Starting phenix.real_space_refine on Wed Mar 4 20:03:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4v_24179/03_2026/7n4v_24179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4v_24179/03_2026/7n4v_24179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n4v_24179/03_2026/7n4v_24179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4v_24179/03_2026/7n4v_24179.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4v_24179/03_2026/7n4v_24179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4v_24179/03_2026/7n4v_24179.cif" } resolution = 3.58 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= 0.045 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 10064 2.51 5 N 2434 2.21 5 O 2800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 15390 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: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'CLR': 3, 'NAG': 4, 'POV': 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: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'CLR': 3, 'NAG': 4, 'POV': 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: 3.17, per 1000 atoms: 0.21 Number of scatterers: 15390 At special positions: 0 Unit cell: (109.956, 133.28, 134.946, 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 2800 8.00 N 2434 7.00 C 10064 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=2.04 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=2.04 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=2.91 Simple disulfide: pdb=" SG CYS B 980 " - pdb=" SG CYS B 989 " distance=2.09 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 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: 1.49 Conformation dependent library (CDL) restraints added in 649.3 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: 84 helices and 16 sheets defined 62.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.594A 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 removed outlier: 3.603A pdb=" N THR A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 388 through 402 removed outlier: 3.569A pdb=" N GLY A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 436 Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.614A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 4.157A pdb=" N ILE A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 removed outlier: 3.745A pdb=" N TYR A 493 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.822A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 Processing helix chain 'A' and resid 583 through 607 removed outlier: 3.803A pdb=" N ALA A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.573A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.863A pdb=" N GLU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 652 removed outlier: 3.978A pdb=" N PHE A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.961A 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 removed outlier: 3.687A pdb=" N GLY A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 701 through 711 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: 3.715A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.593A 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: 3.634A pdb=" N ARG A 846 " --> pdb=" O HIS A 842 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 894 removed outlier: 4.157A pdb=" N ASP A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 929 through 938 Processing helix chain 'A' and resid 952 through 961 removed outlier: 3.833A pdb=" N ASP A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1016 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 3.930A pdb=" N SER A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.659A pdb=" N TYR A1062 " --> pdb=" O ASN A1058 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1100 removed outlier: 3.886A pdb=" N ASN A1099 " --> pdb=" O THR A1096 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A1100 " --> pdb=" O ILE A1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1096 through 1100' Processing helix chain 'A' and resid 1103 through 1106 Processing helix chain 'A' and resid 1107 through 1131 removed outlier: 4.050A pdb=" N GLU A1111 " --> pdb=" O THR A1107 " (cutoff:3.500A) Proline residue: A1122 - end of helix removed outlier: 3.593A pdb=" N LEU A1129 " --> pdb=" O ALA A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1160 removed outlier: 4.146A pdb=" N LEU A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1191 removed outlier: 4.236A pdb=" N VAL A1179 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1228 removed outlier: 4.147A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix removed outlier: 4.330A pdb=" N VAL A1226 " --> pdb=" O PRO A1222 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A1227 " --> pdb=" O GLY A1223 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A1228 " --> pdb=" O ILE A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1239 through 1266 removed outlier: 4.704A pdb=" N LEU A1258 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1277 through 1281 Processing helix chain 'B' and resid 334 through 349 Processing helix chain 'B' and resid 351 through 368 removed outlier: 3.594A 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 removed outlier: 3.602A pdb=" N THR B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 388 through 402 removed outlier: 3.568A pdb=" N GLY B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 436 Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.612A