Starting phenix.real_space_refine on Wed Mar 4 20:38:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4u_24178/03_2026/7n4u_24178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4u_24178/03_2026/7n4u_24178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n4u_24178/03_2026/7n4u_24178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4u_24178/03_2026/7n4u_24178.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4u_24178/03_2026/7n4u_24178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4u_24178/03_2026/7n4u_24178.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 90 5.16 5 C 10068 2.51 5 N 2434 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15396 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7426 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "B" Number of atoms: 7426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7426 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" 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: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 188 Unusual residues: {'CLR': 2, 'NAG': 4, 'POV': 1, 'VIV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 188 Unusual residues: {'CLR': 2, 'NAG': 4, 'POV': 1, 'VIV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.74, per 1000 atoms: 0.24 Number of scatterers: 15396 At special positions: 0 Unit cell: (134.113, 89.131, 136.612, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 2 15.00 O 2802 8.00 N 2434 7.00 C 10068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1024 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B 966 " - pdb=" SG CYS B1024 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 993 " distance=2.03 Simple disulfide: pdb=" SG CYS B 980 " - pdb=" SG CYS B 989 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM15032 O5 NAG A1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM15265 O5 NAG B1602 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1401 " - " ASN A 431 " " NAG A1402 " - " ASN A 464 " " NAG A1403 " - " ASN A1075 " " NAG A1404 " - " ASN A 506 " " NAG B1602 " - " ASN B 431 " " NAG B1603 " - " ASN B 464 " " NAG B1604 " - " ASN B1075 " " NAG B1605 " - " ASN B 506 " " NAG C 1 " - " ASN A 497 " " NAG D 1 " - " ASN A 909 " " NAG E 1 " - " ASN A1037 " " NAG F 1 " - " ASN B 497 " " NAG G 1 " - " ASN B 909 " " NAG H 1 " - " ASN B1037 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 688.4 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 14 sheets defined 62.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.552A pdb=" N ILE A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.642A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 4.012A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.742A pdb=" N ALA A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 555' Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 583 through 607 removed outlier: 4.039A pdb=" N ALA A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.721A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 4.066A pdb=" N GLU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.635A pdb=" N PHE A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 652 removed outlier: 4.019A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 690 Processing helix chain 'A' and resid 695 through 710 removed outlier: 3.602A pdb=" N LEU A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Proline residue: A 703 - end of helix removed outlier: 3.612A pdb=" N LEU A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 724 Processing helix chain 'A' and resid 731 through 762 Proline residue: A 745 - end of helix Processing helix chain 'A' and resid 766 through 804 removed outlier: 3.751A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'A' and resid 842 through 864 removed outlier: 4.419A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 882 through 894 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.758A pdb=" N MET A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 938 Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 986 through 990 removed outlier: 4.184A pdb=" N CYS A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1017 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.552A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1106 Processing helix chain 'A' and resid 1107 through 1131 removed outlier: 4.015A pdb=" N GLU A1111 " --> pdb=" O THR A1107 " (cutoff:3.500A) Proline residue: A1122 - end of helix removed outlier: 3.720A pdb=" N LEU A1129 " --> pdb=" O ALA A1125 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A1131 " --> pdb=" O SER A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1160 Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1178 through 1191 removed outlier: 5.076A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1226 removed outlier: 3.967A pdb=" N SER A1210 " --> pdb=" O ILE A1206 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A1211 " --> pdb=" O SER A1207 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix removed outlier: 3.880A pdb=" N VAL A1226 " --> pdb=" O PRO A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1230 Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1239 through 1266 removed outlier: 5.318A pdb=" N LEU A1258 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1270 through 1274 removed outlier: 3.511A pdb=" N LEU A1273 " --> pdb=" O ASN A1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 349 Processing helix chain 'B' and resid 351 through 368 removed outlier: 3.554A pdb=" N ILE B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Proline residue: B 362 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 388 through 402 Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.643A pdb=" N LEU B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 517 through 528 removed outlier: 4.013A pdb=" N HIS