Starting phenix.real_space_refine on Thu Feb 15 07:32:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh4_12893/02_2024/7oh4_12893_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh4_12893/02_2024/7oh4_12893.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh4_12893/02_2024/7oh4_12893_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh4_12893/02_2024/7oh4_12893_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh4_12893/02_2024/7oh4_12893_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh4_12893/02_2024/7oh4_12893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh4_12893/02_2024/7oh4_12893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh4_12893/02_2024/7oh4_12893_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh4_12893/02_2024/7oh4_12893_updated.pdb" } resolution = 3.0 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7452 2.51 5 N 1859 2.21 5 O 2173 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ASP 584": "OD1" <-> "OD2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1117": "NH1" <-> "NH2" Residue "A PHE 1160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "A TYR 1244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 359": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11535 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1064, 8504 Classifications: {'peptide': 1064} Link IDs: {'PTRANS': 30, 'TRANS': 1033} Chain: "C" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2842 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} 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 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, '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: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {' MG': 1, '2Y5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 6.70, per 1000 atoms: 0.58 Number of scatterers: 11535 At special positions: 0 Unit cell: (77.34, 108.276, 175.304, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 2 15.00 Mg 1 11.99 O 2173 8.00 N 1859 7.00 C 7452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.04 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 BETA1-3 " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG C 501 " - " ASN C 237 " " NAG D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 2.3 seconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 10 sheets defined 38.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 214 through 222 removed outlier: 4.309A pdb=" N PHE A 219 " --> pdb=" O PRO A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.768A pdb=" N GLN A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 280 removed outlier: 3.855A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 439 through 472 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 487 through 505 removed outlier: 3.641A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 497 " --> pdb=" O LYS A 493 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 501 " --> pdb=" O THR A 497 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 removed outlier: 4.355A pdb=" N GLU A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 605 through 612 Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.816A pdb=" N ALA A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 663 Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 739 through 750 removed outlier: 3.552A pdb=" N TYR A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 781 Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.743A pdb=" N HIS A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 866 through 881 Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 899 through 904 Processing helix chain 'A' and resid 911 through 918 Processing helix chain 'A' and resid 932 through 939 removed outlier: 4.238A pdb=" N VAL A 937 " --> pdb=" O LYS A 934 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 939 " --> pdb=" O LEU A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 959 through 962 No H-bonds generated for 'chain 'A' and resid 959 through 962' Processing helix chain 'A' and resid 991 through 996 removed outlier: 3.506A pdb=" N LYS A 994 " --> pdb=" O LYS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1026 removed outlier: 4.311A pdb=" N ILE A1008 " --> pdb=" O SER A1004 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A1009 " --> pdb=" O TYR A1005 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1010 