pdb=" N LEU B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 removed outlier: 4.157A pdb=" N ILE B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.744A pdb=" N TYR B 493 " --> pdb=" O LEU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 517 through 528 removed outlier: 3.822A pdb=" N HIS B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 583 through 607 removed outlier: 3.803A pdb=" N ALA B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.572A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 removed outlier: 3.863A pdb=" N GLU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 652 removed outlier: 3.979A pdb=" N PHE B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.962A 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 removed outlier: 3.688A pdb=" N GLY B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 701 through 711 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: 3.716A pdb=" N SER B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) removed outlier: 4.593A 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: 3.635A pdb=" N ARG B 846 " --> pdb=" O HIS B 842 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 894 removed outlier: 4.157A pdb=" N ASP B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 Processing helix chain 'B' and resid 929 through 938 Processing helix chain 'B' and resid 952 through 961 removed outlier: 3.834A pdb=" N ASP B 956 " --> pdb=" O SER B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1016 Proline residue: B1013 - end of helix Processing helix chain 'B' and resid 1028 through 1033 removed outlier: 3.930A pdb=" N SER B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1081 removed outlier: 3.659A pdb=" N TYR B1062 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B1079 " --> pdb=" O ASN B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1100 removed outlier: 3.884A pdb=" N ASN B1099 " --> pdb=" O THR B1096 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B1100 " --> pdb=" O ILE B1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1096 through 1100' Processing helix chain 'B' and resid 1103 through 1106 Processing helix chain 'B' and resid 1107 through 1131 removed outlier: 4.049A pdb=" N GLU B1111 " --> pdb=" O THR B1107 " (cutoff:3.500A) Proline residue: B1122 - end of helix removed outlier: 3.593A pdb=" N LEU B1129 " --> pdb=" O ALA B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1160 removed outlier: 4.150A pdb=" N LEU B1140 " --> pdb=" O ARG B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1191 removed outlier: 4.236A pdb=" N VAL B1179 " --> pdb=" O VAL B1175 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B1181 " --> pdb=" O MET B1177 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS B1184 " --> pdb=" O GLU B1180 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1196 through 1228 removed outlier: 4.145A pdb=" N MET B1218 " --> pdb=" O ALA B1214 " (cutoff:3.500A) Proline residue: B1222 - end of helix removed outlier: 4.330A pdb=" N VAL B1226 " --> pdb=" O PRO B1222 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B1227 " --> pdb=" O GLY B1223 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B1228 " --> pdb=" O ILE B1224 " (cutoff:3.500A) Processing helix chain 'B' and resid 1232 through 1239 Processing helix chain 'B' and resid 1239 through 1266 removed outlier: 4.708A pdb=" N LEU B1258 " --> pdb=" O GLY B1254 " (cutoff:3.500A) Proline residue: B1259 - end of helix Processing helix chain 'B' and resid 1277 through 1281 Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.570A pdb=" N LYS A 430 " --> pdb=" O TYR A 422 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 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 556 through 557 Processing sheet with id=AA6, first strand: chain 'A' and resid 948 through 951 removed outlier: 5.177A pdb=" N TYR A1052 " --> pdb=" O PRO A 949 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET A1050 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 979 through 980 removed outlier: 3.924A pdb=" N ARG A 968 " --> pdb=" O CYS A 980 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 991 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.933A pdb=" N THR A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AB1, first strand: chain 'B' and resid 420 through 423 removed outlier: 3.569A pdb=" N LYS B 430 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 487 through 488 Processing sheet with id=AB3, first strand: chain 'B' and resid 505 through 509 Processing sheet with id=AB4, first strand: chain 'B' and resid 556 through 557 Processing sheet with id=AB5, first strand: chain 'B' and resid 948 through 951 removed outlier: 5.177A pdb=" N TYR B1052 " --> pdb=" O PRO B 949 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET B1050 " --> pdb=" O SER B 951 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 968 through 969 removed outlier: 4.367A pdb=" N LYS B 991 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.933A pdb=" N THR B1046 " --> pdb=" O ASN B1037 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2316 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: 2.39 Time building geometry restraints manager: 1.88 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: 2382 1.31 - 1.44: 4275 1.44 - 1.57: 8975 1.57 - 1.69: 4 1.69 - 1.82: 138 Bond restraints: 15774 Sorted by residual: bond pdb=" N ILE B 470 " pdb=" CA ILE B 470 " ideal