusoidal: 4423 harmonic: 6293 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 174.29 -81.29 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS A 316 " pdb=" SG CYS A 316 " pdb=" SG CYS A 332 " pdb=" CB CYS A 332 " ideal model delta sinusoidal sigma weight residual -86.00 -148.84 62.84 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual -86.00 -140.31 54.31 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 10713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.932: 2760 0.932 - 1.865: 0 1.865 - 2.797: 0 2.797 - 3.729: 0 3.729 - 4.662: 1 Chirality restraints: 2761 Sorted by residual: chirality pdb=" N14 WB9 A2303 " pdb=" C15 WB9 A2303 " pdb=" C19 WB9 A2303 " pdb=" C20 WB9 A2303 " both_signs ideal model delta sigma weight residual False 2.35 -2.32 4.66 2.00e-01 2.50e+01 5.43e+02 chirality pdb=" C1 NAG E 3 " pdb=" O4 NAG E 2 " pdb=" C2 NAG E 3 " pdb=" O5 NAG E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.38e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.12e+02 ... (remaining 2758 not shown) Planarity restraints: 3005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 4 " -0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 4 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 4 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG E 4 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG E 4 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 3 " -0.321 2.00e-02 2.50e+03 2.71e-01 9.15e+02 pdb=" C7 NAG E 3 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 3 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG E 3 " 0.468 2.00e-02 2.50e+03 pdb=" O7 NAG E 3 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.103 2.00e-02 2.50e+03 8.30e-02 8.62e+01 pdb=" C7 NAG E 2 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.129 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.025 2.00e-02 2.50e+03 ... (remaining 3002 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 194 2.52 - 3.12: 14905 3.12 - 3.71: 26976 3.71 - 4.31: 38305 4.31 - 4.90: 60252 Nonbonded interactions: 140632 Sorted by model distance: nonbonded pdb=" NH2 ARG A 511 " pdb=" CE2 PHE A 512 " model vdw 1.927 3.420 nonbonded pdb=" CZ ARG A 511 " pdb=" CE2 PHE A 512 " model vdw 1.966 3.570 nonbonded pdb=" OH TYR D 788 " pdb=" O THR D 868 " model vdw 2.197 2.440 nonbonded pdb=" O4 NAG C 2 " pdb=" O7 NAG C 2 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR D 599 " pdb=" OD2 ASP D 854 " model vdw 2.203 2.440 ... (remaining 140627 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 'C' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.510 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 49.070 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.275 17552 Z= 0.570 Angle : 1.288 40.671 23822 Z= 0.774 Chirality : 0.108 4.662 2761 Planarity : 0.009 0.291 2998 Dihedral : 19.613 138.585 6612 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 29.12 Ramachandran Plot: Outliers : 1.70 % Allowed : 9.40 % Favored : 88.89 % Rotamer: Outliers : 5.51 % Allowed : 23.80 % Favored : 70.69 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.17), residues: 2116 helix: -1.30 (0.15), residues: 1042 sheet: -0.95 (0.38), residues: 190 loop : -2.59 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 336 HIS 0.004 0.001 HIS A1540 PHE 0.024 0.001 PHE D 686 TYR 0.025 0.001 TYR A 144 ARG 0.013 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 474 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5775 (OUTLIER) cc_final: 0.5355 (mt) REVERT: A 175 PHE cc_start: 0.7273 (t80) cc_final: 0.6950 (t80) REVERT: A 214 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6261 (tt0) REVERT: A 234 LYS cc_start: 0.5331 (OUTLIER) cc_final: 0.5025 (ttmm) REVERT: A 263 LYS cc_start: 0.7276 (tptt) cc_final: 0.6481 (mptt) REVERT: A 267 PRO cc_start: 0.8161 (Cg_exo) cc_final: 0.7824 (Cg_endo) REVERT: A 322 HIS cc_start: 0.3873 (OUTLIER) cc_final: 0.2724 (t70) REVERT: A 337 ASP cc_start: 0.4996 (OUTLIER) cc_final: 0.4043 (t0) REVERT: A 531 ILE cc_start: 0.7509 (mp) cc_final: 0.7276 (mm) REVERT: A 625 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7342 (tp) REVERT: A 713 TYR cc_start: 0.5840 (m-10) cc_final: 0.5518 (m-80) REVERT: A 1070 LEU cc_start: 0.8569 (mt) cc_final: 0.8365 (mt) REVERT: A 1102 ASP cc_start: 0.7065 (p0) cc_final: 0.6803 (p0) REVERT: A 1126 MET cc_start: 0.8149 (ptp) cc_final: 0.7776 (ptt) REVERT: A 1159 ARG cc_start: 0.5400 (ttp-110) cc_final: 0.4884 (ttt180) REVERT: A 1161 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5795 (mp0) REVERT: A 1218 PRO cc_start: 0.6318 (Cg_endo) cc_final: 0.5884 (Cg_exo) REVERT: A 1316 ILE cc_start: 0.7708 (pt) cc_final: 0.7439 (pt) REVERT: A 1509 MET cc_start: 0.8055 (mmt) cc_final: 0.7593 (mmt) REVERT: A 1594 MET cc_start: -0.0176 (pmm) cc_final: -0.0399 (mpp) REVERT: D 578 MET cc_start: 0.8747 (mtp) cc_final: 0.8299 (mtp) REVERT: D 595 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7527 (tp40) REVERT: D 678 GLU cc_start: 0.8627 (pt0) cc_final: 0.7971 (mm-30) REVERT: D 680 LEU cc_start: 0.8379 (tp) cc_final: 0.8108 (tt) REVERT: D 719 TYR cc_start: 0.7785 (t80) cc_final: 0.7468 (t80) REVERT: D 848 MET cc_start: 0.4981 (mmm) cc_final: 0.4079 (mmt) REVERT: D 869 ASN cc_start: 0.8866 (t0) cc_final: 0.8471 (t0) REVERT: D 875 PHE cc_start: 0.7172 (t80) cc_final: 0.6778 (t80) REVERT: D 1010 ASN cc_start: 0.7582 (m110) cc_final: 0.7292 (t0) REVERT: D 1017 MET cc_start: 0.6958 (ttm) cc_final: 0.6353 (tpt) outliers start: 99 outliers final: 29 residues processed: 542 average time/residue: 0.2964 time to fit residues: 237.7888 Evaluate side-chains 337 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 301 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 234 LYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 900 THR Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain A residue 969 ILE Chi-restraints excluded: chain A residue 1161 GLU Chi-restraints excluded: chain A residue 1260 HIS Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 852 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 0.0270 chunk 124 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 259 ASN A 341 HIS A 510 ASN A 556 GLN A 560 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN A1103 HIS A1113 ASN A1157 ASN A1205 ASN A1252 ASN A1259 GLN A1260 HIS A1452 GLN D 77 GLN D 314 ASN D 324 ASN D 406 ASN D 652 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1004 HIS D1010 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17552 Z= 0.253 Angle : 0.919 33.908 23822 Z= 0.419 Chirality : 0.063 2.195 2761 Planarity : 0.006 0.083 2998 Dihedral : 14.888 149.578 2809 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.29 % Favored : 93.43 % Rotamer: Outliers : 5.56 % Allowed : 25.42 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.58 (0.18), residues: 2116 helix: -0.25 (0.16), residues: 1042 sheet: -0.97 (0.35), residues: 209 loop : -2.01 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 382 HIS 0.005 0.001 HIS A1260 PHE 0.048 0.002 PHE A 909 TYR 0.039 0.002 TYR A1169 ARG 0.006 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 309 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5718 (OUTLIER) cc_final: 0.5139 (mt) REVERT: A 259 ASN cc_start: 0.7588 (m110) cc_final: 0.7256 (m110) REVERT: A 263 LYS cc_start: 0.7177 (tptt) cc_final: 0.6279 (mmtp) REVERT: A 532 PHE cc_start: 0.7620 (t80) cc_final: 0.6564 (t80) REVERT: A 620 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7741 (mtp85) REVERT: A 706 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6585 (tt0) REVERT: A 713 TYR cc_start: 0.6636 (m-10) cc_final: 0.6151 (m-80) REVERT: A 972 MET cc_start: 0.5721 (mmm) cc_final: 0.5350 (mmm) REVERT: A 1117 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7326 (p0) REVERT: A 1126 MET cc_start: 0.7945 (ptp) cc_final: 0.7564 (ptt) REVERT: A 1239 THR cc_start: 0.6753 (OUTLIER) cc_final: 0.6491 (p) REVERT: A 1242 GLU cc_start: 0.7488 (mp0) cc_final: 0.7240 (mp0) REVERT: A 1406 GLN cc_start: 0.6616 (mp10) cc_final: 0.6253 (tp40) REVERT: A 1470 MET cc_start: 0.7071 (tmm) cc_final: 0.6600 (ptp) REVERT: A 1509 MET cc_start: 0.7909 (mmt) cc_final: 0.7610 (mmt) REVERT: A 1541 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6055 (m90) REVERT: A 1619 ARG cc_start: 0.4578 (OUTLIER) cc_final: 0.3467 (ptt90) REVERT: A 1646 MET cc_start: 0.4017 (pmm) cc_final: 0.3538 (pmm) REVERT: D 41 GLN cc_start: 0.7540 (tt0) cc_final: 0.6967 (tm-30) REVERT: D 578 MET cc_start: 0.8564 (mtp) cc_final: 0.8267 (mtp) REVERT: D 589 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7472 (ttm170) REVERT: D 678 GLU cc_start: 0.8429 (pt0) cc_final: 0.7790 (mm-30) REVERT: D 848 MET cc_start: 0.5178 (mmm) cc_final: 0.4278 (mmt) REVERT: D 869 ASN cc_start: 0.8892 (t0) cc_final: 0.8438 (t0) REVERT: D 875 PHE cc_start: 0.7375 (t80) cc_final: 0.6956 (t80) REVERT: D 1017 MET cc_start: 0.7111 (ttm) cc_final: 0.6329 (tpt) outliers start: 100 outliers final: 43 residues processed: 379 average time/residue: 0.2568 time to fit residues: 151.8126 Evaluate side-chains 310 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 261 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1260 HIS Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1479 CYS Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1547 ARG Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 324 ASN Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 655 GLU