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A1020 " --> pdb=" O PHE A1016 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET A1024 " --> pdb=" O THR A1020 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR A1025 " --> pdb=" O ALA A1021 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1049 Processing helix chain 'A' and resid 1057 through 1063 Processing helix chain 'A' and resid 1070 through 1073 No H-bonds generated for 'chain 'A' and resid 1070 through 1073' Processing helix chain 'A' and resid 1077 through 1085 removed outlier: 4.407A pdb=" N LYS A1085 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1113 removed outlier: 3.624A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1153 removed outlier: 4.053A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1186 Proline residue: A1166 - end of helix Proline residue: A1177 - end of helix Proline residue: A1184 - end of helix Processing helix chain 'A' and resid 1190 through 1192 No H-bonds generated for 'chain 'A' and resid 1190 through 1192' Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1205 through 1229 removed outlier: 4.386A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) Proline residue: A1213 - end of helix removed outlier: 5.073A pdb=" N ARG A1219 " --> pdb=" O PHE A1215 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1244 removed outlier: 3.864A pdb=" N GLU A1240 " --> pdb=" O HIS A1236 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 68 Proline residue: C 47 - end of helix Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 80 through 83 No H-bonds generated for 'chain 'C' and resid 80 through 83' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 192 through 195 No H-bonds generated for 'chain 'C' and resid 192 through 195' Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 331 through 356 removed outlier: 3.616A pdb=" N ILE C 348 " --> pdb=" O ALA C 344 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.970A pdb=" N LYS A 369 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY A 384 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 283 through 287 Processing sheet with id= C, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.960A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.652A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.529A pdb=" N TYR A 556 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE A 952 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE A 558 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS A 830 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N SER A 559 " --> pdb=" O LYS A 830 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP A 832 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 923 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN A 857 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A 896 " --> pdb=" O ASN A 857 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 637 through 639 Processing sheet with id= G, first strand: chain 'A' and resid 667 through 669 Processing sheet with id= H, first strand: chain 'A' and resid 571 through 577 removed outlier: 3.553A pdb=" N GLU A 571 " --> pdb=" O GLU A 810 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE A 577 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N ILE A 804 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 694 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.405A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 110 through 115 removed outlier: 4.423A pdb=" N LYS C 297 " --> pdb=" O ILE C 209 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1131 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: 4.14 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1860 1.31 - 1.44: 3218 1.44 - 1.57: 6637 1.57 - 1.70: 3 1.70 - 1.82: 77 Bond restraints: 11795 Sorted by residual: bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C35 2Y5 A1501 " pdb=" C36 2Y5 A1501 " ideal model delta sigma weight residual 1.568 1.527 0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C34 2Y5 A1501 " pdb=" C35 2Y5 A1501 " ideal model delta sigma weight residual 1.564 1.526 0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C1 BMA E 4 " pdb=" C2 BMA E 4 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C33 2Y5 A1501 " pdb=" C34 2Y5 A1501 " ideal model delta sigma weight residual 1.560 1.527 0.033 2.00e-02 2.50e+03 2.80e+00 ... (remaining 11790 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 