Starting phenix.real_space_refine on Thu Feb 15 13:51:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcp_0872/02_2024/6lcp_0872_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcp_0872/02_2024/6lcp_0872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcp_0872/02_2024/6lcp_0872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcp_0872/02_2024/6lcp_0872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcp_0872/02_2024/6lcp_0872_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lcp_0872/02_2024/6lcp_0872_updated.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 63 5.16 5 Be 1 3.05 5 C 7979 2.51 5 N 2058 2.21 5 O 2313 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 372": "OD1" <-> "OD2" Residue "A ASP 394": "OD1" <-> "OD2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A PHE 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A ASP 640": "OD1" <-> "OD2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A GLU 657": "OE1" <-> "OE2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ASP 689": "OD1" <-> "OD2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A ASP 727": "OD1" <-> "OD2" Residue "A ASP 759": "OD1" <-> "OD2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 845": "OE1" <-> "OE2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ASP 899": "OD1" <-> "OD2" Residue "A ASP 903": "OD1" <-> "OD2" Residue "A ASP 941": "OD1" <-> "OD2" Residue "A ASP 951": "OD1" <-> "OD2" Residue "A ASP 956": "OD1" <-> "OD2" Residue "A ASP 978": "OD1" <-> "OD2" Residue "A GLU 980": "OE1" <-> "OE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1049": "OD1" <-> "OD2" Residue "A ASP 1057": "OD1" <-> "OD2" Residue "A GLU 1077": "OE1" <-> "OE2" Residue "A GLU 1078": "OE1" <-> "OE2" Residue "A ASP 1087": "OD1" <-> "OD2" Residue "A PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A GLU 1145": "OE1" <-> "OE2" Residue "A PHE 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1173": "OD1" <-> "OD2" Residue "A TYR 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A PHE 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1320": "NH1" <-> "NH2" Residue "A PHE 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1336": "OD1" <-> "OD2" Residue "A ASP 1346": "OD1" <-> "OD2" Residue "A PHE 1347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 194": "OD1" <-> "OD2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12421 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9082 Classifications: {'peptide': 1140} Link IDs: {'PTRANS': 46, 'TRANS': 1093} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3061 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 26, 'TRANS': 349} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'MAN': 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: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 111 Unusual residues: {' MG': 1, 'BEF': 1, 'POV': 2} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" 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 Time building chain proxies: 7.33, per 1000 atoms: 0.59 Number of scatterers: 12421 At special positions: 0 Unit cell: (147.7, 110.775, 128.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 63 16.00 P 3 15.00 Mg 1 11.99 F 3 9.00 O 2313 8.00 N 2058 7.00 C 7979 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 139 " 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=1, symmetry=0 Links applied ALPHA1-3 " MAN C 1 " - " MAN C 2 " " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 501 " - " ASN B 131 " " NAG B 509 " - " ASN B 241 " " NAG D 1 " - " ASN B 189 " " NAG E 1 " - " ASN B 219 " " NAG F 1 " - " ASN B 314 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.51 Conformation dependent library (CDL) restraints added in 2.2 seconds 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2860 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 10 sheets defined 39.5% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 162 through 191 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 484 through 514 Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.637A pdb=" N PHE A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 533 through 547 Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 554 through 572 removed outlier: 3.745A pdb=" N TYR A 557 