model delta sigma weight residual 1.456 1.500 -0.044 9.50e-03 1.11e+04 2.13e+01 bond pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta sigma weight residual 1.456 1.499 -0.043 9.50e-03 1.11e+04 2.05e+01 bond pdb=" N VAL A 701 " pdb=" CA VAL A 701 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.97e+01 bond pdb=" N VAL B 701 " pdb=" CA VAL B 701 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.91e+01 bond pdb=" N LEU A1012 " pdb=" CA LEU A1012 " ideal model delta sigma weight residual 1.463 1.492 -0.029 6.90e-03 2.10e+04 1.80e+01 ... (remaining 15769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 17325 2.37 - 4.73: 4001 4.73 - 7.10: 156 7.10 - 9.47: 20 9.47 - 11.83: 4 Bond angle restraints: 21506 Sorted by residual: angle pdb=" C ALA B 914 " pdb=" N GLY B 915 " pdb=" CA GLY B 915 " ideal model delta sigma weight residual 119.94 125.22 -5.28 1.11e+00 8.12e-01 2.26e+01 angle pdb=" C SER B 433 " pdb=" N GLY B 434 " pdb=" CA GLY B 434 " ideal model delta sigma weight residual 119.98 125.24 -5.26 1.11e+00 8.12e-01 2.25e+01 angle pdb=" C ALA A 914 " pdb=" N GLY A 915 " pdb=" CA GLY A 915 " ideal model delta sigma weight residual 119.94 125.19 -5.25 1.11e+00 8.12e-01 2.24e+01 angle pdb=" C SER A1137 " pdb=" N GLY A1138 " pdb=" CA GLY A1138 " ideal model delta sigma weight residual 119.98 125.22 -5.24 1.11e+00 8.12e-01 2.23e+01 angle pdb=" C SER B1137 " pdb=" N GLY B1138 " pdb=" CA GLY B1138 " ideal model delta sigma weight residual 119.98 125.22 -5.24 1.11e+00 8.12e-01 2.23e+01 ... (remaining 21501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 9490 30.32 - 60.63: 363 60.63 - 90.95: 55 90.95 - 121.27: 16 121.27 - 151.59: 2 Dihedral angle restraints: 9926 sinusoidal: 4374 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 93.00 162.69 -69.69 1 1.00e+01 1.00e-02 6.27e+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 93.00 162.66 -69.66 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS A 966 " pdb=" SG CYS A 966 " pdb=" SG CYS A1024 " pdb=" CB CYS A1024 " ideal model delta sinusoidal sigma weight residual 93.00 158.05 -65.05 1 1.00e+01 1.00e-02 5.55e+01 ... (remaining 9923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.932: 2546 0.932 - 1.864: 0 1.864 - 2.796: 0 2.796 - 3.727: 0 3.727 - 4.659: 4 Chirality restraints: 2550 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 2.26 -4.66 2.00e-02 2.50e+03 5.43e+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 2.26 -4.66 2.00e-02 2.50e+03 5.42e+04 chirality pdb=" C1 NAG A1403 " pdb=" ND2 ASN A1075 " pdb=" C2 NAG A1403 " pdb=" O5 NAG A1403 " both_signs ideal model delta sigma weight residual False -2.40 2.24 -4.64 2.00e-01 2.50e+01 5.37e+02 ... (remaining 2547 not shown) Planarity restraints: 2662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1602 " -0.335 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG B1602 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG B1602 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG B1602 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG B1602 " -0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1401 " 0.335 2.00e-02 2.50e+03 2.89e-01 1.05e+03 pdb=" C7 NAG A1401 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1401 " 0.043 2.00e-02 2.50e+03 pdb=" N2 NAG A1401 " -0.507 2.00e-02 2.50e+03 pdb=" O7 NAG A1401 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.252 2.00e-02 2.50e+03 2.12e-01 5.61e+02 pdb=" C7 NAG F 1 " 0.135 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.202 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.319 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.001 2.00e-02 2.50e+03 ... (remaining 2659 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2166 2.81 - 3.33: 16307 3.33 - 3.86: 23807 3.86 - 4.38: 30269 4.38 - 4.90: 50150 Nonbonded interactions: 122699 Sorted by model distance: nonbonded pdb=" ND2 ASN A1170 " pdb=" O PHE A1238 " model vdw 2.288 3.120 nonbonded pdb=" ND2 ASN B1170 " pdb=" O PHE B1238 " model vdw 2.289 3.120 nonbonded pdb=" OG SER B 433 " pdb=" O ALA B 567 " model vdw 2.308 3.040 nonbonded pdb=" OG SER A 433 " pdb=" O ALA A 567 " model vdw 2.309 3.040 nonbonded pdb=" O SER B1207 " pdb=" OG SER B1210 " model vdw 2.313 3.040 ... (remaining 122694 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 333 through 1285 or resid 1402 through 1404 or resid 1406 \ through 1407)) selection = (chain 'B' and (resid 333 through 1285 or resid 1602 through 1604 or resid 1606 \ through 1607)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.990 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.016 0.881 15806 Z= 1.115 Angle : 1.813 27.401 21590 Z= 1.313 Chirality : 0.203 4.659 2550 Planarity : 0.012 0.290 2648 Dihedral : 16.543 151.585 6310 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % 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: -3.22 (0.16), residues: 1902 helix: -1.55 (0.13), residues: 1052 sheet: -3.15 (0.33), residues: 130 loop : -2.66 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1070 TYR 0.029 0.003 TYR A 646 PHE 0.027 0.003 PHE A 791 TRP 0.017 0.003 TRP B 457 HIS 0.010 0.003 HIS B1184 Details of bonding type rmsd covalent geometry : bond 0.01391 (15774) covalent geometry : angle 1.77562 (21506) SS BOND : bond 0.25486 ( 12) SS BOND : angle 6.81880 ( 24) hydrogen bonds : bond 0.16252 ( 802) hydrogen bonds : angle 6.90951 ( 2316) link_BETA1-4 : bond 0.00344 ( 6) link_BETA1-4 : angle 3.27541 ( 18) link_NAG-ASN : bond 