301 107.13 - 113.85: 6749 113.85 - 120.58: 4677 120.58 - 127.30: 4144 127.30 - 134.02: 119 Bond angle restraints: 15990 Sorted by residual: angle pdb=" C21 2Y5 A1501 " pdb=" C22 2Y5 A1501 " pdb=" C23 2Y5 A1501 " ideal model delta sigma weight residual 85.82 120.51 -34.69 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C24 2Y5 A1501 " pdb=" C25 2Y5 A1501 " pdb=" C26 2Y5 A1501 " ideal model delta sigma weight residual 152.70 120.16 32.54 3.00e+00 1.11e-01 1.18e+02 angle pdb=" C18 2Y5 A1501 " pdb=" C19 2Y5 A1501 " pdb=" C20 2Y5 A1501 " ideal model delta sigma weight residual 152.65 120.63 32.02 3.00e+00 1.11e-01 1.14e+02 angle pdb=" C15 2Y5 A1501 " pdb=" C16 2Y5 A1501 " pdb=" C17 2Y5 A1501 " ideal model delta sigma weight residual 152.62 120.79 31.83 3.00e+00 1.11e-01 1.13e+02 angle pdb=" C17 2Y5 A1501 " pdb=" C18 2Y5 A1501 " pdb=" C19 2Y5 A1501 " ideal model delta sigma weight residual 112.15 120.66 -8.51 3.00e+00 1.11e-01 8.05e+00 ... (remaining 15985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.96: 7029 32.96 - 65.92: 83 65.92 - 98.88: 20 98.88 - 131.84: 12 131.84 - 164.79: 2 Dihedral angle restraints: 7146 sinusoidal: 2996 harmonic: 4150 Sorted by residual: dihedral pdb=" C24 2Y5 A1501 " pdb=" C25 2Y5 A1501 " pdb=" C26 2Y5 A1501 " pdb=" C27 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 329.24 164.45 164.79 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C1 2Y5 A1501 " pdb=" O1 2Y5 A1501 " pdb=" P1 2Y5 A1501 " pdb=" O13 2Y5 A1501 " ideal model delta sinusoidal sigma weight residual 64.28 -148.14 -147.58 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C1 NAG C 501 " pdb=" C5 NAG C 501 " pdb=" O5 NAG C 501 " pdb=" C4 NAG C 501 " ideal model delta sinusoidal sigma weight residual -64.11 51.54 -115.65 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 7143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1560 0.055 - 0.109: 243 0.109 - 0.164: 29 0.164 - 0.219: 1 0.219 - 0.274: 2 Chirality restraints: 1835 Sorted by residual: chirality pdb=" C5 BMA E 4 " pdb=" C4 BMA E 4 " pdb=" C6 BMA E 4 " pdb=" O5 BMA E 4 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 237 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.48e-01 ... (remaining 1832 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A1056 " -0.027 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO A1057 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1057 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1057 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 188 " -0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO C 189 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 189 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 189 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1183 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A1184 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1184 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A1184 " 0.020 5.00e-02 4.00e+02 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 102 2.60 - 3.17: 9830 3.17 - 3.75: 17049 3.75 - 4.32: 24346 4.32 - 4.90: 40169 Nonbonded interactions: 91496 Sorted by model distance: nonbonded pdb="MG MG A1502 " pdb=" O HOH A1603 " model vdw 2.021 2.170 nonbonded pdb="MG MG A1502 " pdb=" O HOH A1602 " model vdw 2.044 2.170 nonbonded pdb="MG MG A1502 " pdb=" O HOH A1601 " model vdw 2.057 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1502 " model vdw 2.083 2.170 nonbonded pdb=" OD2 ASP A 560 " pdb="MG MG A1502 " model vdw 2.114 2.170 ... (remaining 91491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.250 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: 4.200 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 36.460 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 : 0.003 0.079 11795 Z= 0.171 Angle : 0.727 34.689 15990 Z= 0.315 Chirality : 0.041 0.274 1835 Planarity : 0.003 0.040 1995 Dihedral : 13.288 164.795 4464 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.36 % Allowed : 5.03 % Favored : 93.62 % 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: -3.11 (0.19), residues: 1410 helix: -1.74 (0.19), residues: 594 sheet: -1.81 (0.31), residues: 219 loop : -2.37 (0.21), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1134 HIS 0.003 0.001 HIS A 580 PHE 0.014 0.001 PHE A1205 TYR 0.012 0.001 TYR C 141 ARG 0.003 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 HIS