B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.743A pdb=" N ALA B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 555' Processing helix chain 'B' and resid 563 through 567 Processing helix chain 'B' and resid 583 through 607 removed outlier: 4.039A pdb=" N ALA B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.721A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 removed outlier: 4.066A pdb=" N GLU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.638A pdb=" N PHE B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 652 removed outlier: 4.019A pdb=" N ILE B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 665 through 690 Processing helix chain 'B' and resid 695 through 710 removed outlier: 3.602A pdb=" N LEU B 699 " --> pdb=" O SER B 695 " (cutoff:3.500A) Proline residue: B 703 - end of helix removed outlier: 3.611A pdb=" N LEU B 707 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 Processing helix chain 'B' and resid 731 through 762 Proline residue: B 745 - end of helix Processing helix chain 'B' and resid 766 through 804 removed outlier: 3.749A pdb=" N SER B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 792 " --> pdb=" O MET B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 835 Processing helix chain 'B' and resid 835 through 841 Processing helix chain 'B' and resid 842 through 864 removed outlier: 4.420A pdb=" N GLY B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 882 through 894 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.757A pdb=" N MET B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 938 Processing helix chain 'B' and resid 952 through 961 Processing helix chain 'B' and resid 986 through 990 removed outlier: 4.185A pdb=" N CYS B 989 " --> pdb=" O SER B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1017 Proline residue: B1013 - end of helix Processing helix chain 'B' and resid 1058 through 1081 removed outlier: 3.553A pdb=" N ASP B1079 " --> pdb=" O ASN B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1106 Processing helix chain 'B' and resid 1107 through 1131 removed outlier: 4.012A pdb=" N GLU B1111 " --> pdb=" O THR B1107 " (cutoff:3.500A) Proline residue: B1122 - end of helix removed outlier: 3.718A pdb=" N LEU B1129 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B1131 " --> pdb=" O SER B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1160 Processing helix chain 'B' and resid 1164 through 1178 Processing helix chain 'B' and resid 1178 through 1191 removed outlier: 5.076A pdb=" N HIS B1184 " --> pdb=" O GLU B1180 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1196 through 1226 removed outlier: 3.968A pdb=" N SER B1210 " --> pdb=" O ILE B1206 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B1211 " --> pdb=" O SER B1207 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET B1218 " --> pdb=" O ALA B1214 " (cutoff:3.500A) Proline residue: B1222 - end of helix removed outlier: 3.878A pdb=" N VAL B1226 " --> pdb=" O PRO B1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 1227 through 1230 Processing helix chain 'B' and resid 1232 through 1239 Processing helix chain 'B' and resid 1239 through 1266 removed outlier: 5.323A pdb=" N LEU B1258 " --> pdb=" O GLY B1254 " (cutoff:3.500A) Proline residue: B1259 - end of helix Processing helix chain 'B' and resid 1270 through 1274 removed outlier: 3.512A pdb=" N LEU B1273 " --> pdb=" O ASN B1270 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 423 Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 509 Processing sheet with id=AA5, first strand: chain 'A' and resid 948 through 951 removed outlier: 5.155A pdb=" N TYR A1052 " --> pdb=" O PRO A 949 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET A1050 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 979 through 980 removed outlier: 4.144A pdb=" N ARG A 968 " --> pdb=" O CYS A 980 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 991 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.762A pdb=" N THR A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 487 through 489 Processing sheet with id=AA9, first strand: chain 'B' and resid 487 through 489 Processing sheet with id=AB1, first strand: chain 'B' and resid 419 through 423 Processing sheet with id=AB2, first strand: chain 'B' and resid 505 through 509 Processing sheet with id=AB3, first strand: chain 'B' and resid 948 through 951 removed outlier: 5.154A pdb=" N TYR B1052 " --> pdb=" O PRO B 949 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET B1050 " --> pdb=" O SER B 951 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 979 through 980 removed outlier: 4.144A pdb=" N ARG B 968 " --> pdb=" O CYS B 980 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 991 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.762A pdb=" N THR B1046 " --> pdb=" O ASN B1037 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2337 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: 2.93 Time building geometry restraints manager: 1.99 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: 2384 1.31 - 1.44: 4270 1.44 - 1.57: 8980 1.57 - 1.69: 4 1.69 - 1.82: 138 Bond restraints: 15776 Sorted by residual: bond pdb=" C4 VIV B1608 " pdb=" O1 VIV B1608 " ideal model delta sigma weight residual 1.358 1.463 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C4 VIV A1407 " pdb=" O1 VIV A1407 " ideal model delta sigma weight residual 1.358 1.463 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" N VAL A 662 " pdb=" CA VAL A 662 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.09e+01 bond pdb=" N VAL B 662 " pdb=" CA VAL B 662 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.07e+01 bond pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.69e+01 ... (remaining 15771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 17246 2.36 - 4.72: 4015 4.72 - 7.09: 