0.02342 ( 14) link_NAG-ASN : angle 6.61318 ( 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 198 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 TYR cc_start: 0.8582 (t80) cc_final: 0.8342 (t80) REVERT: A 487 ILE cc_start: 0.8406 (mt) cc_final: 0.8101 (mp) REVERT: A 623 ASP cc_start: 0.7479 (t0) cc_final: 0.7072 (t0) REVERT: A 743 VAL cc_start: 0.7736 (m) cc_final: 0.7504 (p) REVERT: A 894 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: A 1011 TYR cc_start: 0.7871 (m-10) cc_final: 0.7294 (m-10) REVERT: A 1218 MET cc_start: 0.8177 (mmt) cc_final: 0.7951 (mmm) REVERT: B 457 TRP cc_start: 0.6069 (t-100) cc_final: 0.5224 (t-100) REVERT: B 588 GLN cc_start: 0.8065 (mt0) cc_final: 0.7631 (mm-40) REVERT: B 591 LEU cc_start: 0.8114 (mt) cc_final: 0.7863 (mt) REVERT: B 894 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8171 (m-10) REVERT: B 1064 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6493 (mp0) REVERT: B 1091 GLU cc_start: 0.7366 (pt0) cc_final: 0.6999 (tt0) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.1251 time to fit residues: 36.7773 Evaluate side-chains 135 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain B residue 894 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.7980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 488 ASN A1043 GLN B 339 GLN B1043 GLN B1236 GLN B1253 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.111196 restraints weight = 20817.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111637 restraints weight = 15196.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.113135 restraints weight = 12550.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113926 restraints weight = 10243.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113943 restraints weight = 9500.174| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15806 Z= 0.134 Angle : 0.735 14.702 21590 Z= 0.333 Chirality : 0.048 0.751 2550 Planarity : 0.004 0.039 2648 Dihedral : 12.341 130.177 2936 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.36 % Allowed : 10.11 % Favored : 88.53 % 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 (0.19), residues: 1902 helix: 0.53 (0.16), residues: 1070 sheet: -2.46 (0.36), residues: 130 loop : -1.70 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 693 TYR 0.022 0.001 TYR A 886 PHE 0.023 0.001 PHE B 930 TRP 0.012 0.001 TRP A 953 HIS 0.005 0.001 HIS A1009 Details of bonding type rmsd covalent geometry : bond 0.00275 (15774) covalent geometry : angle 0.70728 (21506) SS BOND : bond 0.00220 ( 12) SS BOND : angle 1.33139 ( 24) hydrogen bonds : bond 0.04610 ( 802) hydrogen bonds : angle 4.90461 ( 2316) link_BETA1-4 : bond 0.00661 ( 6) link_BETA1-4 : angle 2.43919 ( 18) link_NAG-ASN : bond 0.00383 ( 14) link_NAG-ASN : angle 4.25718 ( 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 176 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 PHE cc_start: 0.8038 (m-80) cc_final: 0.7810 (m-10) REVERT: A 457 TRP cc_start: 0.6922 (t-100) cc_final: 0.6249 (t-100) REVERT: A 662 VAL cc_start: 0.7925 (OUTLIER) cc_final: 0.7708 (p) REVERT: A 783 ASP cc_start: 0.8057 (t70) cc_final: 0.7773 (t0) REVERT: A 1011 TYR cc_start: 0.7992 (m-10) cc_final: 0.7624 (m-80) REVERT: A 1064 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6852 (mp0) REVERT: B 457 TRP cc_start: 0.6268 (t-100) cc_final: 0.5770 (t-100) REVERT: B 579 TYR cc_start: 0.7964 (m-80) cc_final: 0.7520 (m-80) REVERT: B 588 GLN cc_start: 0.7976 (mt0) cc_final: 0.7704 (mm-40) outliers start: 22 outliers final: 9 residues processed: 165 average time/residue: 0.1129 time to fit residues: 28.5764 Evaluate side-chains 140 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 1162 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 64 optimal weight: 20.0000 chunk 179 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN A 409 GLN A1009 HIS A1253 HIS B 448 GLN B 496 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.147058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107929 restraints weight = 21399.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110342 restraints weight = 16241.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111537 restraints weight = 11627.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112173 restraints weight = 9602.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112405 restraints weight = 9059.515| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15806 Z= 0.163 Angle : 0.663 12.522 21590 Z= 0.308 Chirality : 0.044 0.343 2550 Planarity : 0.004 0.047 2648 Dihedral : 9.989 119.251 2936 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.85 % Allowed : 12.39 % Favored : 85.76 % 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: -0.43 (0.20), residues: 1902 helix: 0.81 (0.16), residues: 1066 sheet: -2.29 (0.39), residues: 130 loop : -1.56 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 693 TYR 0.018 0.001 TYR B 836 PHE 0.018 0.001 PHE B 930 TRP 0.011 0.001 TRP B1014 HIS 0.006 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00386 (15774) covalent geometry : angle 0.64732 (21506) SS BOND : bond 0.00408 ( 12) SS BOND : angle 1.17924 ( 24) hydrogen bonds : bond 0.04462 ( 802) hydrogen bonds : angle 4.72413 ( 2316) link_BETA1-4 : bond 0.00717 ( 6) link_BETA1-4 : angle 2.13662 ( 18) link_NAG-ASN : bond 0.00415 ( 14) link_NAG-ASN : angle 2.90185 ( 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 173 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 