cc_start: 0.8237 (t-90) cc_final: 0.7835 (p90) REVERT: A 299 TRP cc_start: 0.6890 (m-10) cc_final: 0.6115 (m100) REVERT: A 647 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8156 (mmpt) REVERT: A 961 MET cc_start: 0.7757 (ttm) cc_final: 0.7556 (ttt) REVERT: A 1042 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: A 1212 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6175 (mp) outliers start: 17 outliers final: 3 residues processed: 152 average time/residue: 0.9859 time to fit residues: 165.8999 Evaluate side-chains 93 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 3.9990 chunk 106 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 110 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 280 ASN A 338 ASN A 883 HIS A 888 HIS C 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11795 Z= 0.151 Angle : 0.548 12.888 15990 Z= 0.263 Chirality : 0.042 0.181 1835 Planarity : 0.004 0.059 1995 Dihedral : 12.973 152.504 1765 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.39 % Allowed : 10.85 % Favored : 86.75 % 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: -2.17 (0.21), residues: 1410 helix: -0.79 (0.21), residues: 590 sheet: -1.45 (0.31), residues: 221 loop : -2.01 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1056 HIS 0.008 0.001 HIS A 883 PHE 0.021 0.001 PHE A1109 TYR 0.016 0.001 TYR C 147 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 HIS cc_start: 0.7908 (t-90) cc_final: 0.7629 (p90) REVERT: A 280 ASN cc_start: 0.5383 (OUTLIER) cc_final: 0.4944 (t0) REVERT: A 299 TRP cc_start: 0.6957 (m-10) cc_final: 0.6040 (m100) REVERT: A 359 ASP cc_start: 0.7260 (t0) cc_final: 0.6710 (t0) REVERT: A 1241 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6582 (ttm) outliers start: 30 outliers final: 15 residues processed: 106 average time/residue: 0.9890 time to fit residues: 116.9056 Evaluate side-chains 97 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 106 optimal weight: 0.0970 chunk 87 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 138 optimal weight: 0.9990 chunk 114 optimal weight: 0.0040 chunk 127 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS A 888 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11795 Z= 0.132 Angle : 0.530 12.941 15990 Z= 0.253 Chirality : 0.041 0.194 1835 Planarity : 0.003 0.061 1995 Dihedral : 11.538 153.145 1759 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.08 % Allowed : 11.81 % Favored : 86.11 % 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: -1.64 (0.22), residues: 1410 helix: -0.37 (0.22), residues: 588 sheet: -1.17 (0.32), residues: 219 loop : -1.69 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1028 HIS 0.006 0.001 HIS A 888 PHE 0.020 0.001 PHE A 669 TYR 0.019 0.001 TYR C 147 ARG 0.001 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 HIS cc_start: 0.7930 (t-90) cc_final: 0.7660 (p-80) REVERT: A 299 TRP cc_start: 0.7011 (m-10) cc_final: 0.6122 (m100) REVERT: A 359 ASP cc_start: 0.7267 (t0) cc_final: 0.6688 (t0) outliers start: 26 outliers final: 14 residues processed: 97 average time/residue: 0.9047 time to fit residues: 98.9523 Evaluate side-chains 90 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 50.0000 chunk 86 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 883 HIS A 888 HIS C 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11795 Z= 0.201 Angle : 0.567 12.894 15990 Z= 0.273 Chirality : 0.043 0.236 1835 Planarity : 0.004 0.060 1995 Dihedral : 10.863 154.006 1759 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.55 % Allowed : 12.37 % Favored : 85.08 % 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: -1.54 (0.22), residues: 1410 helix: -0.38 (0.22), residues: 588 sheet: -1.00 (0.33), residues: 213 loop : -1.58 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1028 HIS 0.010 0.001 HIS A 883 PHE 0.017 0.002 PHE A1205 TYR 0.025 0.001 TYR C 147 ARG 0.002 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 299 TRP cc_start: 0.7122 (m-10) cc_final: 0.6523 (m-10) REVERT: A 359 ASP cc_start: 0.7397 (t0) cc_final: 0.6806 (t0) outliers start: 32 outliers final: 18 residues processed: 95 average time/residue: 0.9754 time to fit residues: 103.7692 Evaluate side-chains 92 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 69 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS A 888 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11795 Z= 0.265 Angle : 0.620 12.963 15990 Z= 