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE A 558 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 577 No H-bonds generated for 'chain 'A' and resid 575 through 577' Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 634 through 642 Processing helix chain 'A' and resid 649 through 671 Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 700 through 712 removed outlier: 3.895A pdb=" N GLN A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'A' and resid 807 through 810 No H-bonds generated for 'chain 'A' and resid 807 through 810' Processing helix chain 'A' and resid 820 through 835 Processing helix chain 'A' and resid 850 through 865 Processing helix chain 'A' and resid 870 through 879 Processing helix chain 'A' and resid 901 through 911 Processing helix chain 'A' and resid 923 through 932 removed outlier: 3.674A pdb=" N ILE A 927 " --> pdb=" O VAL A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 972 Processing helix chain 'A' and resid 980 through 983 No H-bonds generated for 'chain 'A' and resid 980 through 983' Processing helix chain 'A' and resid 1002 through 1008 Processing helix chain 'A' and resid 1013 through 1023 Processing helix chain 'A' and resid 1034 through 1047 Processing helix chain 'A' and resid 1059 through 1067 removed outlier: 3.544A pdb=" N GLU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1102 Processing helix chain 'A' and resid 1105 through 1136 Processing helix chain 'A' and resid 1148 through 1151 No H-bonds generated for 'chain 'A' and resid 1148 through 1151' Processing helix chain 'A' and resid 1158 through 1166 Processing helix chain 'A' and resid 1175 through 1178 No H-bonds generated for 'chain 'A' and resid 1175 through 1178' Processing helix chain 'A' and resid 1180 through 1187 Processing helix chain 'A' and resid 1196 through 1220 Proline residue: A1215 - end of helix Processing helix chain 'A' and resid 1237 through 1256 Proline residue: A1245 - end of helix Processing helix chain 'A' and resid 1263 through 1285 removed outlier: 4.495A pdb=" N ALA A1285 " --> pdb=" O GLY A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1299 No H-bonds generated for 'chain 'A' and resid 1296 through 1299' Processing helix chain 'A' and resid 1303 through 1329 Proline residue: A1313 - end of helix Proline residue: A1319 - end of helix Processing helix chain 'A' and resid 1334 through 1344 removed outlier: 4.114A pdb=" N ARG A1344 " --> pdb=" O GLU A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1355 Processing helix chain 'B' and resid 50 through 74 Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 212 through 215 No H-bonds generated for 'chain 'B' and resid 212 through 215' Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 293 through 298 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 356 through 381 Processing sheet with id= A, first strand: chain 'A' and resid 86 through 89 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 196 Processing sheet with id= C, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= D, first strand: chain 'A' and resid 377 through 381 Processing sheet with id= E, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 5.750A pdb=" N VAL A1027 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASP A 941 " --> pdb=" O ALA A 997 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 999 " --> pdb=" O ASP A 941 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU A 943 " --> pdb=" O VAL A 999 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ASP A1001 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEU A 945 " --> pdb=" O ASP A1001 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 720 through 723 Processing sheet with id= G, first strand: chain 'A' and resid 753 through 755 removed outlier: 4.199A pdb=" N ASN A 763 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 616 through 623 removed outlier: 6.900A pdb=" N ALA A 892 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ALA A 621 " --> pdb=" O GLY A 890 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY A 890 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE A 623 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N LEU A 888 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 843 " --> pdb=" O LEU A 888 