217 7.09 - 9.45: 16 9.45 - 11.81: 6 Bond angle restraints: 21500 Sorted by residual: angle pdb=" C GLY B 671 " pdb=" N GLY B 672 " pdb=" CA GLY B 672 " ideal model delta sigma weight residual 119.94 125.32 -5.38 1.11e+00 8.12e-01 2.35e+01 angle pdb=" C GLY A 671 " pdb=" N GLY A 672 " pdb=" CA GLY A 672 " ideal model delta sigma weight residual 119.94 125.30 -5.36 1.11e+00 8.12e-01 2.33e+01 angle pdb=" C GLN A 342 " pdb=" N GLY A 343 " pdb=" CA GLY A 343 " ideal model delta sigma weight residual 119.94 125.09 -5.15 1.11e+00 8.12e-01 2.16e+01 angle pdb=" C GLN B 342 " pdb=" N GLY B 343 " pdb=" CA GLY B 343 " ideal model delta sigma weight residual 119.94 125.08 -5.14 1.11e+00 8.12e-01 2.15e+01 angle pdb=" C ALA A 914 " pdb=" N GLY A 915 " pdb=" CA GLY A 915 " ideal model delta sigma weight residual 119.94 125.04 -5.10 1.11e+00 8.12e-01 2.11e+01 ... (remaining 21495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 9440 31.97 - 63.95: 334 63.95 - 95.92: 54 95.92 - 127.89: 22 127.89 - 159.87: 2 Dihedral angle restraints: 9852 sinusoidal: 4300 harmonic: 5552 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.81 -66.81 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" SG CYS B 542 " pdb=" CB CYS B 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.76 -66.76 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS B 966 " pdb=" SG CYS B 966 " pdb=" SG CYS B1024 " pdb=" CB CYS B1024 " ideal model delta sinusoidal sigma weight residual 93.00 143.82 -50.82 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 2526 0.948 - 1.896: 2 1.896 - 2.844: 2 2.844 - 3.792: 2 3.792 - 4.740: 8 Chirality restraints: 2540 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 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 2.27 -4.67 2.00e-02 2.50e+03 5.45e+04 ... (remaining 2537 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG D 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.147 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG G 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1602 " 0.218 2.00e-02 2.50e+03 1.86e-01 4.31e+02 pdb=" C7 NAG B1602 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B1602 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG B1602 " -0.304 2.00e-02 2.50e+03 pdb=" O7 NAG B1602 " 0.169 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 188 2.66 - 3.22: 13837 3.22 - 3.78: 23853 3.78 - 4.34: 30309 4.34 - 4.90: 53852 Nonbonded interactions: 122039 Sorted by model distance: nonbonded pdb=" O VAL B 660 " pdb=" OD2 ASP B 808 " model vdw 2.102 3.040 nonbonded pdb=" O VAL A 660 " pdb=" OD2 ASP A 808 " model vdw 2.103 3.040 nonbonded pdb=" O VAL B 380 " pdb=" OG SER B 384 " model vdw 2.273 3.040 nonbonded pdb=" O VAL A 380 " pdb=" OG SER A 384 " model vdw 2.274 3.040 nonbonded pdb=" O MET A 661 " pdb=" N ASP A 808 " model vdw 2.360 3.120 ... (remaining 122034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 333 through 1285 or resid 1402 through 1404 or resid 1406) \ ) selection = (chain 'B' and (resid 333 through 1285 or resid 1602 through 1604 or resid 1606) \ ) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.990 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.363 15808 Z= 1.105 Angle : 1.877 29.589 21584 Z= 1.339 Chirality : 0.294 4.740 2540 Planarity : 0.011 0.303 2650 Dihedral : 17.763 159.868 6236 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 1.79 % Allowed : 7.52 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.17), residues: 1902 helix: -1.48 (0.13), residues: 1062 sheet: -2.56 (0.40), residues: 126 loop : -1.97 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1070 TYR 0.033 0.003 TYR B1062 PHE 0.040 0.002 PHE A 791 TRP 0.014 0.002 TRP B 518 HIS 0.005 0.002 HIS B 521 Details of bonding type rmsd covalent geometry : bond 0.01419 (15776) covalent geometry : angle 1.79505 (21500) SS BOND : bond 0.00247 ( 12) SS BOND : angle 1.34494 ( 24) hydrogen bonds : bond 0.15854 ( 807) hydrogen bonds : angle 6.52210 ( 2337) link_BETA1-4 : bond 0.00220 ( 6) link_BETA1-4 : angle 1.14893 ( 18) link_NAG-ASN : bond 0.16311 ( 14) link_NAG-ASN : angle 12.61341 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ASN cc_start: 0.8461 (t0) cc_final: 0.7944 (t0) REVERT: A 524 TYR cc_start: 0.7666 (t80) cc_final: 0.7206 (t80) REVERT: A 566 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7456 (mp0) REVERT: A 818 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7997 (tp) REVERT: A 994 MET cc_start: 0.7523 (ptp) cc_final: 0.7119 (ppp) REVERT: A 998 MET cc_start: 0.7203 (pmm) cc_final: 0.6584 (pmm) REVERT: A 1102 TYR cc_start: 0.8478 (m-10) cc_final: 0.8015 (m-10) REVERT: A 1103 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: A 1198 LEU cc_start: 0.7637 (mt) cc_final: 0.7296 (tt) REVERT: A 1242 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6458 (tt) REVERT: B 476 ASN cc_start: 0.8353 (t0) cc_final: 0.7817 (t0) REVERT: B 524 TYR cc_start: 0.7651 (t80) cc_final: 0.7172 (t80) REVERT: B 566 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7430 (mp0) REVERT: B 818 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8184 (tp) REVERT: B 994 MET cc_start: 0.7248 (ptp) cc_final: 0.6880 (ppp) REVERT: B 998 MET cc_start: 0.7291 (pmm) cc_final: 0.6676 (pmm) REVERT: B 1102 TYR cc_start: 0.8475 (m-10) cc_final: 0.7981 (m-10) REVERT: B 1198 LEU cc_start: 0.7681 (mt) cc_final: 0.7426 (tt) outliers start: 29 outliers final: 11 residues processed: 206 average time/residue: 0.1156 time to fit residues: 36.9686 Evaluate side-chains 135 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 1103 GLU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 872 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 409 GLN A 527 ASN A1184 HIS A1233 GLN A1253 HIS B 339 GLN B 409 GLN B 527 ASN B1184 HIS B1220 ASN B1233 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.089429 