0.301 Chirality : 0.045 0.240 1835 Planarity : 0.004 0.057 1995 Dihedral : 10.562 155.132 1759 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.19 % Allowed : 12.85 % Favored : 83.96 % 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: -1.56 (0.22), residues: 1410 helix: -0.50 (0.22), residues: 582 sheet: -0.86 (0.33), residues: 214 loop : -1.53 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1206 HIS 0.010 0.001 HIS A 883 PHE 0.018 0.002 PHE A1205 TYR 0.028 0.002 TYR C 147 ARG 0.005 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 73 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 205 THR cc_start: 0.7182 (p) cc_final: 0.6954 (p) REVERT: A 299 TRP cc_start: 0.6943 (m-10) cc_final: 0.6320 (m100) REVERT: A 359 ASP cc_start: 0.7367 (t0) cc_final: 0.6776 (t0) outliers start: 40 outliers final: 23 residues processed: 103 average time/residue: 1.0468 time to fit residues: 120.0795 Evaluate side-chains 94 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.9990 chunk 122 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS A 888 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11795 Z= 0.146 Angle : 0.560 12.806 15990 Z= 0.267 Chirality : 0.042 0.192 1835 Planarity : 0.003 0.051 1995 Dihedral : 9.808 155.683 1759 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.47 % Allowed : 14.21 % Favored : 83.32 % 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: -1.20 (0.22), residues: 1410 helix: -0.14 (0.23), residues: 584 sheet: -0.76 (0.32), residues: 212 loop : -1.37 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1028 HIS 0.012 0.001 HIS A 883 PHE 0.012 0.001 PHE A1205 TYR 0.017 0.001 TYR C 147 ARG 0.004 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 75 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 THR cc_start: 0.6977 (p) cc_final: 0.6697 (p) REVERT: A 299 TRP cc_start: 0.7012 (m-10) cc_final: 0.6399 (m100) REVERT: A 359 ASP cc_start: 0.7392 (t0) cc_final: 0.6812 (t0) REVERT: A 464 ILE cc_start: 0.6071 (OUTLIER) cc_final: 0.5453 (mp) outliers start: 31 outliers final: 20 residues processed: 97 average time/residue: 0.8991 time to fit residues: 98.1284 Evaluate side-chains 91 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1113 ILE Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 54 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 HIS A 888 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11795 Z= 0.248 Angle : 0.607 12.959 15990 Z= 0.294 Chirality : 0.044 0.184 1835 Planarity : 0.004 0.045 1995 Dihedral : 9.629 155.507 1759 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.03 % Allowed : 14.05 % Favored : 82.92 % 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: -1.32 (0.22), residues: 1410 helix: -0.31 (0.22), residues: 583 sheet: -0.64 (0.33), residues: 212 loop : -1.42 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1206 HIS 0.012 0.001 HIS A 883 PHE 0.020 0.002 PHE A1205 TYR 0.024 0.001 TYR C 147 ARG 0.004 0.000 ARG A1228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 71 time to evaluate : 1.397 Fit side-chains revert: symmetry clash REVERT: A 205 THR cc_start: 0.6976 (p) cc_final: 0.6681 (p) REVERT: A 299 TRP cc_start: 0.7087 (m-10) cc_final: 0.6472 (m100) REVERT: A 359 ASP cc_start: 0.7401 (t0) cc_final: 0.6805 (t0) REVERT: A 464 ILE cc_start: 0.6151 (OUTLIER) cc_final: 0.5621 (mp) REVERT: A 1042 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: C 61 ILE cc_start: 0.6520 (OUTLIER) cc_final: 0.6161 (mt) outliers start: 38 outliers final: 20 residues processed: 99 average time/residue: 0.8959 time to fit residues: 100.3303 Evaluate side-chains 92 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1042 GLU Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11795 Z= 0.148 Angle : 0.551 12.795 15990 Z= 0.264 Chirality : 0.042 0.189 1835 Planarity : 0.003 0.044 1995 Dihedral : 9.102 155.734 1759 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.31 % Allowed : 15.24 % Favored : 82.44 % 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: -1.03 (0.22), residues: 1410 helix: -0.01 (0.23), residues: 584 sheet: -0.68 (0.32), residues: 216 loop : -1.25 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1028 HIS 0.003 0.001 HIS A 888 PHE 0.013 0.001 PHE A1205 TYR 0.015 0.001 TYR C 147 ARG 0.003 0.000 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 75 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 205 THR cc_start: 0.6603 (p) cc_final: 0.6286 (p) REVERT: A 299 TRP cc_start: 0.7049 (m-10) cc_final: 0.6456 (m100) REVERT: A 359 ASP cc_start: 0.7401 (t0) cc_final: 0.6794 (t0) REVERT: A 366 MET cc_start: 0.3476 (tpp) cc_final: 0.0401 (mtm) REVERT: A 464 ILE cc_start: 0.6096 (OUTLIER) cc_final: 0.5522 (mp) REVERT: A 1192 TYR cc_start: 0.7493 (m-80) cc_final: 0.7039 (m-80) REVERT: C 135 LYS cc_start: 0.8259 (mmmt) cc_final: 0.8038 (mmmt) outliers start: 29 outliers final: 19 residues processed: 99 average time/residue: 0.9021 time to fit residues: 101.0637 Evaluate side-chains 91 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.0040 chunk 99 optimal weight: 0.7980 chunk 38 optimal weight: 0.0470 chunk 114 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.5090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11795 Z= 0.142 Angle : 0.547 12.831 15990 Z= 0.261 Chirality : 0.041 0.193 1835 Planarity : 0.003 0.045 1995 Dihedral : 8.466 154.739 1756 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.52 % Allowed : 15.80 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1410 helix: 0.24 (0.23), residues: 575 sheet: -0.57 (0.32), residues: 221 loop : -1.12 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1028 HIS 0.003 0.001 HIS A 634 PHE 0.013 0.001 PHE A1205 TYR 0.013 0.001 TYR C 147 ARG 0.004 0.000 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 1.321 Fit side-chains revert: symmetry clash REVERT: A 299 TRP cc_start: 0.6950 (m-10) cc_final: 0.6358 (m100) REVERT: A 359 ASP cc_start: 0.7422 (t0) cc_final: 0.6814 (t0) REVERT: A 366 MET cc_start: 0.3507 (tpp) cc_final: 0.0352 (mtm) REVERT: A 464 ILE cc_start: 0.6091 (OUTLIER) cc_final: 0.5552 (mp) REVERT: A 863 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7155 (mt-10) REVERT: C 135 LYS cc_start: 0.8255 (mmmt) cc_final: 0.8037 (mmmt) outliers start: 19 outliers final: 15 residues processed: 92 average time/residue: 0.9558 time to fit residues: 99.0524 Evaluate side-chains 87 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 0.0670 chunk 93 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 11 optimal weight: 20.0000 chunk 86 optimal weight: 0.0370 chunk 68 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN A 888 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11795 Z= 0.242 Angle : 0.620 12.944 15990 Z= 0.301 Chirality : 0.044 0.174 1835 Planarity : 0.004 0.041 1995 Dihedral : 8.590 154.499 1753 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.76 % Allowed : 15.88 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1410 helix: -0.18 (0.22), residues: 588 sheet: -0.47 (0.32), residues: 221 loop : -1.36 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1056 HIS 0.005 0.001 HIS A 202 PHE 0.020 0.002 PHE A1205 TYR 0.023 0.001 TYR C 147 ARG 0.005 0.000 ARG A1228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 71 time to evaluate : 1.425 Fit side-chains REVERT: A 299 TRP cc_start: 0.7021 (m-10) cc_final: 0.6409 (m100) REVERT: A 359 ASP cc_start: 0.7442 (t0) cc_final: 0.6828 (t0) REVERT: A 464 ILE cc_start: 0.6043 (OUTLIER) cc_final: 0.5475 (mp) outliers start: 22 outliers final: 14 residues processed: 86 average time/residue: 0.8793 time to fit residues: 86.0181 Evaluate side-chains 83 residues out of total 1253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 1040 ILE Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 365 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 46 optimal weight: 30.0000 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.175076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.108248 restraints weight = 14544.355| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.68 r_work: 0.3570 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11795 Z= 0.164 Angle : 0.575 12.802 15990 Z= 0.276 Chirality : 0.042 0.184 1835 Planarity : 0.003 0.041 1995 Dihedral : 8.299 154.520 1753 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.68 % Allowed : 15.96 % Favored : 82.36 % 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: -1.00 (0.22), residues: 1410 helix: -0.01 (0.23), residues: 587 sheet: -0.52 (0.32), residues: 224 loop : -1.29 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1134 HIS 0.003 0.001 HIS A 888 PHE 0.015 0.001 PHE A1205 TYR 0.016 0.001 TYR C 147 ARG 0.005 0.000 ARG C 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.56 seconds wall clock time: 64 minutes 43.30 seconds (3883.30 seconds total)