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY A 890 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU A 841 " --> pdb=" O GLY A 890 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA A 892 " --> pdb=" O ARG A 839 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ARG A 839 " --> pdb=" O ALA A 892 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ARG A 793 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 775 " --> pdb=" O ARG A 793 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.550A pdb=" N ARG B 340 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR B 157 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LEU B 310 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU B 159 " --> pdb=" O TYR B 308 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR B 308 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 119 through 126 492 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 5.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 2018 1.28 - 1.41: 3213 1.41 - 1.55: 7363 1.55 - 1.68: 11 1.68 - 1.81: 103 Bond restraints: 12708 Sorted by residual: bond pdb=" BE BEF A2002 " pdb=" F3 BEF A2002 " ideal model delta sigma weight residual 1.476 1.765 -0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" BE BEF A2002 " pdb=" F2 BEF A2002 " ideal model delta sigma weight residual 1.476 1.764 -0.288 2.00e-02 2.50e+03 2.07e+02 bond pdb=" BE BEF A2002 " pdb=" F1 BEF A2002 " ideal model delta sigma weight residual 1.476 1.761 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C ARG A1320 " pdb=" O ARG A1320 " ideal model delta sigma weight residual 1.236 1.144 0.093 1.26e-02 6.30e+03 5.41e+01 bond pdb=" C31 POV A2003 " pdb=" O31 POV A2003 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.04e+01 ... (remaining 12703 not shown) Histogram of bond angle deviations from ideal: 97.56 - 105.12: 260 105.12 - 112.68: 6714 112.68 - 120.24: 5136 120.24 - 127.80: 5013 127.80 - 135.35: 122 Bond angle restraints: 17245 Sorted by residual: angle pdb=" N GLY A 527 " pdb=" CA GLY A 527 " pdb=" C GLY A 527 " ideal model delta sigma weight residual 110.91 127.16 -16.25 1.49e+00 4.50e-01 1.19e+02 angle pdb=" C PRO B 151 " pdb=" N THR B 152 " pdb=" CA THR B 152 " ideal model delta sigma weight residual 121.54 135.35 -13.81 1.91e+00 2.74e-01 5.23e+01 angle pdb=" N ILE B 153 " pdb=" CA ILE B 153 " pdb=" CB ILE B 153 " ideal model delta sigma weight residual 110.82 103.29 7.53 1.11e+00 8.12e-01 4.60e+01 angle pdb=" CA GLY A 527 " pdb=" C GLY A 527 " pdb=" N SER A 528 " ideal model delta sigma weight residual 114.84 107.92 6.92 1.06e+00 8.90e-01 4.27e+01 angle pdb=" C ARG A1320 " pdb=" CA ARG A1320 " pdb=" CB ARG A1320 " ideal model delta sigma weight residual 110.67 99.03 11.64 1.92e+00 2.71e-01 3.67e+01 ... (remaining 17240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.52: 7316 26.52 - 53.04: 369 53.04 - 79.56: 48 79.56 - 106.08: 22 106.08 - 132.60: 6 Dihedral angle restraints: 7761 sinusoidal: 3330 harmonic: 4431 Sorted by residual: dihedral pdb=" C PRO B 151 " pdb=" N PRO B 151 " pdb=" CA PRO B 151 " pdb=" CB PRO B 151 " ideal model delta harmonic sigma weight residual -120.70 -139.69 18.99 0 2.50e+00 1.60e-01 5.77e+01 dihedral pdb=" N PRO B 151 " pdb=" C PRO B 151 " pdb=" CA PRO B 151 " pdb=" CB PRO B 151 " ideal model delta harmonic sigma weight residual 115.10 133.88 -18.78 0 2.50e+00 1.60e-01 5.64e+01 dihedral pdb=" C THR B 152 " pdb=" N THR B 152 " pdb=" CA THR B 152 " pdb=" CB THR B 152 " ideal model delta harmonic sigma weight residual -122.00 -136.85 14.85 0 2.50e+00 1.60e-01 3.53e+01 ... (remaining 7758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.230: 1928 0.230 - 0.460: 5 0.460 - 0.690: 2 0.690 - 0.920: 2 0.920 - 1.150: 2 Chirality restraints: 1939 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-02 2.50e+03 1.47e+03 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 -1.90 -0.50 2.00e-02 2.50e+03 6.25e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.92e+02 ... (remaining 1936 not shown) Planarity restraints: 2191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 314 " -0.098 2.00e-02 2.50e+03 1.05e-01 1.39e+02 pdb=" CG ASN B 314 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 314 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 