restraints weight = 24693.877| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.86 r_work: 0.3075 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15808 Z= 0.143 Angle : 0.801 23.267 21584 Z= 0.349 Chirality : 0.055 1.054 2540 Planarity : 0.004 0.039 2650 Dihedral : 13.561 133.893 2887 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.58 % Favored : 97.32 % Rotamer: Outliers : 3.51 % Allowed : 10.79 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1902 helix: 0.76 (0.16), residues: 1052 sheet: -2.00 (0.42), residues: 126 loop : -1.35 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 498 TYR 0.015 0.001 TYR A 836 PHE 0.015 0.001 PHE A 704 TRP 0.010 0.001 TRP A 518 HIS 0.005 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00307 (15776) covalent geometry : angle 0.72313 (21500) SS BOND : bond 0.00291 ( 12) SS BOND : angle 1.12898 ( 24) hydrogen bonds : bond 0.04318 ( 807) hydrogen bonds : angle 4.56185 ( 2337) link_BETA1-4 : bond 0.02126 ( 6) link_BETA1-4 : angle 4.58873 ( 18) link_NAG-ASN : bond 0.00596 ( 14) link_NAG-ASN : angle 7.23950 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 0.566 Fit side-chains REVERT: A 398 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: A 476 ASN cc_start: 0.8576 (t0) cc_final: 0.8188 (t0) REVERT: A 524 TYR cc_start: 0.7919 (t80) cc_final: 0.7616 (t80) REVERT: A 566 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7850 (mp0) REVERT: A 607 MET cc_start: 0.8310 (mmm) cc_final: 0.7284 (mmm) REVERT: A 818 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8112 (tp) REVERT: A 994 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7137 (ppp) REVERT: A 998 MET cc_start: 0.7024 (pmm) cc_final: 0.6335 (pmm) REVERT: A 1023 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8385 (mttp) REVERT: A 1102 TYR cc_start: 0.8656 (m-10) cc_final: 0.8286 (m-10) REVERT: A 1198 LEU cc_start: 0.8484 (mt) cc_final: 0.8143 (tt) REVERT: A 1261 ILE cc_start: 0.8455 (tt) cc_final: 0.8179 (tt) REVERT: B 476 ASN cc_start: 0.8444 (t0) cc_final: 0.8016 (t0) REVERT: B 524 TYR cc_start: 0.7969 (t80) cc_final: 0.7676 (t80) REVERT: B 566 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7888 (mp0) REVERT: B 1023 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8468 (mttp) REVERT: B 1102 TYR cc_start: 0.8642 (m-10) cc_final: 0.8247 (m-10) REVERT: B 1103 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: B 1198 LEU cc_start: 0.8486 (mt) cc_final: 0.8253 (tt) outliers start: 57 outliers final: 23 residues processed: 187 average time/residue: 0.1055 time to fit residues: 32.0798 Evaluate side-chains 140 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1103 GLU Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 92 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1220 ASN B1253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087461 restraints weight = 25223.850| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.04 r_work: 0.3039 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15808 Z= 0.124 Angle : 0.673 18.706 21584 Z= 0.303 Chirality : 0.046 0.812 2540 Planarity : 0.003 0.032 2650 Dihedral : 10.773 115.569 2875 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.42 % Favored : 96.48 % Rotamer: Outliers : 3.27 % Allowed : 12.58 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1902 helix: 1.22 (0.16), residues: 1056 sheet: -1.90 (0.47), residues: 102 loop : -1.06 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 406 TYR 0.014 0.001 TYR B 646 PHE 0.015 0.001 PHE A 930 TRP 0.011 0.001 TRP A 518 HIS 0.005 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00275 (15776) covalent geometry : angle 0.62369 (21500) SS BOND : bond 0.00284 ( 12) SS BOND : angle 0.96822 ( 24) hydrogen bonds : bond 0.03839 ( 807) hydrogen bonds : angle 4.32038 ( 2337) link_BETA1-4 : bond 0.01154 ( 6) link_BETA1-4 : angle 3.02407 ( 18) link_NAG-ASN : bond 0.00724 ( 14) link_NAG-ASN : angle 5.39649 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 126 time to evaluate : 0.581 Fit side-chains REVERT: A 398 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: A 476 ASN cc_start: 0.8567 (t0) cc_final: 0.8138 (t0) REVERT: A 524 TYR cc_start: 0.7814 (t80) cc_final: 0.7464 (t80) REVERT: A 566 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7743 (mp0) REVERT: A 607 MET cc_start: 0.8198 (mmm) cc_final: 0.7370 (mmm) REVERT: A 818 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8334 (tp) REVERT: A 836 TYR cc_start: 0.8011 (t80) cc_final: 0.7690 (t80) REVERT: A 994 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7236 (ppp) REVERT: A 998 MET cc_start: 0.7227 (pmm) cc_final: 0.6545 (pmm) REVERT: A 1023 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8430 (mttp) REVERT: A 1050 MET cc_start: 0.8359 (ttt) cc_final: 0.7491 (ttt) REVERT: A 1102 TYR cc_start: 0.8686 (m-10) cc_final: 0.8261 (m-10) REVERT: A 1128 CYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8421 (m) REVERT: A 1198 LEU cc_start: 0.8352 (mt) cc_final: 0.7967 (tt) REVERT: A 1261 ILE cc_start: 0.8208 (tt) cc_final: 0.7982 (tp) REVERT: B 476 ASN cc_start: 0.8468 (t0) cc_final: 0.7987 (t0) REVERT: B 524 TYR cc_start: 0.7855 (t80) cc_final: 0.7434 (t80) REVERT: B 566 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7804 (mp0) REVERT: B 607 MET cc_start: 0.8179 (mmm) cc_final: 0.7268 (mmm) REVERT: B 836 TYR cc_start: 0.7964 (t80) cc_final: 0.7573 (t80) REVERT: B 994 MET cc_start: 0.7683 (ppp) cc_final: 0.7052 (ppp) REVERT: B 1023 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8497 (mttp) REVERT: B 1050 MET cc_start: 0.8378 (ttt) cc_final: 0.7486 (ttt) REVERT: B 1102 TYR cc_start: 0.8675 (m-10) cc_final: 0.8222 (m-10) REVERT: B 1128 CYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8434 (m) REVERT: B 1198 LEU cc_start: 0.8308 (mt) cc_final: 0.8032 (tt) outliers start: 53 outliers final: 37 residues