457 TRP cc_start: 0.6857 (t-100) cc_final: 0.6320 (t-100) REVERT: A 707 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7393 (tp) REVERT: A 783 ASP cc_start: 0.8129 (t70) cc_final: 0.7848 (t0) REVERT: A 1008 PHE cc_start: 0.8501 (t80) cc_final: 0.8292 (t80) REVERT: A 1050 MET cc_start: 0.8609 (ttt) cc_final: 0.8266 (ttt) REVERT: B 457 TRP cc_start: 0.6241 (t-100) cc_final: 0.5845 (t-100) REVERT: B 579 TYR cc_start: 0.8027 (m-80) cc_final: 0.7659 (m-80) REVERT: B 1064 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6546 (mp0) outliers start: 30 outliers final: 16 residues processed: 160 average time/residue: 0.1076 time to fit residues: 26.5754 Evaluate side-chains 147 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 1162 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN B 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.145782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107433 restraints weight = 21465.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108325 restraints weight = 16040.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109321 restraints weight = 13674.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110288 restraints weight = 10988.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110477 restraints weight = 9775.910| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15806 Z= 0.181 Angle : 0.650 9.454 21590 Z= 0.307 Chirality : 0.043 0.272 2550 Planarity : 0.004 0.050 2648 Dihedral : 9.492 108.968 2936 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.47 % Allowed : 13.63 % Favored : 83.91 % 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: 0.83 (0.16), residues: 1076 sheet: -2.37 (0.40), residues: 132 loop : -1.50 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 605 TYR 0.017 0.001 TYR A 646 PHE 0.016 0.001 PHE A 791 TRP 0.011 0.001 TRP B1014 HIS 0.006 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00434 (15774) covalent geometry : angle 0.63730 (21506) SS BOND : bond 0.00324 ( 12) SS BOND : angle 1.05630 ( 24) hydrogen bonds : bond 0.04385 ( 802) hydrogen bonds : angle 4.72837 ( 2316) link_BETA1-4 : bond 0.00524 ( 6) link_BETA1-4 : angle 2.08511 ( 18) link_NAG-ASN : bond 0.00322 ( 14) link_NAG-ASN : angle 2.55754 ( 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 174 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 457 TRP cc_start: 0.6768 (t-100) cc_final: 0.6261 (t-100) REVERT: A 664 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7932 (p) REVERT: A 707 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7367 (tp) REVERT: A 1008 PHE cc_start: 0.8340 (t80) cc_final: 0.8107 (t80) REVERT: A 1050 MET cc_start: 0.8637 (ttt) cc_final: 0.8265 (ttt) REVERT: A 1064 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6610 (mp0) REVERT: B 457 TRP cc_start: 0.6299 (t-100) cc_final: 0.5880 (t-100) REVERT: B 579 TYR cc_start: 0.8045 (m-80) cc_final: 0.7718 (m-80) REVERT: B 607 MET cc_start: 0.7722 (mpp) cc_final: 0.7496 (mpp) REVERT: B 1064 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6664 (mp0) outliers start: 40 outliers final: 24 residues processed: 158 average time/residue: 0.1042 time to fit residues: 26.2492 Evaluate side-chains 152 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 153 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 ASN ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.147799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.109283 restraints weight = 21365.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.110611 restraints weight = 16005.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.112149 restraints weight = 12203.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112639 restraints weight = 10253.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112931 restraints weight = 9768.039| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15806 Z= 0.123 Angle : 0.589 11.198 21590 Z= 0.277 Chirality : 0.040 0.228 2550 Planarity : 0.004 0.050 2648 Dihedral : 9.199 107.508 2936 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.71 % Allowed : 14.00 % Favored : 83.29 % 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: -0.09 (0.20), residues: 1902 helix: 1.01 (0.16), residues: 1086 sheet: -2.32 (0.40), residues: 132 loop : -1.28 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 693 TYR 0.019 0.001 TYR A 646 PHE 0.014 0.001 PHE B 930 TRP 0.014 0.001 TRP B1014 HIS 0.003 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00278 (15774) covalent geometry : angle 0.58003 (21506) SS BOND : bond 0.00309 ( 12) SS BOND : angle 0.90754 ( 24) hydrogen bonds : bond 0.03943 ( 802) hydrogen bonds : angle 4.55040 ( 2316) link_BETA1-4 : bond 0.00547 ( 6) link_BETA1-4 : angle 1.83732 ( 18) link_NAG-ASN : bond 0.00268 ( 14) link_NAG-ASN : angle 2.08309 ( 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 185 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.606 Fit side-chains revert: symmetry clash REVERT: A 411 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8208 (mm) REVERT: A 457 TRP cc_start: 0.6610 (t-100) cc_final: 0.6029 (t-100) REVERT: A 664 SER cc_start: 0.8272 (OUTLIER) cc_final: 0.7970 (p) REVERT: A 707 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7401 (tp) REVERT: A 990 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8627 (mm) REVERT: A 1064 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6595 (mp0) REVERT: B 421 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7842 (tmm160) REVERT: B 457 TRP cc_start: 0.6151 (t-100) cc_final: 0.5858 (t-100) REVERT: B 579 TYR cc_start: 0.8018 (m-80) cc_final: 0.7703 (m-80) REVERT: B 607 MET cc_start: 0.7647 (mpp) cc_final: 0.7364 (mpp) REVERT: B 750 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7629 (m) REVERT: B 990 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7971 (mt) REVERT: B 1064 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6684 (mp0) REVERT: B 1218 MET cc_start: 0.8413 (mmm) cc_final: 0.8073 (mmm) outliers start: 44 outliers final: 21 residues processed: 172 average time/residue: 0.1042 time to fit residues: 28.5711 Evaluate side-chains 150 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 750 CYS Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 108 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 156 optimal weight: 0.0040 chunk 47 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.146131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.107418 restraints weight = 21257.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108851 restraints weight = 16314.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.110180 restraints weight = 12638.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110600 restraints weight = 10551.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110914 restraints weight = 9681.992| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15806 Z= 0.151 Angle : 0.604 10.066 21590 Z= 0.286 Chirality : 0.041 0.240 2550 Planarity : 0.004 0.052 2648 Dihedral : 9.157 106.127 2936 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.02 % Allowed : 14.67 % Favored : 82.31 % 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: -0.10 (0.20), residues: 1902 helix: 1.05 (0.16), residues: 1064 sheet: -2.24 (0.41), residues: 132 loop : -1.31 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 693 TYR 0.017 0.001 TYR A 646 PHE 0.014 0.001 PHE A 791 TRP 0.012 0.001 TRP B1014 HIS 0.003 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00361 (15774) covalent geometry : angle 0.59533 (21506) SS BOND : bond 0.00344 ( 12) SS BOND : angle 1.08979 ( 24) hydrogen bonds : bond 0.04051 ( 802) hydrogen bonds : angle 4.55481 ( 2316) link_BETA1-4 : bond 0.00493 ( 6) link_BETA1-4 : angle 1.78822 ( 18) link_NAG-ASN : bond 0.00274 ( 14) link_NAG-ASN : angle 2.02562 ( 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 179 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 0.513 Fit side-chains REVERT: A 411 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8217 (mm) REVERT: A 457 TRP cc_start: 0.6596 (t-100) cc_final: 0.6060 (t-100) REVERT: A 664 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8023 (p) REVERT: A 707 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7689 (tp) REVERT: A 990 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8606 (mm) REVERT: A 994 MET cc_start: 0.8135 (mmm) cc_final: 0.7600 (tpt) REVERT: A 1064 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6677 (mp0) REVERT: B 421 ARG cc_start: 0.8269 (mmm160) cc_final: 0.8017 (mmm160) REVERT: B 457 TRP cc_start: 0.6214 (t-100) cc_final: 0.5874 (t-100) REVERT: B 579 TYR cc_start: 0.8032 (m-80) cc_final: 0.7719 (m-80) REVERT: B 607 MET cc_start: 0.7649 (mpp) cc_final: 0.7389 (mpp) REVERT: B 990 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8137 (mm) REVERT: B 1008 PHE cc_start: 0.8269 (t80) cc_final: 0.7758 (m-80) REVERT: B 1050 MET cc_start: 0.8630 (ttt) cc_final: 0.8178 (ttt) outliers start: 49 outliers final: 31 residues processed: 164 average time/residue: 0.1049 time to fit residues: 27.5314 Evaluate side-chains 164 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 766 MET Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 184 optimal weight: 0.3980 chunk 129 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109349 restraints weight = 21151.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109350 restraints weight = 15393.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110693 restraints weight = 12023.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111270 restraints weight = 10683.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111612 restraints weight = 9901.609| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15806 Z= 0.124 Angle : 0.585 12.016 21590 Z= 0.276 Chirality : 0.040 0.232 2550 Planarity : 0.004 0.061 2648 Dihedral : 8.984 105.680 2936 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.90 % Allowed : 15.17 % Favored : 81.94 % 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: 0.04 (0.20), residues: 1902 helix: 1.15 (0.16), residues: 1068 sheet: -2.19 (0.42), residues: 132 loop : -1.23 (0.25), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 693 TYR 0.019 0.001 TYR A 646 PHE 0.012 0.001 PHE A 930 TRP 0.012 0.001 TRP B1014 HIS 0.003 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00285 (15774) covalent geometry : angle 0.57699 (21506) SS BOND : bond 0.00330 ( 12) SS BOND : angle 1.06675 ( 24) hydrogen bonds : bond 0.03879 ( 802) hydrogen bonds : angle 4.50187 ( 2316) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 1.65116 ( 18) link_NAG-ASN : bond 0.00269 ( 14) link_NAG-ASN : angle 1.86561 ( 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 184 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 411 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 457 TRP cc_start: 0.6531 (t-100) cc_final: 0.5937 (t-100) REVERT: A 664 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7987 (p) REVERT: A 707 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7683 (tp) REVERT: A 990 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8569 (mm) REVERT: A 1064 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6625 (mp0) REVERT: B 421 ARG cc_start: 0.8279 (mmm160) cc_final: 0.8026 (mmm160) REVERT: B 457 TRP cc_start: 0.6160 (t-100) cc_final: 0.5826 (t-100) REVERT: B 579 TYR cc_start: 0.8012 (m-80) cc_final: 0.7723 (m-80) REVERT: B 607 MET cc_start: 0.7632 (mpp) cc_final: 0.7373 (mpp) REVERT: B 990 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8112 (mm) REVERT: B 1008 PHE cc_start: 0.8207 (t80) cc_final: 0.7883 (m-80) REVERT: B 1064 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6616 (mp0) REVERT: B 1218 MET cc_start: 0.8369 (mmm) cc_final: 0.8026 (mmm) outliers start: 47 outliers final: 31 residues processed: 170 average time/residue: 0.1108 time to fit residues: 29.7227 Evaluate side-chains 164 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 47 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.147341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108296 restraints weight = 21393.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109811 restraints weight = 16201.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111386 restraints weight = 12175.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111805 restraints weight = 9827.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111937 restraints weight = 9420.890| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15806 Z= 0.135 Angle : 0.599 12.391 21590 Z= 0.282 Chirality : 0.041 0.221 2550 Planarity : 0.004 0.053 2648 Dihedral : 8.772 104.743 2936 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.59 % Allowed : 15.66 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.05 (0.20), residues: 1902 helix: 1.14 (0.16), residues: 1076 sheet: -2.20 (0.41), residues: 132 loop : -1.23 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 421 TYR 0.018 0.001 TYR A 646 PHE 0.016 0.001 PHE A 853 TRP 0.024 0.001 TRP B1014 HIS 0.003 0.001 HIS A 521 Details of bonding type rmsd covalent geometry : bond 0.00317 (15774) covalent geometry : angle 0.59177 (21506) SS BOND : bond 0.00281 ( 12) SS BOND : angle 1.09483 ( 24) hydrogen bonds : bond 0.03910 ( 802) hydrogen bonds : angle 4.48842 ( 2316) link_BETA1-4 : bond 0.00462 ( 6) link_BETA1-4 : angle 1.59649 ( 18) link_NAG-ASN : bond 0.00275 ( 14) link_NAG-ASN : angle 1.85004 ( 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 177 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 411 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8213 (mm) REVERT: A 457 TRP cc_start: 0.6512 (t-100) cc_final: 0.6002 (t-100) REVERT: A 664 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 707 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7692 (tp) REVERT: A 990 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8567 (mm) REVERT: A 1064 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6624 (mp0) REVERT: B 457 TRP cc_start: 0.6152 (t-100) cc_final: 0.5873 (t-100) REVERT: B 579 TYR cc_start: 0.8006 (m-80) cc_final: 0.7737 (m-80) REVERT: B 607 MET cc_start: 0.7588 (mpp) cc_final: 0.7360 (mpp) REVERT: B 990 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8153 (mm) REVERT: B 1064 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6594 (mp0) REVERT: B 1218 MET cc_start: 0.8345 (mmm) cc_final: 0.8011 (mmm) outliers start: 42 outliers final: 32 residues processed: 165 average time/residue: 0.1023 time to fit residues: 26.8289 Evaluate side-chains 165 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 104 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 125 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.147753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.109706 restraints weight = 21256.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110048 restraints weight = 15355.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110897 restraints weight = 12353.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111898 restraints weight = 11123.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112066 restraints weight = 9850.578| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15806 Z= 0.128 Angle : 0.597 12.282 21590 Z= 0.280 Chirality : 0.040 0.224 2550 Planarity : 0.004 0.053 2648 Dihedral : 8.595 104.349 2936 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.59 % Allowed : 16.21 % Favored : 81.20 % 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: 0.08 (0.20), residues: 1902 helix: 1.18 (0.16), residues: 1076 sheet: -2.44 (0.39), residues: 144 loop : -1.14 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 421 TYR 0.018 0.001 TYR A 646 PHE 0.012 0.001 PHE A 930 TRP 0.022 0.001 TRP B1014 HIS 0.003 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00297 (15774) covalent geometry : angle 0.59098 (21506) SS BOND : bond 0.00251 ( 12) SS BOND : angle 0.98046 ( 24) hydrogen bonds : bond 0.03848 ( 802) hydrogen bonds : angle 4.44171 ( 2316) link_BETA1-4 : bond 0.00489 ( 6) link_BETA1-4 : angle 1.50515 ( 18) link_NAG-ASN : bond 0.00252 ( 14) link_NAG-ASN : angle 1.73564 ( 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 177 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 411 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8178 (mm) REVERT: A 457 TRP cc_start: 0.6448 (t-100) cc_final: 0.5943 (t-100) REVERT: A 664 