314 " 0.167 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 269 " 0.093 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO B 270 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 270 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 270 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 152 " 0.022 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C THR B 152 " -0.077 2.00e-02 2.50e+03 pdb=" O THR B 152 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE B 153 " 0.025 2.00e-02 2.50e+03 ... (remaining 2188 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 65 2.42 - 3.04: 8142 3.04 - 3.66: 18540 3.66 - 4.28: 28424 4.28 - 4.90: 47566 Nonbonded interactions: 102737 Sorted by model distance: nonbonded pdb=" NH2 ARG A 114 " pdb=" CD1 ILE A 476 " model vdw 1.795 3.540 nonbonded pdb=" OD1 ASP A 606 " pdb=" F1 BEF A2002 " model vdw 1.807 2.390 nonbonded pdb=" OD2 ASP A 606 " pdb="MG MG A2001 " model vdw 1.968 2.170 nonbonded pdb=" O ASN A 948 " pdb=" N SER A 950 " model vdw 2.037 2.520 nonbonded pdb=" N ASP B 148 " pdb=" OD1 ASP B 148 " model vdw 2.073 2.520 ... (remaining 102732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.240 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 37.040 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 0.289 12708 Z= 0.586 Angle : 0.970 16.247 17245 Z= 0.528 Chirality : 0.068 1.150 1939 Planarity : 0.007 0.142 2186 Dihedral : 16.804 132.598 4898 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.83 % Favored : 89.97 % Rotamer: Outliers : 0.99 % Allowed : 8.72 % Favored : 90.29 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.18), residues: 1506 helix: -1.91 (0.16), residues: 644 sheet: -2.63 (0.32), residues: 209 loop : -3.61 (0.20), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 120 HIS 0.003 0.001 HIS A 717 PHE 0.028 0.002 PHE A 524 TYR 0.020 0.002 TYR A1293 ARG 0.009 0.001 ARG A1320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 231 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 326 PHE cc_start: 0.7832 (m-80) cc_final: 0.6866 (m-80) REVERT: A 399 GLN cc_start: 0.7329 (tt0) cc_final: 0.6768 (tp40) REVERT: A 441 ILE cc_start: 0.8437 (mm) cc_final: 0.8142 (mm) REVERT: A 476 ILE cc_start: 0.7330 (OUTLIER) cc_final: 0.7095 (mp) REVERT: A 501 ILE cc_start: 0.8193 (mm) cc_final: 0.7894 (mt) REVERT: A 788 MET cc_start: 0.7634 (tmm) cc_final: 0.7412 (tmm) REVERT: A 854 ARG cc_start: 0.6902 (ppt170) cc_final: 0.6696 (ppt170) REVERT: A 924 GLU cc_start: 0.5975 (mm-30) cc_final: 0.5700 (mm-30) REVERT: A 1145 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6766 (tm-30) REVERT: A 1151 MET cc_start: 0.7816 (mtp) cc_final: 0.7566 (mtp) REVERT: B 135 ASN cc_start: 0.8141 (p0) cc_final: 0.7736 (p0) REVERT: B 270 PRO cc_start: 0.8578 (Cg_endo) cc_final: 0.8330 (Cg_exo) outliers start: 13 outliers final: 8 residues processed: 244 average time/residue: 0.3184 time to fit residues: 105.8231 Evaluate side-chains 181 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 172 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 478 PRO Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 955 GLU Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 153 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 370 ASN A 408 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN A 613 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 646 ASN A 704 GLN A 717 HIS A 928 ASN A 990 ASN A1015 GLN A1023 GLN A1046 ASN A1251 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12708 Z= 0.229 Angle : 0.699 8.666 17245 Z= 0.360 Chirality : 0.045 0.211 1939 Planarity : 0.006 0.095 2186 Dihedral : 12.508 144.633 2020 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.64 % Favored : 92.23 % Rotamer: Outliers : 2.22 % Allowed : 15.83 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.20), residues: 1506 helix: -0.70 (0.19), residues: 651 sheet: -2.17 (0.33), residues: 212 loop : -3.23 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 120 HIS 0.003 0.001 HIS A 673 PHE 0.032 0.002 PHE A 709 TYR 0.020 0.002 TYR A 853 ARG 0.003 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 1.472 Fit side-chains revert: symmetry clash REVERT: A 326 PHE cc_start: 0.7455 (m-80) cc_final: 0.6818 (m-80) REVERT: A 441 ILE cc_start: 