processed: 164 average time/residue: 0.1025 time to fit residues: 27.8731 Evaluate side-chains 157 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 7 optimal weight: 0.0570 chunk 5 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 chunk 189 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.115343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.084671 restraints weight = 26464.673| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.06 r_work: 0.3089 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15808 Z= 0.136 Angle : 0.634 16.512 21584 Z= 0.289 Chirality : 0.044 0.681 2540 Planarity : 0.003 0.028 2650 Dihedral : 10.061 106.110 2872 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.10 % Favored : 96.79 % Rotamer: Outliers : 3.64 % Allowed : 12.95 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1902 helix: 1.20 (0.16), residues: 1064 sheet: -1.87 (0.48), residues: 102 loop : -0.87 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1002 TYR 0.013 0.001 TYR B 646 PHE 0.015 0.001 PHE A 839 TRP 0.009 0.001 TRP A 592 HIS 0.004 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00315 (15776) covalent geometry : angle 0.59328 (21500) SS BOND : bond 0.00335 ( 12) SS BOND : angle 0.98161 ( 24) hydrogen bonds : bond 0.03761 ( 807) hydrogen bonds : angle 4.25703 ( 2337) link_BETA1-4 : bond 0.01300 ( 6) link_BETA1-4 : angle 3.36558 ( 18) link_NAG-ASN : bond 0.00458 ( 14) link_NAG-ASN : angle 4.60609 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 118 time to evaluate : 0.600 Fit side-chains REVERT: A 398 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7680 (m-30) REVERT: A 476 ASN cc_start: 0.8564 (t0) cc_final: 0.8204 (t0) REVERT: A 524 TYR cc_start: 0.8027 (t80) cc_final: 0.7677 (t80) REVERT: A 566 GLU cc_start: 0.8651 (mt-10) cc_final: 0.7860 (mp0) REVERT: A 607 MET cc_start: 0.8232 (mmm) cc_final: 0.7255 (mmm) REVERT: A 818 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8316 (tp) REVERT: A 836 TYR cc_start: 0.8201 (t80) cc_final: 0.7953 (t80) REVERT: A 998 MET cc_start: 0.7113 (pmm) cc_final: 0.6517 (pmm) REVERT: A 1023 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8396 (mttp) REVERT: A 1102 TYR cc_start: 0.8846 (m-10) cc_final: 0.8602 (m-10) REVERT: A 1128 CYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8624 (m) REVERT: A 1198 LEU cc_start: 0.8504 (mt) cc_final: 0.8182 (tt) REVERT: A 1261 ILE cc_start: 0.8426 (tt) cc_final: 0.8176 (tp) REVERT: B 476 ASN cc_start: 0.8478 (t0) cc_final: 0.8072 (t0) REVERT: B 524 TYR cc_start: 0.8052 (t80) cc_final: 0.7733 (t80) REVERT: B 566 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7949 (mp0) REVERT: B 607 MET cc_start: 0.8175 (mmm) cc_final: 0.7734 (mmm) REVERT: B 836 TYR cc_start: 0.8232 (t80) cc_final: 0.7929 (t80) REVERT: B 894 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: B 994 MET cc_start: 0.7714 (ppp) cc_final: 0.7209 (ppp) REVERT: B 1023 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8489 (mttp) REVERT: B 1102 TYR cc_start: 0.8801 (m-10) cc_final: 0.8487 (m-10) REVERT: B 1103 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8239 (pt0) REVERT: B 1128 CYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8633 (m) REVERT: B 1198 LEU cc_start: 0.8483 (mt) cc_final: 0.8229 (tt) outliers start: 59 outliers final: 34 residues processed: 162 average time/residue: 0.1075 time to fit residues: 28.1520 Evaluate side-chains 155 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1022 ILE Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1103 GLU Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 128 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.114838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.084277 restraints weight = 26416.679| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.04 r_work: 0.3082 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15808 Z= 0.143 Angle : 0.630 15.426 21584 Z= 0.286 Chirality : 0.043 0.619 2540 Planarity : 0.003 0.028 2650 Dihedral : 9.734 105.729 2872 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.68 % Favored : 96.21 % Rotamer: Outliers : 3.45 % Allowed : 13.01 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1902 helix: 1.23 (0.16), residues: 1062 sheet: -1.89 (0.48), residues: 102 loop : -0.80 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 417 TYR 0.013 0.001 TYR B 646 PHE 0.015 0.001 PHE B 839 TRP 0.010 0.001 TRP A 518 HIS 0.004 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00334 (15776) covalent geometry : angle 0.59557 (21500) SS BOND : bond 0.00356 ( 12) SS BOND : angle 0.99704 ( 24) hydrogen bonds : bond 0.03742 ( 807) hydrogen bonds : angle 4.23321 ( 2337) link_BETA1-4 : bond 0.01107 ( 6) link_BETA1-4 : angle 3.21080 ( 18) link_NAG-ASN : bond 0.00423 ( 14) link_NAG-ASN : angle 4.18194 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 0.588 Fit side-chains REVERT: A 476 ASN cc_start: 0.8547 (t0) cc_final: 0.8197 (t0) REVERT: A 524 TYR cc_start: 0.8066 (t80) cc_final: 0.7735 (t80) REVERT: A 566 GLU cc_start: 0.8714 (mt-10) cc_final: 0.7927 (mp0) REVERT: A 607 MET cc_start: 0.7890 (mmm) cc_final: 0.7671 (mmm) REVERT: A 616 MET cc_start: 0.8726 (ptm) cc_final: 0.8463 (tmm) REVERT: A 818 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8293 (tp) REVERT: A 836 TYR cc_start: 0.8208 (t80) cc_final: 0.8007 (t80) REVERT: A 998 MET cc_start: 0.7180 (pmm) cc_final: 0.6641 (pmm) REVERT: A 1023 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8392 (mttp) REVERT: A 1102 TYR cc_start: 0.8870 (m-10) cc_final: 0.8619 (m-10) REVERT: A 1128 CYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8610 (m) REVERT: A 1198 LEU cc_start: 0.8515 (mt) cc_final: 0.8195 (tt) REVERT: A 1261 ILE cc_start: 0.8415 (tt) cc_final: 0.8112 (tt) REVERT: B 476 ASN cc_start: 0.8488 (t0) cc_final: 0.8091 (t0) REVERT: B 524 TYR cc_start: 0.8094 (t80) cc_final: 0.7750 (t80) REVERT: B 566 GLU cc_start: 0.8622 (mt-10) cc_final: 0.7912 (mp0) REVERT: B 616 MET cc_start: 0.8690 (ptm) cc_final: 0.8478 (tmm) REVERT: B 836 TYR cc_start: 0.8212 (t80) cc_final: 0.7964 (t80) REVERT: B 894 PHE cc_start: 0.8398 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: B 994 MET cc_start: 0.7757 (ppp) cc_final: 0.7244 (ppp) REVERT: B 1023 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8449 (mttp) REVERT: B 1102 TYR cc_start: 0.8835 (m-10) cc_final: 0.8526 (m-10) REVERT: B 1103 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8204 (pt0) REVERT: B 1128 CYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8631 (m) REVERT: B 1198 LEU cc_start: 0.8500 (mt) cc_final: 0.8244 (tt) outliers start: 56 outliers final: 41 residues processed: 164 average time/residue: 0.1091 time to fit residues: 28.7278 Evaluate side-chains 159 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 111 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1103 GLU Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 43 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 49 optimal weight: 0.0170 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 176 optimal weight: 0.3980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.116941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.086680 restraints weight = 26135.372| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.04 r_work: 0.3120 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15808 Z= 0.101 Angle : 0.588 14.594 21584 Z= 0.267 Chirality : 0.042 0.576 2540 Planarity : 0.003 0.027 2650 Dihedral : 9.349 106.501 2872 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.02 % Allowed : 14.12 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1902 helix: 1.38 (0.16), residues: 1064 sheet: -1.71 (0.48), residues: 102 loop : -0.64 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1002 TYR 0.012 0.001 TYR B 646 PHE 0.019 0.001 PHE A 839 TRP 0.010 0.001 TRP A 518 HIS 0.003 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00216 (15776) covalent geometry : angle 0.55430 (21500) SS BOND : bond 0.00270 ( 12) SS BOND : angle 0.90231 ( 24) hydrogen bonds : bond 0.03396 ( 807) hydrogen bonds : angle 4.15660 ( 2337) link_BETA1-4 : bond 0.01209 ( 6) link_BETA1-4 : angle 3.28489 ( 18) link_NAG-ASN : bond 0.00445 ( 14) link_NAG-ASN : angle 3.89747 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.608 Fit side-chains REVERT: A 476 ASN cc_start: 0.8509 (t0) cc_final: 0.8195 (t0) REVERT: A 524 TYR cc_start: 0.8029 (t80) cc_final: 0.7649 (t80) REVERT: A 566 GLU cc_start: 0.8609 (mt-10) cc_final: 0.7894 (mp0) REVERT: A 818 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8298 (tp) REVERT: A 994 MET cc_start: 0.7731 (ppp) cc_final: 0.7527 (ppp) REVERT: A 998 MET cc_start: 0.7144 (pmm) cc_final: 0.6652 (pmm) REVERT: A 1023 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8368 (mttp) REVERT: A 1050 MET cc_start: 0.8176 (ttt) cc_final: 0.7410 (ttt) REVERT: A 1128 CYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8621 (m) REVERT: A 1139 LEU cc_start: 0.8230 (tp) cc_final: 0.8011 (tp) REVERT: A 1198 LEU cc_start: 0.8498 (mt) cc_final: 0.8181 (tt) REVERT: A 1282 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: B 476 ASN cc_start: 0.8406 (t0) cc_final: 0.8022 (t0) REVERT: B 524 TYR cc_start: 0.8098 (t80) cc_final: 0.7727 (t80) REVERT: B 566 GLU cc_start: 0.8583 (mt-10) cc_final: 0.7905 (mp0) REVERT: B 607 MET cc_start: 0.8179 (mmm) cc_final: 0.7368 (mmm) REVERT: B 836 TYR cc_start: 0.8058 (t80) cc_final: 0.7818 (t80) REVERT: B 894 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7952 (m-80) REVERT: B 994 MET cc_start: 0.7689 (ppp) cc_final: 0.7176 (ppp) REVERT: B 1023 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8444 (mttp) REVERT: B 1050 MET cc_start: 0.8138 (ttt) cc_final: 0.7367 (ttt) REVERT: B 1102 TYR cc_start: 0.8780 (m-10) cc_final: 0.8493 (m-10) REVERT: B 1128 CYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8625 (m) REVERT: B 1198 LEU cc_start: 0.8506 (mt) cc_final: 0.8234 (tt) REVERT: B 1282 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7074 (pm20) outliers start: 49 outliers final: 29 residues processed: 161 average time/residue: 0.1187 time to fit residues: 29.9576 Evaluate side-chains 148 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 67 optimal weight: 0.7980 chunk 47 optimal weight: 0.0060 chunk 9 optimal weight: 0.0870 chunk 18 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087020 restraints weight = 26272.576| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.04 r_work: 0.3127 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15808 Z= 0.099 Angle : 0.575 13.630 21584 Z= 0.261 Chirality : 0.041 0.538 2540 Planarity : 0.003 0.027 2650 Dihedral : 9.143 105.622 2872 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.90 % Allowed : 14.24 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1902 helix: 1.44 (0.16), residues: 1068 sheet: -1.54 (0.48), residues: 102 loop : -0.51 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 742 TYR 0.012 0.001 TYR B 646 PHE 0.017 0.001 PHE B 839 TRP 0.009 0.001 TRP A 518 HIS 0.003 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00214 (15776) covalent geometry : angle 0.54428 (21500) SS BOND : bond 0.00258 ( 12) SS BOND : angle 0.85890 ( 24) hydrogen bonds : bond 0.03289 ( 807) hydrogen bonds : angle 4.05731 ( 2337) link_BETA1-4 : bond 0.01132 ( 6) link_BETA1-4 : angle 3.21165 ( 18) link_NAG-ASN : bond 0.00448 ( 14) link_NAG-ASN : angle 3.65048 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 115 time to evaluate : 0.617 Fit side-chains REVERT: A 476 ASN cc_start: 0.8505 (t0) cc_final: 0.8201 (t0) REVERT: A 524 TYR cc_start: 0.8064 (t80) cc_final: 0.7669 (t80) REVERT: A 566 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7874 (mp0) REVERT: A 607 MET cc_start: 0.8021 (mmt) cc_final: 0.7458 (mmm) REVERT: A 994 MET cc_start: 0.7725 (ppp) cc_final: 0.7453 (ppp) REVERT: A 998 MET cc_start: 0.7191 (pmm) cc_final: 0.6718 (pmm) REVERT: A 1023 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8364 (mttp) REVERT: A 1128 CYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8620 (m) REVERT: A 1139 LEU cc_start: 0.8194 (tp) cc_final: 0.7978 (tp) REVERT: A 1198 LEU cc_start: 0.8502 (mt) cc_final: 0.8184 (tt) REVERT: A 1282 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: B 476 ASN cc_start: 0.8382 (t0) cc_final: 0.8030 (t0) REVERT: B 524 TYR cc_start: 0.8118 (t80) cc_final: 0.7710 (t80) REVERT: B 566 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7898 (mp0) REVERT: B 836 TYR cc_start: 0.8008 (t80) cc_final: 0.7781 (t80) REVERT: B 894 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7945 (m-80) REVERT: B 994 MET cc_start: 0.7665 (ppp) cc_final: 0.7104 (ppp) REVERT: B 1023 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8422 (mttp) REVERT: B 1102 TYR cc_start: 0.8799 (m-10) cc_final: 0.8472 (m-10) REVERT: B 1128 CYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8617 (m) REVERT: B 1198 LEU cc_start: 0.8535 (mt) cc_final: 0.8252 (tt) outliers start: 47 outliers final: 35 residues processed: 149 average time/residue: 0.1145 time to fit residues: 27.4108 Evaluate side-chains 155 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 93 optimal weight: 0.0050 chunk 95 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086980 restraints weight = 26468.769| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.04 r_work: 0.3126 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15808 Z= 0.103 Angle : 0.570 13.167 21584 Z= 0.259 Chirality : 0.041 0.519 2540 Planarity : 0.003 0.027 2650 Dihedral : 9.018 105.458 2870 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.77 % Allowed : 14.86 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.20), residues: 1902 helix: 1.50 (0.16), residues: 1068 sheet: -1.40 (0.50), residues: 102 loop : -0.39 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 742 TYR 0.013 0.001 TYR A1105 PHE 0.017 0.001 PHE A 839 TRP 0.007 0.001 TRP A 518 HIS 0.003 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00226 (15776) covalent geometry : angle 0.54123 (21500) SS BOND : bond 0.00257 ( 12) SS BOND : angle 0.85238 ( 24) hydrogen bonds : bond 0.03277 ( 807) hydrogen bonds : angle 4.06337 ( 2337) link_BETA1-4 : bond 0.01200 ( 6) link_BETA1-4 : angle 3.18399 ( 18) link_NAG-ASN : bond 0.00447 ( 14) link_NAG-ASN : angle 3.52881 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 0.603 Fit side-chains REVERT: A 476 ASN cc_start: 0.8498 (t0) cc_final: 0.8194 (t0) REVERT: A 524 TYR cc_start: 0.8083 (t80) cc_final: 0.7654 (t80) REVERT: A 566 GLU cc_start: 0.8618 (mt-10) cc_final: 0.7904 (mp0) REVERT: A 607 MET cc_start: 0.7989 (mmt) cc_final: 0.7427 (mmm) REVERT: A 994 MET cc_start: 0.7756 (ppp) cc_final: 0.7438 (ppp) REVERT: A 998 MET cc_start: 0.7207 (pmm) cc_final: 0.6749 (pmm) REVERT: A 1023 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8374 (mttp) REVERT: A 1128 CYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8598 (m) REVERT: A 1139 LEU cc_start: 0.8182 (tp) cc_final: 0.7961 (tp) REVERT: A 1198 LEU cc_start: 0.8508 (mt) cc_final: 0.8192 (tt) REVERT: A 1282 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: B 476 ASN cc_start: 0.8400 (t0) cc_final: 0.8072 (t0) REVERT: B 524 TYR cc_start: 0.8089 (t80) cc_final: 0.7687 (t80) REVERT: B 566 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7904 (mp0) REVERT: B 836 TYR cc_start: 0.8031 (t80) cc_final: 0.7817 (t80) REVERT: B 894 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7968 (m-80) REVERT: B 994 MET cc_start: 0.7620 (ppp) cc_final: 0.7055 (ppp) REVERT: B 1023 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8420 (mttp) REVERT: B 1102 TYR cc_start: 0.8803 (m-10) cc_final: 0.8554 (m-10) REVERT: B 1128 CYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8604 (m) REVERT: B 1198 LEU cc_start: 0.8526 (mt) cc_final: 0.8243 (tt) REVERT: B 1282 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7048 (pm20) outliers start: 45 outliers final: 33 residues processed: 151 average time/residue: 0.1147 time to fit residues: 27.7246 Evaluate side-chains 153 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 178 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 71 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 67 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 626 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.087211 restraints weight = 26209.863| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.01 r_work: 0.3130 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15808 Z= 0.101 Angle : 0.576 12.755 21584 Z= 0.260 Chirality : 0.041 0.501 2540 Planarity : 0.003 0.027 2650 Dihedral : 8.794 105.395 2870 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.65 % Allowed : 14.92 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1902 helix: 1.56 (0.16), residues: 1068 sheet: -1.40 (0.49), residues: 102 loop : -0.34 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.012 0.001 TYR B 646 PHE 0.018 0.001 PHE B 839 TRP 0.008 0.001 TRP A 518 HIS 0.003 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00220 (15776) covalent geometry : angle 0.54938 (21500) SS BOND : bond 0.00252 ( 12) SS BOND : angle 0.83676 ( 24) hydrogen bonds : bond 0.03254 ( 807) hydrogen bonds : angle 4.01906 ( 2337) link_BETA1-4 : bond 0.01185 ( 6) link_BETA1-4 : angle 3.14770 ( 18) link_NAG-ASN : bond 0.00453 ( 14) link_NAG-ASN : angle 3.41055 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.613 Fit side-chains REVERT: A 476 ASN cc_start: 0.8508 (t0) cc_final: 0.8203 (t0) REVERT: A 524 TYR cc_start: 0.8087 (t80) cc_final: 0.7659 (t80) REVERT: A 566 