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.7999 (p) REVERT: A 707 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7708 (tp) REVERT: A 990 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8546 (mm) REVERT: A 1064 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6653 (mp0) REVERT: B 457 TRP cc_start: 0.6158 (t-100) cc_final: 0.5853 (t-100) REVERT: B 579 TYR cc_start: 0.8001 (m-80) cc_final: 0.7769 (m-80) REVERT: B 610 MET cc_start: 0.7024 (ttp) cc_final: 0.6774 (ttp) REVERT: B 990 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8149 (mm) REVERT: B 1064 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6628 (mp0) outliers start: 42 outliers final: 31 residues processed: 165 average time/residue: 0.1063 time to fit residues: 27.8754 Evaluate side-chains 167 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 54 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.109697 restraints weight = 21435.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.109599 restraints weight = 15611.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110350 restraints weight = 12478.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111296 restraints weight = 11587.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111646 restraints weight = 10182.791| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15806 Z= 0.132 Angle : 0.609 13.055 21590 Z= 0.285 Chirality : 0.040 0.223 2550 Planarity : 0.004 0.054 2648 Dihedral : 8.519 103.645 2936 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.34 % Allowed : 16.46 % Favored : 81.20 % 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: 0.10 (0.20), residues: 1902 helix: 1.18 (0.16), residues: 1076 sheet: -2.39 (0.39), residues: 144 loop : -1.11 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 421 TYR 0.018 0.001 TYR A 646 PHE 0.013 0.001 PHE A 791 TRP 0.021 0.001 TRP B1014 HIS 0.003 0.001 HIS A1053 Details of bonding type rmsd covalent geometry : bond 0.00309 (15774) covalent geometry : angle 0.60391 (21506) SS BOND : bond 0.00256 ( 12) SS BOND : angle 1.01374 ( 24) hydrogen bonds : bond 0.03861 ( 802) hydrogen bonds : angle 4.46654 ( 2316) link_BETA1-4 : bond 0.00443 ( 6) link_BETA1-4 : angle 1.47831 ( 18) link_NAG-ASN : bond 0.00250 ( 14) link_NAG-ASN : angle 1.64134 ( 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 168 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A 411 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8168 (mm) REVERT: A 457 TRP cc_start: 0.6437 (t-100) cc_final: 0.5939 (t-100) REVERT: A 664 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7973 (p) REVERT: A 707 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7691 (tp) REVERT: A 766 MET cc_start: 0.8166 (mmt) cc_final: 0.7735 (mmt) REVERT: A 814 LYS cc_start: 0.6333 (mmtm) cc_final: 0.5925 (tppt) REVERT: A 990 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 1064 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6690 (mp0) REVERT: A 1143 LEU cc_start: 0.8047 (tp) cc_final: 0.7826 (tt) REVERT: A 1147 MET cc_start: 0.8429 (mtm) cc_final: 0.8177 (mtt) REVERT: B 457 TRP cc_start: 0.6152 (t-100) cc_final: 0.5847 (t-100) REVERT: B 579 TYR cc_start: 0.8007 (m-80) cc_final: 0.7743 (m-80) REVERT: B 990 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8153 (mm) REVERT: B 1064 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6630 (mp0) outliers start: 38 outliers final: 32 residues processed: 156 average time/residue: 0.1021 time to fit residues: 25.5367 Evaluate side-chains 164 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 664 SER Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1212 VAL Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 155 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 159 optimal weight: 0.0010 chunk 144 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1104 GLN ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.148140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.110188 restraints weight = 21085.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111481 restraints weight = 15008.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112607 restraints weight = 11613.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113195 restraints weight = 10242.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113408 restraints weight = 9339.963| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15806 Z= 0.114 Angle : 0.589 12.684 21590 Z= 0.275 Chirality : 0.040 0.223 2550 Planarity : 0.004 0.053 2648 Dihedral : 8.347 103.354 2936 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.34 % Allowed : 16.58 % Favored : 81.07 % 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: 0.15 (0.20), residues: 1902 helix: 1.20 (0.16), residues: 1086 sheet: -2.31 (0.39), residues: 144 loop : -1.09 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 421 TYR 0.019 0.001 TYR A 646 PHE 0.013 0.001 PHE A 930 TRP 0.026 0.001 TRP B1014 HIS 0.002 0.001 HIS B1053 Details of bonding type rmsd covalent geometry : bond 0.00260 (15774) covalent geometry : angle 0.58382 (21506) SS BOND : bond 0.00257 ( 12) SS BOND : angle 1.01927 ( 24) hydrogen bonds : bond 0.03713 ( 802) hydrogen bonds : angle 4.40891 ( 2316) link_BETA1-4 : bond 0.00465 ( 6) link_BETA1-4 : angle 1.40039 ( 18) link_NAG-ASN : bond 0.00223 ( 14) link_NAG-ASN : angle 1.52984 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2142.42 seconds wall clock time: 37 minutes 53.01 seconds (2273.01 seconds total)