0.8430 (mm) cc_final: 0.8124 (mm) REVERT: A 481 ARG cc_start: 0.7758 (mtp-110) cc_final: 0.7506 (mtp-110) REVERT: A 501 ILE cc_start: 0.8208 (mm) cc_final: 0.7958 (mt) REVERT: A 630 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6408 (mm-30) REVERT: A 924 GLU cc_start: 0.5793 (mm-30) cc_final: 0.5582 (mm-30) REVERT: A 1131 TRP cc_start: 0.8735 (m100) cc_final: 0.8533 (m100) REVERT: A 1145 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6764 (tm-30) REVERT: B 43 CYS cc_start: 0.8685 (p) cc_final: 0.8360 (p) REVERT: B 135 ASN cc_start: 0.8121 (p0) cc_final: 0.7774 (p0) REVERT: B 270 PRO cc_start: 0.8386 (Cg_endo) cc_final: 0.8065 (Cg_exo) outliers start: 29 outliers final: 16 residues processed: 236 average time/residue: 0.2756 time to fit residues: 91.1391 Evaluate side-chains 197 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 148 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 137 optimal weight: 0.7980 chunk 148 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 127 ASN A 399 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1244 HIS ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12708 Z= 0.225 Angle : 0.662 8.785 17245 Z= 0.341 Chirality : 0.044 0.167 1939 Planarity : 0.005 0.089 2186 Dihedral : 11.225 140.756 2007 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.30 % Favored : 92.56 % Rotamer: Outliers : 2.98 % Allowed : 18.81 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.20), residues: 1506 helix: -0.27 (0.19), residues: 646 sheet: -2.07 (0.33), residues: 217 loop : -3.00 (0.22), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 120 HIS 0.002 0.000 HIS A 717 PHE 0.027 0.002 PHE A 781 TYR 0.027 0.002 TYR A 853 ARG 0.009 0.000 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 194 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 PHE cc_start: 0.7405 (m-80) cc_final: 0.6789 (m-80) REVERT: A 441 ILE cc_start: 0.8491 (mm) cc_final: 0.8153 (mm) REVERT: A 501 ILE cc_start: 0.8234 (mm) cc_final: 0.7995 (mt) REVERT: A 713 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 841 LEU cc_start: 0.8001 (mp) cc_final: 0.7707 (mp) REVERT: A 924 GLU cc_start: 0.5769 (mm-30) cc_final: 0.5473 (mm-30) REVERT: A 1145 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: B 43 CYS cc_start: 0.8672 (p) cc_final: 0.8353 (p) REVERT: B 135 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7917 (p0) REVERT: B 168 ARG cc_start: 0.8229 (tpt170) cc_final: 0.7794 (ttt90) REVERT: B 270 PRO cc_start: 0.8308 (Cg_endo) cc_final: 0.7959 (Cg_exo) outliers start: 39 outliers final: 22 residues processed: 221 average time/residue: 0.2755 time to fit residues: 85.7484 Evaluate side-chains 199 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 174 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 327 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 12708 Z= 0.361 Angle : 0.717 8.510 17245 Z= 0.370 Chirality : 0.046 0.199 1939 Planarity : 0.005 0.092 2186 Dihedral : 10.511 139.124 2005 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.90 % Favored : 91.97 % Rotamer: Outliers : 4.59 % Allowed : 19.04 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.20), residues: 1506 helix: -0.33 (0.19), residues: 653 sheet: -2.07 (0.32), residues: 219 loop : -2.91 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 120 HIS 0.002 0.001 HIS B 317 PHE 0.023 0.002 PHE A 781 TYR 0.030 0.002 TYR A 853 ARG 0.006 0.001 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 187 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 PHE cc_start: 0.7256 (m-80) cc_final: 0.6603 (m-80) REVERT: A 441 ILE cc_start: 0.8505 (mm) cc_final: 0.8188 (mm) REVERT: A 472 MET cc_start: 0.7837 (ttt) cc_final: 0.7548 (ttm) REVERT: A 501 ILE cc_start: 0.8284 (mm) cc_final: 0.8021 (mt) REVERT: A 713 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8028 (mp) REVERT: A 841 LEU cc_start: 0.8060 (mp) cc_final: 0.7705 (mp) REVERT: A 924 GLU cc_start: 0.6040 (mm-30) cc_final: 0.5773 (mm-30) REVERT: A 974 ASN cc_start: 0.8257 (t0) cc_final: 0.8038 (t0) REVERT: A 1145 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: B 43 CYS cc_start: 0.8655 (p) cc_final: 0.8344 (p) REVERT: B 168 ARG cc_start: 0.8253 (tpt170) cc_final: 0.7807 (ttt90) outliers start: 60 outliers final: 39 residues