GLU cc_start: 0.8636 (mt-10) cc_final: 0.7876 (mp0) REVERT: A 607 MET cc_start: 0.7978 (mmt) cc_final: 0.7340 (mmm) REVERT: A 994 MET cc_start: 0.7753 (ppp) cc_final: 0.7428 (ppp) REVERT: A 998 MET cc_start: 0.7216 (pmm) cc_final: 0.6775 (pmm) REVERT: A 1023 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8382 (mttp) REVERT: A 1128 CYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8608 (m) REVERT: A 1139 LEU cc_start: 0.8160 (tp) cc_final: 0.7944 (tp) REVERT: A 1198 LEU cc_start: 0.8513 (mt) cc_final: 0.8198 (tt) REVERT: B 476 ASN cc_start: 0.8382 (t0) cc_final: 0.8055 (t0) REVERT: B 524 TYR cc_start: 0.8086 (t80) cc_final: 0.7663 (t80) REVERT: B 566 GLU cc_start: 0.8598 (mt-10) cc_final: 0.7904 (mp0) REVERT: B 836 TYR cc_start: 0.8009 (t80) cc_final: 0.7800 (t80) REVERT: B 894 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: B 994 MET cc_start: 0.7612 (ppp) cc_final: 0.7044 (ppp) REVERT: B 1023 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8418 (mttp) REVERT: B 1128 CYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8592 (m) REVERT: B 1198 LEU cc_start: 0.8524 (mt) cc_final: 0.8234 (tt) REVERT: B 1218 MET cc_start: 0.8651 (mmm) cc_final: 0.8393 (mmm) REVERT: B 1282 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7069 (pm20) outliers start: 43 outliers final: 32 residues processed: 149 average time/residue: 0.1210 time to fit residues: 28.1047 Evaluate side-chains 151 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 133 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 0.0270 chunk 132 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087201 restraints weight = 26464.761| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.01 r_work: 0.3130 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15808 Z= 0.103 Angle : 0.578 12.374 21584 Z= 0.262 Chirality : 0.041 0.485 2540 Planarity : 0.003 0.027 2650 Dihedral : 8.631 105.177 2870 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.59 % Allowed : 14.92 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.20), residues: 1902 helix: 1.59 (0.16), residues: 1068 sheet: -1.39 (0.49), residues: 102 loop : -0.32 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 742 TYR 0.013 0.001 TYR B 646 PHE 0.019 0.001 PHE A 839 TRP 0.007 0.001 TRP A 592 HIS 0.003 0.000 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00225 (15776) covalent geometry : angle 0.55217 (21500) SS BOND : bond 0.00258 ( 12) SS BOND : angle 0.87293 ( 24) hydrogen bonds : bond 0.03238 ( 807) hydrogen bonds : angle 4.00730 ( 2337) link_BETA1-4 : bond 0.01157 ( 6) link_BETA1-4 : angle 3.10272 ( 18) link_NAG-ASN : bond 0.00436 ( 14) link_NAG-ASN : angle 3.28825 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 0.567 Fit side-chains REVERT: A 476 ASN cc_start: 0.8450 (t0) cc_final: 0.8156 (t0) REVERT: A 524 TYR cc_start: 0.8092 (t80) cc_final: 0.7657 (t80) REVERT: A 566 GLU cc_start: 0.8636 (mt-10) cc_final: 0.7887 (mp0) REVERT: A 607 MET cc_start: 0.7979 (mmt) cc_final: 0.7368 (mmm) REVERT: A 994 MET cc_start: 0.7754 (ppp) cc_final: 0.7428 (ppp) REVERT: A 998 MET cc_start: 0.7223 (pmm) cc_final: 0.6800 (pmm) REVERT: A 1023 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8382 (mttp) REVERT: A 1128 CYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8609 (m) REVERT: A 1139 LEU cc_start: 0.8172 (tp) cc_final: 0.7950 (tp) REVERT: A 1198 LEU cc_start: 0.8511 (mt) cc_final: 0.8196 (tt) REVERT: A 1282 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: B 476 ASN cc_start: 0.8411 (t0) cc_final: 0.8091 (t0) REVERT: B 524 TYR cc_start: 0.8093 (t80) cc_final: 0.7663 (t80) REVERT: B 566 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7923 (mp0) REVERT: B 836 TYR cc_start: 0.8012 (t80) cc_final: 0.7804 (t80) REVERT: B 894 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: B 994 MET cc_start: 0.7619 (ppp) cc_final: 0.7094 (ppp) REVERT: B 1023 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8418 (mttp) REVERT: B 1128 CYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8583 (m) REVERT: B 1198 LEU cc_start: 0.8538 (mt) cc_final: 0.8253 (tt) REVERT: B 1218 MET cc_start: 0.8660 (mmm) cc_final: 0.8403 (mmm) REVERT: B 1282 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7103 (pm20) outliers start: 42 outliers final: 33 residues processed: 152 average time/residue: 0.1222 time to fit residues: 29.0914 Evaluate side-chains 153 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 811 CYS Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 36 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 178 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.115584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.086893 restraints weight = 25686.231| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.80 r_work: 0.3137 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15808 Z= 0.110 Angle : 0.584 12.100 21584 Z= 0.265 Chirality : 0.041 0.474 2540 Planarity : 0.003 0.028 2650 Dihedral : 8.524 104.866 2870 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.53 % Allowed : 14.98 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1902 helix: 1.59 (0.16), residues: 1068 sheet: -1.46 (0.49), residues: 102 loop : -0.33 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 742 TYR 0.015 0.001 TYR B1105 PHE 0.028 0.001 PHE B 839 TRP 0.007 0.001 TRP A 592 HIS 0.003 0.000 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00247 (15776) covalent geometry : angle 0.55933 (21500) SS BOND : bond 0.00287 ( 12) SS BOND : angle 1.07062 ( 24) hydrogen bonds : bond 0.03284 ( 807) hydrogen bonds : angle 3.98498 ( 2337) link_BETA1-4 : bond 0.01222 ( 6) link_BETA1-4 : angle 3.08122 ( 18) link_NAG-ASN : bond 0.00421 ( 14) link_NAG-ASN : angle 3.19564 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.81 seconds wall clock time: 56 minutes 42.82 seconds (3402.82 seconds total)