Chi-restraints excluded: chain D residue 711 PHE Chi-restraints excluded: chain D residue 716 VAL Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 771 ASP Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1037 THR Chi-restraints excluded: chain D residue 1058 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 53 optimal weight: 0.0670 chunk 194 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 173 optimal weight: 0.0970 chunk 193 optimal weight: 0.1980 chunk 66 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN A1252 ASN ** A1573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 374 ASN D 406 ASN ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 885 HIS ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17552 Z= 0.232 Angle : 0.858 31.930 23822 Z= 0.381 Chirality : 0.060 2.101 2761 Planarity : 0.005 0.079 2998 Dihedral : 12.859 157.444 2767 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 5.45 % Allowed : 25.64 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.10 (0.18), residues: 2116 helix: 0.23 (0.16), residues: 1032 sheet: -0.91 (0.35), residues: 205 loop : -1.82 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 185 HIS 0.006 0.001 HIS A1260 PHE 0.045 0.002 PHE A 909 TYR 0.020 0.001 TYR A1169 ARG 0.011 0.000 ARG A1559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 283 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5657 (OUTLIER) cc_final: 0.4345 (tp) REVERT: A 151 ASP cc_start: 0.8653 (p0) cc_final: 0.7524 (p0) REVERT: A 263 LYS cc_start: 0.7179 (tptt) cc_final: 0.6312 (mptt) REVERT: A 291 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7103 (tmm) REVERT: A 531 ILE cc_start: 0.7668 (mm) cc_final: 0.7466 (mm) REVERT: A 532 PHE cc_start: 0.7622 (t80) cc_final: 0.6527 (t80) REVERT: A 546 TYR cc_start: 0.7089 (t80) cc_final: 0.6746 (t80) REVERT: A 655 LEU cc_start: 0.7654 (mt) cc_final: 0.7271 (mp) REVERT: A 683 GLN cc_start: 0.5420 (tp40) cc_final: 0.5037 (mp10) REVERT: A 706 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6602 (tt0) REVERT: A 713 TYR cc_start: 0.6947 (m-10) cc_final: 0.6198 (m-80) REVERT: A 972 MET cc_start: 0.5831 (mmm) cc_final: 0.3505 (ttt) REVERT: A 1063 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7401 (t80) REVERT: A 1117 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7324 (p0) REVERT: A 1126 MET cc_start: 0.7880 (ptp) cc_final: 0.7592 (ptt) REVERT: A 1129 PHE cc_start: 0.7958 (t80) cc_final: 0.7741 (t80) REVERT: A 1242 GLU cc_start: 0.7511 (mp0) cc_final: 0.7176 (mp0) REVERT: A 1405 PHE cc_start: 0.7060 (t80) cc_final: 0.6745 (t80) REVERT: A 1470 MET cc_start: 0.7297 (tmm) cc_final: 0.7023 (ptm) REVERT: A 1509 MET cc_start: 0.7894 (mmt) cc_final: 0.7530 (mmt) REVERT: A 1541 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.5829 (m90) REVERT: A 1544 GLU cc_start: 0.7630 (mp0) cc_final: 0.7070 (mp0) REVERT: D 41 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: D 84 ARG cc_start: 0.8190 (mtm-85) cc_final: 0.7892 (mpp80) REVERT: D 424 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: D 578 MET cc_start: 0.8541 (mtp) cc_final: 0.8284 (mtp) REVERT: D 589 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7444 (ttm170) REVERT: D 678 GLU cc_start: 0.8409 (pt0) cc_final: 0.7809 (mm-30) REVERT: D 861 MET cc_start: 0.6149 (ptt) cc_final: 0.5898 (ptp) REVERT: D 869 ASN cc_start: 0.8871 (t0) cc_final: 0.8415 (t0) REVERT: D 875 PHE cc_start: 0.7410 (t80) cc_final: 0.6990 (t80) REVERT: D 1017 MET cc_start: 0.7131 (ttm) cc_final: 0.6417 (tpt) outliers start: 98 outliers final: 48 residues processed: 352 average time/residue: 0.2612 time to fit residues: 142.8094 Evaluate side-chains 320 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 264 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 655 GLU Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 767 SER Chi-restraints excluded: chain D residue 771 ASP Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1030 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 6.9990 chunk 146 optimal weight: 0.0030 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 195 optimal weight: 5.9990 chunk 206 optimal weight: 0.1980 chunk 102 optimal weight: 0.5980 chunk 185 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 HIS D 374 ASN D 641 GLN ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17552 Z= 0.184 Angle : 0.806 31.079 23822 Z= 0.354 Chirality : 0.059 2.090 2761 Planarity : 0.005 0.077 2998 Dihedral : 11.491 162.872 2760 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 4.17 % Allowed : 25.92 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2116 helix: 0.55 (0.16), residues: 1026 sheet: -0.80 (0.35), residues: 205 loop : -1.73 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 