processed: 229 average time/residue: 0.2713 time to fit residues: 88.3618 Evaluate side-chains 213 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1050 VAL Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 351 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 0.0010 chunk 108 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 131 optimal weight: 0.8980 chunk 36 optimal weight: 0.0040 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12708 Z= 0.183 Angle : 0.645 8.295 17245 Z= 0.331 Chirality : 0.044 0.190 1939 Planarity : 0.005 0.088 2186 Dihedral : 9.520 132.881 2005 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.37 % Favored : 93.49 % Rotamer: Outliers : 3.75 % Allowed : 19.80 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.21), residues: 1506 helix: 0.07 (0.20), residues: 642 sheet: -1.90 (0.31), residues: 229 loop : -2.77 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 120 HIS 0.002 0.000 HIS A 860 PHE 0.018 0.001 PHE A 538 TYR 0.031 0.001 TYR A 853 ARG 0.011 0.000 ARG A 858 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.6520 (mtt180) cc_final: 0.5922 (mmp80) REVERT: A 326 PHE cc_start: 0.7232 (m-80) cc_final: 0.6693 (m-80) REVERT: A 472 MET cc_start: 0.7691 (ttt) cc_final: 0.7452 (ttm) REVERT: A 501 ILE cc_start: 0.8232 (mm) cc_final: 0.7960 (mt) REVERT: A 682 ASP cc_start: 0.7824 (t70) cc_final: 0.7504 (t0) REVERT: A 713 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7971 (mp) REVERT: A 841 LEU cc_start: 0.7998 (mp) cc_final: 0.7680 (mp) REVERT: A 924 GLU cc_start: 0.5808 (mm-30) cc_final: 0.5545 (mm-30) REVERT: A 1145 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6897 (tm-30) REVERT: B 43 CYS cc_start: 0.8648 (p) cc_final: 0.8312 (p) REVERT: B 168 ARG cc_start: 0.8189 (tpt170) cc_final: 0.7865 (ttt90) outliers start: 49 outliers final: 34 residues processed: 243 average time/residue: 0.2820 time to fit residues: 98.9362 Evaluate side-chains 213 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 ASN Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 645 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 351 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 146 optimal weight: 0.5980 chunk 121 optimal weight: 0.0040 chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.0040 chunk 76 optimal weight: 2.9990 overall best weight: 0.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12708 Z= 0.171 Angle : 0.618 8.931 17245 Z= 0.318 Chirality : 0.043 0.191 1939 Planarity : 0.005 0.087 2186 Dihedral : 8.761 127.704 2003 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.64 % Favored : 93.23 % Rotamer: Outliers : 3.44 % Allowed : 20.95 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1506 helix: 0.20 (0.20), residues: 663 sheet: -1.64 (0.32), residues: 226 loop : -2.70 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 120 HIS 0.001 0.000 HIS A 673 PHE 0.021 0.001 PHE A 538 TYR 0.026 0.001 TYR A 853 ARG 0.007 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.6480 (mtt180) cc_final: 0.5874 (mmp80) REVERT: A 326 PHE cc_start: 0.7175 (m-80) cc_final: 0.6623 (m-80) REVERT: A 472 MET cc_start: 0.7634 (ttt) cc_final: 0.7361 (ttm) REVERT: A 501 ILE cc_start: 0.8237 (mm) cc_final: 0.7978 (mt) REVERT: A 630 GLU cc_start: 0.5875 (mm-30) cc_final: 0.5515 (tp30) REVERT: A 641 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7723 (ttp-170) REVERT: A 656 GLU cc_start: 0.7488 (tp30) cc_final: 0.7287 (tp30) REVERT: A 682 ASP cc_start: 0.7745 (t70) cc_final: 0.7519 (t0) REVERT: A 683 MET cc_start: 0.8590 (ptm) cc_final: 0.8350 (ptp) REVERT: A 713 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7952 (mp) REVERT: A 841 LEU cc_start: 0.7969 (mp) cc_final: 0.7665 (mp) REVERT: A 924 GLU cc_start: 0.5730 (mm-30) cc_final: 0.5478 (mm-30) REVERT: A 1051 MET cc_start: 0.7893 (tpp) cc_final: 0.7623 (tpp) REVERT: A 1145 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: B 43 CYS cc_start: 0.8629 (p) cc_final: 0.8289 (p) REVERT: B 168 ARG cc_start: 0.8170 (tpt170) cc_final: 0.7818 (ttt90) outliers start: 45 outliers final: 33 residues processed: 231 average time/residue: 0.2637 time to fit residues: 86.6480 Evaluate side-chains 217 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 182 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12708 