185 HIS 0.003 0.001 HIS A1260 PHE 0.022 0.002 PHE D 686 TYR 0.038 0.001 TYR A 299 ARG 0.004 0.000 ARG A1547 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 273 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5706 (OUTLIER) cc_final: 0.4521 (tp) REVERT: A 263 LYS cc_start: 0.7180 (tptt) cc_final: 0.6307 (mptt) REVERT: A 273 LEU cc_start: 0.8175 (tp) cc_final: 0.7963 (tp) REVERT: A 362 MET cc_start: 0.7302 (mtm) cc_final: 0.7050 (mpp) REVERT: A 526 PHE cc_start: 0.6221 (OUTLIER) cc_final: 0.5862 (p90) REVERT: A 532 PHE cc_start: 0.7742 (t80) cc_final: 0.6701 (t80) REVERT: A 538 THR cc_start: 0.8613 (m) cc_final: 0.8400 (m) REVERT: A 706 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6587 (tt0) REVERT: A 972 MET cc_start: 0.6014 (mmm) cc_final: 0.5711 (mmm) REVERT: A 1117 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7455 (p0) REVERT: A 1125 MET cc_start: 0.8690 (mtp) cc_final: 0.8473 (mtp) REVERT: A 1126 MET cc_start: 0.7941 (ptp) cc_final: 0.7712 (ptt) REVERT: A 1129 PHE cc_start: 0.7982 (t80) cc_final: 0.7769 (t80) REVERT: A 1405 PHE cc_start: 0.7286 (t80) cc_final: 0.7063 (t80) REVERT: A 1509 MET cc_start: 0.7908 (mmt) cc_final: 0.7541 (mmt) REVERT: A 1541 HIS cc_start: 0.6669 (OUTLIER) cc_final: 0.5689 (m90) REVERT: A 1646 MET cc_start: 0.3140 (pmm) cc_final: 0.2789 (pmm) REVERT: D 41 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: D 84 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7914 (mpp80) REVERT: D 424 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: D 578 MET cc_start: 0.8427 (mtp) cc_final: 0.8211 (mtp) REVERT: D 589 ARG cc_start: 0.7702 (ttm170) cc_final: 0.7467 (ttm170) REVERT: D 678 GLU cc_start: 0.8366 (pt0) cc_final: 0.7809 (mm-30) REVERT: D 848 MET cc_start: 0.5203 (mmp) cc_final: 0.1869 (ptt) REVERT: D 861 MET cc_start: 0.6533 (ptt) cc_final: 0.6187 (ptt) REVERT: D 869 ASN cc_start: 0.8886 (t0) cc_final: 0.8412 (t0) REVERT: D 875 PHE cc_start: 0.7420 (t80) cc_final: 0.6975 (t80) REVERT: D 1017 MET cc_start: 0.7101 (ttm) cc_final: 0.6579 (tpt) outliers start: 75 outliers final: 42 residues processed: 322 average time/residue: 0.2642 time to fit residues: 133.3811 Evaluate side-chains 285 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 237 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1116 PHE Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1421 ILE Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1541 HIS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 655 GLU Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 771 ASP Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 891 VAL Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1011 THR Chi-restraints excluded: chain D residue 1030 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 ASN A1205 ASN D 374 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17552 Z= 0.237 Angle : 0.816 31.195 23822 Z= 0.359 Chirality : 0.060 1.999 2761 Planarity : 0.005 0.083 2998 Dihedral : 10.495 165.519 2754 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 4.78 % Allowed : 26.59 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.18), residues: 2116 helix: 0.57 (0.16), residues: 1033 sheet: -0.73 (0.35), residues: 205 loop : -1.71 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 185 HIS 0.003 0.001 HIS A 341 PHE 0.020 0.002 PHE D 686 TYR 0.016 0.001 TYR A1169 ARG 0.005 0.000 ARG A1615 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 267 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.5665 (OUTLIER) cc_final: 0.4388 (tp) REVERT: A 179 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7760 (tp) REVERT: A 263 LYS cc_start: 0.7440 (tptt) cc_final: 0.6835 (tppt) REVERT: A 281 ILE cc_start: 0.8657 (mt) cc_final: 0.8288 (tt) REVERT: A 362 MET cc_start: 0.7385 (mtm) cc_final: 0.6947 (mpp) REVERT: A 526 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5752 (p90) REVERT: A 532 PHE cc_start: 0.7940 (t80) cc_final: 0.6912 (t80) REVERT: A 655 LEU cc_start: 0.7762 (mt) cc_final: 0.7359 (mp) REVERT: A 706 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6609 (tt0) REVERT: A 717 MET cc_start: 0.7575 (ttt) cc_final: 0.7319 (tpp) REVERT: A 972 MET cc_start: 0.5690 (mmm) cc_final: 0.5455 (mmm) REVERT: A 1117 ASP cc_start: 0.7802 (OUTLIER) cc_final: 0.7438 (p0) REVERT: A 1126 MET cc_start: 0.8101 (ptp) cc_final: 0.7727 (ptt) REVERT: A 1129 PHE cc_start: 0.8165 (t80) cc_final: 0.7952 (t80) REVERT: A 1509 MET cc_start: 0.8018 (mmt) cc_final: 0.7712 (mmt) REVERT: A 1646 MET cc_start: 0.3251 (pmm) cc_final: 0.2816 (pmm) REVERT: D 41 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: D 84 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7936 (mpp80) REVERT: D 114 ARG cc_start: 0.7324 (ptt90) cc_final: 0.7057 (ptt90) REVERT: D 366 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7372 (mt-10) REVERT: D 424 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8289 (pt0) REVERT: D 589 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7176 (ttm-80) REVERT: D 639 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7935 (mm) REVERT: D 678 GLU cc_start: 0.8360 (pt0) cc_final: 0.7909 (mm-30) REVERT: D 793 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7898 (ttm) REVERT: D 848 MET cc_start: 0.5563 (mmp) cc_final: 0.2192 (ptt) REVERT: D 861 MET cc_start: 0.6892 (ptt) cc_final: 0.6283 (ptt) REVERT: D 869 ASN cc_start: 0.8885 (t0) cc_final: 0.8409 (t0) REVERT: D 875 PHE cc_start: 0.7552 (t80) cc_final: 0.7095 (t80) REVERT: D 1017 MET cc_start: 0.7036 (ttm) cc_final: 0.6644 (tpt) outliers start: 86 outliers final: 58 residues processed: 322 average time/residue: 0.2720 time to fit residues: 135.2500 Evaluate side-chains 307 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 240 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1205 ASN Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1421 ILE Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1642 LYS Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 41 GLN Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 366 GLU Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1014 ILE Chi-restraints excluded: chain D residue 1030 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 50.0000 chunk 186 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN A1205 ASN A1228 HIS A1252 ASN D 167 HIS D 374 ASN D 526 ASN D 682 ASN D 753 GLN D 864 HIS ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.070 17552 Z= 0.613 Angle : 1.042 31.557 23822 Z= 0.485 Chirality : 0.066 1.982 2761 Planarity : 0.007 0.092 2998 Dihedral : 11.165 160.957 2754 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.70 % Favored : 92.20 % Rotamer: Outliers : 6.56 % Allowed : 25.58 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.54 (0.18), residues: 2116 helix: -0.06 (0.16), residues: 1071 sheet: -1.24 (0.35), residues: 196 loop : -2.20 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A1111 HIS 0.009 0.002 HIS D 392 PHE 0.029 0.003 PHE D 294 TYR 0.039 0.003 TYR A 299 ARG 0.006 0.001 ARG D 732 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 273 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8063 (tp) REVERT: A 263 LYS cc_start: 0.8107 (tptt) cc_final: 0.7515 (tppt) REVERT: A 418 ARG cc_start: 0.6437 (mmp80) cc_final: 0.6217 (mmm160) REVERT: A 526 PHE cc_start: 0.6380 (OUTLIER) cc_final: 0.5961 (p90) REVERT: A 567 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.7085 (m-10) REVERT: A 672 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.7593 (tp) REVERT: A 688 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8738 (p) REVERT: A 706 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6872 (tt0) REVERT: A 717 MET cc_start: 0.8293 (ttt) cc_final: 0.7989 (tpp) REVERT: A 917 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6043 (pt) REVERT: A 1117 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7478 (p0) REVERT: A 1126 MET cc_start: 0.8227 (ptp) cc_final: 0.7905 (ptm) REVERT: A 1259 GLN cc_start: 0.7958 (mt0) cc_final: 0.7702 (mt0) REVERT: A 1590 ARG cc_start: 0.0410 (ppt170) cc_final: 0.0196 (ptt180) REVERT: A 1646 MET cc_start: 0.3681 (pmm) cc_final: 0.3126 (pmm) REVERT: D 589 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7387 (ttm-80) REVERT: D 678 GLU cc_start: 0.8452 (pt0) cc_final: 0.8072 (mm-30) REVERT: D 707 LEU cc_start: 0.8399 (tt) cc_final: 0.8184 (tt) REVERT: D 848 MET cc_start: 0.5919 (mmp) cc_final: 0.5650 (mmp) REVERT: D 864 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.6652 (m90) REVERT: D 869 ASN cc_start: 0.8985 (t0) cc_final: 0.8657 (t0) REVERT: D 875 PHE cc_start: 0.7727 (t80) cc_final: 0.7328 (t80) REVERT: D 904 CYS cc_start: 0.4994 (p) cc_final: 0.4762 (p) REVERT: D 994 LEU cc_start: 0.8782 (tt) cc_final: 0.8566 (tt) REVERT: D 1017 MET cc_start: 0.7029 (ttm) cc_final: 0.6626 (tpt) outliers start: 118 outliers final: 67 residues processed: 347 average time/residue: 0.2671 time to fit residues: 144.3095 Evaluate side-chains 322 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 246 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1095 THR Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1162 ILE Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1247 VAL Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1421 ILE Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 583 SER Chi-restraints excluded: chain D residue 585 GLU Chi-restraints excluded: chain D residue 589 ARG Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 798 VAL Chi-restraints excluded: chain D residue 864 HIS Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 891 VAL Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1011 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 206 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1252 ASN A1259 GLN D 374 ASN D 481 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17552 Z= 0.209 Angle : 0.829 31.169 23822 Z= 0.371 Chirality : 0.059 2.025 2761 Planarity : 0.005 0.094 2998 Dihedral : 10.323 162.221 2752 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 4.06 % Allowed : 27.31 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2116 helix: 0.43 (0.16), residues: 1046 sheet: -1.15 (0.35), residues: 192 loop : -1.87 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 185 HIS 0.030 0.001 HIS D 864 PHE 0.036 0.002 PHE D 775 TYR 0.027 0.001 TYR D1068 ARG 0.008 0.000 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 263 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7891 (tt) REVERT: A 263 LYS cc_start: 0.8065 (tptt) cc_final: 0.7504 (tppt) REVERT: A 526 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.6058 (p90) REVERT: A 532 PHE cc_start: 0.8065 (t80) cc_final: 0.7103 (t80) REVERT: A 670 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7815 (ptp) REVERT: A 680 ASP cc_start: 0.7658 (m-30) cc_final: 0.7428 (m-30) REVERT: A 717 MET cc_start: 0.8132 (ttt) cc_final: 0.7882 (tpp) REVERT: A 917 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6223 (pt) REVERT: A 972 MET cc_start: 0.5533 (mmm) cc_final: 0.3595 (ttt) REVERT: A 1105 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5822 (pt) REVERT: A 1117 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7558 (p0) REVERT: A 1126 MET cc_start: 0.8043 (ptp) cc_final: 0.7709 (ptm) REVERT: A 1546 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6946 (tttm) REVERT: A 1619 ARG cc_start: 0.5049 (OUTLIER) cc_final: 0.4282 (ptt90) REVERT: A 1646 MET cc_start: 0.3798 (pmm) cc_final: 0.3412 (pmm) REVERT: D 424 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: D 589 ARG cc_start: 0.7612 (ttm170) cc_final: 0.7131 (ttm-80) REVERT: D 639 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7851 (mm) REVERT: D 678 GLU cc_start: 0.8351 (pt0) cc_final: 0.7992 (mm-30) REVERT: D 704 ARG cc_start: 0.7633 (ttt90) cc_final: 0.7153 (tpt90) REVERT: D 848 MET cc_start: 0.6065 (mmp) cc_final: 0.3119 (ptt) REVERT: D 861 MET cc_start: 0.7227 (ptt) cc_final: 0.6699 (ptt) REVERT: D 869 ASN cc_start: 0.8949 (t0) cc_final: 0.8605 (t0) REVERT: D 875 PHE cc_start: 0.7676 (t80) cc_final: 0.7228 (t80) REVERT: D 883 MET cc_start: 0.7933 (tpt) cc_final: 0.7728 (tpp) REVERT: D 904 CYS cc_start: 0.4879 (p) cc_final: 0.4567 (p) REVERT: D 1009 MET cc_start: 0.8531 (mmm) cc_final: 0.8256 (mmm) outliers start: 73 outliers final: 46 residues processed: 310 average time/residue: 0.2696 time to fit residues: 129.4983 Evaluate side-chains 298 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 242 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1105 ILE Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1169 TYR Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 974 CYS Chi-restraints excluded: chain D residue 1030 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 62 optimal weight: 30.0000 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 187 optimal weight: 0.0370 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17552 Z= 0.264 Angle : 0.831 31.287 23822 Z= 0.371 Chirality : 0.059 2.029 2761 Planarity : 0.005 0.086 2998 Dihedral : 10.052 168.342 2752 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.52 % Favored : 93.43 % Rotamer: Outliers : 4.45 % Allowed : 26.86 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2116 helix: 0.52 (0.16), residues: 1048 sheet: -1.23 (0.35), residues: 199 loop : -1.81 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1399 HIS 0.005 0.001 HIS D 864 PHE 0.025 0.002 PHE D 775 TYR 0.022 0.002 TYR A1169 ARG 0.008 0.000 ARG A1547 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 249 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.8139 (tptt) cc_final: 0.7593 (tppt) REVERT: A 526 PHE cc_start: 0.6608 (OUTLIER) cc_final: 0.6249 (p90) REVERT: A 532 PHE cc_start: 0.8114 (t80) cc_final: 0.7141 (t80) REVERT: A 670 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7708 (ptp) REVERT: A 672 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.7328 (tp) REVERT: A 717 MET cc_start: 0.8186 (ttt) cc_final: 0.7983 (tpp) REVERT: A 917 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6467 (pt) REVERT: A 1117 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7582 (p0) REVERT: A 1126 MET cc_start: 0.8086 (ptp) cc_final: 0.7872 (ptt) REVERT: A 1230 TYR cc_start: 0.7417 (t80) cc_final: 0.6902 (t80) REVERT: A 1242 GLU cc_start: 0.7625 (mp0) cc_final: 0.7060 (mp0) REVERT: A 1546 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6719 (tttm) REVERT: A 1619 ARG cc_start: 0.4852 (OUTLIER) cc_final: 0.4089 (ptt90) REVERT: A 1646 MET cc_start: 0.3802 (pmm) cc_final: 0.3502 (pmm) REVERT: D 41 GLN cc_start: 0.7267 (tm-30) cc_final: 0.7032 (tm-30) REVERT: D 114 ARG cc_start: 0.7795 (ptt90) cc_final: 0.7499 (ptt180) REVERT: D 424 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8223 (pt0) REVERT: D 589 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7231 (ttm-80) REVERT: D 604 ASN cc_start: 0.8253 (m-40) cc_final: 0.7970 (m110) REVERT: D 639 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7980 (mm) REVERT: D 678 GLU cc_start: 0.8366 (pt0) cc_final: 0.8026 (mm-30) REVERT: D 704 ARG cc_start: 0.7631 (ttt90) cc_final: 0.7201 (tpt90) REVERT: D 869 ASN cc_start: 0.8939 (t0) cc_final: 0.8615 (t0) outliers start: 80 outliers final: 56 residues processed: 299 average time/residue: 0.2762 time to fit residues: 126.8246 Evaluate side-chains 301 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 236 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 748 PHE Chi-restraints excluded: chain A residue 915 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1470 MET Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 795 SER Chi-restraints excluded: chain D residue 805 LYS Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 892 TYR Chi-restraints excluded: chain D residue 974 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 7.9990 chunk 180 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 115 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 chunk 173 optimal weight: 3.9990 chunk 181 optimal weight: 0.0020 chunk 191 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1446 ASN D 374 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1033 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17552 Z= 0.184 Angle : 0.819 31.533 23822 Z= 0.362 Chirality : 0.058 2.043 2761 Planarity : 0.005 0.090 2998 Dihedral : 9.732 169.758 2752 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 3.56 % Allowed : 28.42 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 2116 helix: 0.69 (0.16), residues: 1048 sheet: -0.86 (0.36), residues: 202 loop : -1.70 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 185 HIS 0.002 0.000 HIS D 306 PHE 0.024 0.001 PHE D 775 TYR 0.027 0.001 TYR D1068 ARG 0.016 0.000 ARG D 643 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 244 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.8068 (tptt) cc_final: 0.7537 (tppt) REVERT: A 526 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6107 (p90) REVERT: A 532 PHE cc_start: 0.8118 (t80) cc_final: 0.7145 (t80) REVERT: A 670 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7487 (ptp) REVERT: A 917 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6551 (pt) REVERT: A 972 MET cc_start: 0.5398 (mmm) cc_final: 0.3635 (ttt) REVERT: A 1117 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7606 (p0) REVERT: A 1230 TYR cc_start: 0.7410 (t80) cc_final: 0.6883 (t80) REVERT: A 1242 GLU cc_start: 0.7664 (mp0) cc_final: 0.7193 (mp0) REVERT: A 1546 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6946 (tttm) REVERT: A 1619 ARG cc_start: 0.4840 (OUTLIER) cc_final: 0.4028 (ptt90) REVERT: D 41 GLN cc_start: 0.7287 (tm-30) cc_final: 0.7054 (tm-30) REVERT: D 114 ARG cc_start: 0.7715 (ptt90) cc_final: 0.7425 (ptt180) REVERT: D 424 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8118 (pt0) REVERT: D 639 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7852 (mm) REVERT: D 678 GLU cc_start: 0.8321 (pt0) cc_final: 0.8003 (mm-30) REVERT: D 704 ARG cc_start: 0.7633 (ttt90) cc_final: 0.7189 (tpt90) REVERT: D 848 MET cc_start: 0.6124 (mmp) cc_final: 0.3000 (ptt) REVERT: D 875 PHE cc_start: 0.7541 (t80) cc_final: 0.6948 (t80) outliers start: 64 outliers final: 45 residues processed: 286 average time/residue: 0.2781 time to fit residues: 122.1460 Evaluate side-chains 283 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 230 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1253 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1446 ASN Chi-restraints excluded: chain A residue 1470 MET Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 455 GLU Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 892 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 213 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 169 optimal weight: 0.0970 chunk 17 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1446 