Z= 0.212 Angle : 0.631 9.133 17245 Z= 0.326 Chirality : 0.043 0.200 1939 Planarity : 0.005 0.088 2186 Dihedral : 8.283 126.454 2001 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.04 % Favored : 92.83 % Rotamer: Outliers : 3.67 % Allowed : 21.56 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.21), residues: 1506 helix: 0.32 (0.20), residues: 652 sheet: -1.57 (0.33), residues: 227 loop : -2.62 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 120 HIS 0.002 0.000 HIS B 166 PHE 0.021 0.001 PHE A 538 TYR 0.018 0.001 TYR A1146 ARG 0.006 0.000 ARG A1260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 188 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.6514 (mtt180) cc_final: 0.5881 (mmp80) REVERT: A 326 PHE cc_start: 0.7100 (m-80) cc_final: 0.6483 (m-80) REVERT: A 472 MET cc_start: 0.7690 (ttt) cc_final: 0.7416 (ttm) REVERT: A 481 ARG cc_start: 0.7675 (mtp-110) cc_final: 0.7431 (mtp-110) REVERT: A 501 ILE cc_start: 0.8208 (mm) cc_final: 0.7944 (mt) REVERT: A 682 ASP cc_start: 0.7725 (t70) cc_final: 0.7517 (t0) REVERT: A 683 MET cc_start: 0.8604 (ptm) cc_final: 0.8369 (ptp) REVERT: A 841 LEU cc_start: 0.7986 (mp) cc_final: 0.7678 (mp) REVERT: A 924 GLU cc_start: 0.5799 (mm-30) cc_final: 0.5486 (mm-30) REVERT: A 1145 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: B 43 CYS cc_start: 0.8578 (p) cc_final: 0.8243 (p) REVERT: B 150 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6991 (tp40) REVERT: B 168 ARG cc_start: 0.8200 (tpt170) cc_final: 0.7869 (ttt90) outliers start: 48 outliers final: 40 residues processed: 215 average time/residue: 0.2677 time to fit residues: 81.5057 Evaluate side-chains 218 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12708 Z= 0.209 Angle : 0.631 9.951 17245 Z= 0.325 Chirality : 0.043 0.196 1939 Planarity : 0.005 0.087 2186 Dihedral : 8.044 125.047 2001 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.44 % Favored : 92.43 % Rotamer: Outliers : 3.67 % Allowed : 21.79 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.21), residues: 1506 helix: 0.37 (0.20), residues: 652 sheet: -1.48 (0.33), residues: 227 loop : -2.57 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 120 HIS 0.001 0.000 HIS B 166 PHE 0.021 0.001 PHE A 538 TYR 0.032 0.001 TYR A 853 ARG 0.005 0.000 ARG A1260 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 187 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.6561 (mtt180) cc_final: 0.5937 (mmp80) REVERT: A 326 PHE cc_start: 0.7085 (m-80) cc_final: 0.6642 (m-80) REVERT: A 501 ILE cc_start: 0.8267 (mm) cc_final: 0.7997 (mt) REVERT: A 682 ASP cc_start: 0.7781 (t70) cc_final: 0.7578 (t0) REVERT: A 841 LEU cc_start: 0.8103 (mp) cc_final: 0.7810 (mp) REVERT: A 924 GLU cc_start: 0.5811 (mm-30) cc_final: 0.5497 (mm-30) REVERT: A 940 MET cc_start: 0.8595 (mtt) cc_final: 0.8367 (mtt) REVERT: A 1145 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: B 43 CYS cc_start: 0.8570 (p) cc_final: 0.8218 (p) REVERT: B 150 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7058 (tp40) REVERT: B 168 ARG cc_start: 0.8185 (tpt170) cc_final: 0.7845 (ttt90) outliers start: 48 outliers final: 42 residues processed: 218 average time/residue: 0.2683 time to fit residues: 83.0237 Evaluate side-chains 228 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 128 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12708 Z= 0.234 Angle : 0.646 10.435 17245 Z= 0.332 Chirality : 0.043 0.201 1939 Planarity : 0.005 0.088 2186 Dihedral : 7.983 125.194 2001 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.50 % Favored : 92.36 % Rotamer: Outliers : 4.05 % Allowed : 21.33 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.21), residues: 1506 helix: 0.37 (0.20), residues: 654 sheet: -1.43 (0.34), residues: 222 loop : -2.51 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 120 HIS 0.002 0.000 HIS A 673 PHE 0.020 0.001 PHE A1278 TYR 0.030 0.002 TYR A 853 ARG 0.007 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 188 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.6594 (mtt180) cc_final: 0.5937 (mmp80) REVERT: A 326 PHE cc_start: 0.7103 (m-80) cc_final: 0.6667 (m-80) REVERT: A 501 ILE cc_start: 0.8205 (mm) cc_final: 0.7943 (mt) REVERT: A 682 ASP cc_start: 0.7821 (t70) cc_final: 0.7583 (t0) REVERT: A 841 LEU cc_start: 0.8145 (mp) cc_final: 0.7847 (mp) REVERT: A 924 GLU cc_start: 0.5794 (mm-30) cc_final: 0.5474 (mm-30) REVERT: A 1145 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6952 (tm-30) REVERT: B 43 CYS cc_start: 0.8567 (p) cc_final: 0.8224 (p) REVERT: B 150 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7023 (tp40) REVERT: B 168 ARG cc_start: 0.8234 (tpt170) cc_final: 0.7914 (ttt90) outliers start: 53 outliers final: 47 residues processed: 220 average time/residue: 0.2797 time to fit residues: 89.0298 Evaluate side-chains 224 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1060 ASN Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain A residue 1333 TYR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.0270 chunk 99 optimal weight: 0.9980 chunk 150 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12708 Z= 0.198 Angle : 0.635 11.073 17245 Z= 0.326 Chirality : 0.042 0.200 1939 Planarity : 0.005 0.087 2186 Dihedral : 7.854 123.376 2001 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.17 % Favored : 92.70 % Rotamer: Outliers : 3.67 % Allowed : 22.25 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.21), residues: 1506 helix: 0.44 (0.20), residues: 661 sheet: -1.31 (0.34), residues: 221 loop : -2.46 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1279 HIS 0.001 0.000 HIS B 166 PHE 0.020 0.001 PHE A1278 TYR 0.030 0.001 TYR A 853 ARG 0.006 0.000 ARG A 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3012 Ramachandran restraints generated. 1506 Oldfield, 0 Emsley, 1506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 190 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 181 ARG cc_start: 0.6519 (mtt180) cc_final: 0.5894 (mmp80) REVERT: A 326 PHE cc_start: 0.7102 (m-80) cc_final: 0.6480 (m-80) REVERT: A 501 ILE cc_start: 0.8250 (mm) cc_final: 0.7987 (mt) REVERT: A 682 ASP cc_start: 0.7796 (t70) cc_final: 0.7571 (t0) REVERT: A 841 LEU cc_start: 0.8169 (mp) cc_final: 0.7870 (mp) REVERT: A 924 GLU cc_start: 0.5750 (mm-30) cc_final: 0.5426 (mm-30) REVERT: A 1145 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: B 43 CYS cc_start: 0.8555 (p) cc_final: 0.8189 (p) REVERT: B 150 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7031 (tp40) REVERT: B 168 ARG cc_start: 0.8227 (tpt170) cc_final: 0.7918 (ttt90) outliers start: 48 outliers final: 44 residues processed: 219 average time/residue: 0.2634 time to fit residues: 82.9848 Evaluate side-chains 228 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 182 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 133 HIS Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 364 CYS Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 412 TYR Chi-restraints excluded: chain A residue 413 LYS Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 526 TYR Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 623 ILE Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 954 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1134 CYS Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1146 TYR Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1308 CYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 150 GLN Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 283 ASN Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 614 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.146900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114756 restraints weight = 16332.903| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.82 r_work: 0.3285 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12708 Z= 0.212 Angle : 0.638 10.986 17245 Z= 0.328 Chirality : 0.043 0.202 1939 Planarity : 0.005 0.087 2186 Dihedral : 7.780 122.808 2001 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.57 % Favored : 92.30 % Rotamer: Outliers : 3.67 % Allowed : 22.32 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.21), residues: 1506 helix: 0.46 (0.20), residues: 653 sheet: -1.33 (0.34), residues: 222 loop : -2.38 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 120 HIS 0.002 0.000 HIS B 166 PHE 0.021 0.001 PHE A1278 TYR 0.028 0.001 TYR A 853 ARG 0.006 0.000 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2958.41 seconds wall clock time: 54 minutes 43.65 seconds (3283.65 seconds total)