ASN D 604 ASN ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1033 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17552 Z= 0.222 Angle : 0.828 31.435 23822 Z= 0.368 Chirality : 0.058 2.043 2761 Planarity : 0.005 0.083 2998 Dihedral : 10.375 172.348 2752 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 3.17 % Allowed : 28.98 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 2116 helix: 0.69 (0.16), residues: 1061 sheet: -0.90 (0.36), residues: 206 loop : -1.70 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1641 HIS 0.002 0.001 HIS D 306 PHE 0.021 0.001 PHE D 775 TYR 0.035 0.001 TYR A 299 ARG 0.008 0.000 ARG A1547 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 242 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LYS cc_start: 0.8111 (tptt) cc_final: 0.7572 (tppt) REVERT: A 526 PHE cc_start: 0.6548 (OUTLIER) cc_final: 0.6163 (p90) REVERT: A 532 PHE cc_start: 0.8124 (t80) cc_final: 0.7161 (t80) REVERT: A 670 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7517 (ptp) REVERT: A 709 ASN cc_start: 0.8146 (p0) cc_final: 0.7837 (p0) REVERT: A 917 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6619 (pt) REVERT: A 972 MET cc_start: 0.5486 (mmm) cc_final: 0.3635 (ttt) REVERT: A 1117 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7276 (p0) REVERT: A 1122 LEU cc_start: 0.8659 (tp) cc_final: 0.8454 (tp) REVERT: A 1230 TYR cc_start: 0.7427 (t80) cc_final: 0.6897 (t80) REVERT: A 1242 GLU cc_start: 0.7648 (mp0) cc_final: 0.7159 (mp0) REVERT: A 1546 LYS cc_start: 0.7200 (OUTLIER) cc_final: 0.6909 (tttm) REVERT: A 1619 ARG cc_start: 0.4994 (OUTLIER) cc_final: 0.4188 (ptt90) REVERT: D 41 GLN cc_start: 0.7320 (tm-30) cc_final: 0.7092 (tm-30) REVERT: D 424 GLN cc_start: 0.9235 (OUTLIER) cc_final: 0.8124 (pt0) REVERT: D 639 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7871 (mm) REVERT: D 678 GLU cc_start: 0.8328 (pt0) cc_final: 0.8024 (mm-30) REVERT: D 704 ARG cc_start: 0.7680 (ttt90) cc_final: 0.7245 (tpt90) REVERT: D 848 MET cc_start: 0.5711 (mmp) cc_final: 0.2802 (ptt) REVERT: D 875 PHE cc_start: 0.7546 (t80) cc_final: 0.7002 (t80) outliers start: 57 outliers final: 43 residues processed: 281 average time/residue: 0.2738 time to fit residues: 118.6735 Evaluate side-chains 290 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 239 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 546 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 567 PHE Chi-restraints excluded: chain A residue 571 MET Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 670 MET Chi-restraints excluded: chain A residue 687 SER Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 917 LEU Chi-restraints excluded: chain A residue 1063 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1232 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1446 ASN Chi-restraints excluded: chain A residue 1470 MET Chi-restraints excluded: chain A residue 1531 THR Chi-restraints excluded: chain A residue 1546 LYS Chi-restraints excluded: chain A residue 1567 THR Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1619 ARG Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 424 GLN Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 463 THR Chi-restraints excluded: chain D residue 507 CYS Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 613 ASN Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 639 ILE Chi-restraints excluded: chain D residue 668 ASN Chi-restraints excluded: chain D residue 892 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.0370 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 40.0000 chunk 149 optimal weight: 0.8980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1259 GLN A1304 ASN A1446 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1033 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.211355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158658 restraints weight = 22815.191| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.54 r_work: 0.3459 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17552 Z= 0.261 Angle : 0.833 31.462 23822 Z= 0.371 Chirality : 0.058 2.038 2761 Planarity : 0.005 0.089 2998 Dihedral : 10.352 173.357 2752 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 3.50 % Allowed : 28.59 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.19), residues: 2116 helix: 0.72 (0.16), residues: 1065 sheet: -0.91 (0.36), residues: 204 loop : -1.68 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1641 HIS 0.003 0.001 HIS D 306 PHE 0.021 0.002 PHE D 775 TYR 0.021 0.001 TYR A1169 ARG 0.007 0.001 ARG A1547 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4036.78 seconds wall clock time: 73 minutes 24.58 seconds (4404.58 seconds total)