Starting phenix.real_space_refine on Tue Jun 17 02:57:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ki0_62361/06_2025/9ki0_62361.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ki0_62361/06_2025/9ki0_62361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ki0_62361/06_2025/9ki0_62361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ki0_62361/06_2025/9ki0_62361.map" model { file = "/net/cci-nas-00/data/ceres_data/9ki0_62361/06_2025/9ki0_62361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ki0_62361/06_2025/9ki0_62361.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.193 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 26 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 12207 2.51 5 N 3365 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19397 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9479 Classifications: {'peptide': 1173} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1139} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 9455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1171, 9455 Classifications: {'peptide': 1171} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1137} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 199 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.94, per 1000 atoms: 0.72 Number of scatterers: 19397 At special positions: 0 Unit cell: (144.358, 113.116, 134.662, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 26 15.00 Mg 2 11.99 O 3747 8.00 N 3365 7.00 C 12207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 4.8 seconds 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4472 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 24 sheets defined 56.6% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.691A pdb=" N GLU A 7 " --> pdb=" O SER A 4 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 9 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.548A pdb=" N SER A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 78 removed outlier: 3.521A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 181 through 209 removed outlier: 3.720A pdb=" N LYS A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 227 through 235 removed outlier: 4.043A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.722A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.619A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 401 through 433 Processing helix chain 'A' and resid 443 through 460 removed outlier: 4.670A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLU A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 475 Processing helix chain 'A' and resid 493 through 498 removed outlier: 3.530A pdb=" N THR A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.573A pdb=" N GLY A 536 " --> pdb=" O MET A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.558A pdb=" N GLY A 593 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.717A pdb=" N ALA A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.508A pdb=" N ILE A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 657 removed outlier: 3.936A pdb=" N SER A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 647 " --> pdb=" O TRP A 643 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 693 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.523A pdb=" N SER A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 737 Processing helix chain 'A' and resid 789 through 808 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 827 through 836 Processing helix chain 'A' and resid 838 through 854 removed outlier: 3.908A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 874 through 880 removed outlier: 3.533A pdb=" N GLU A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.736A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 901 Processing helix chain 'A' and resid 909 through 938 Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 992 through 996 removed outlier: 4.001A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1002 No H-bonds generated for 'chain 'A' and resid 1000 through 1002' Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1014 through 1020 Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.701A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1051 Processing helix chain 'A' and resid 1052 through 1069 Processing helix chain 'A' and resid 1077 through 1081 removed outlier: 3.636A pdb=" N TYR A1081 " --> pdb=" O ASN A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1127 removed outlier: 4.134A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.805A pdb=" N THR B 9 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 removed outlier: 3.732A pdb=" N SER B 29 " --> pdb=" O VAL B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 77 Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 146 through 157 Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.584A pdb=" N GLN B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 186 removed outlier: 3.855A pdb=" N LYS B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE B 186 " --> pdb=" O PRO B 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 181 through 186' Processing helix chain 'B' and resid 188 through 209 removed outlier: 3.633A pdb=" N GLY B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.993A pdb=" N LYS B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.728A pdb=" N GLN B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 401 through 435 removed outlier: 3.545A pdb=" N GLY B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 460 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 474 Processing helix chain 'B' and resid 475 through 478 Processing helix chain 'B' and resid 493 through 497 removed outlier: 3.692A pdb=" N HIS B 496 " --> pdb=" O SER B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 536 removed outlier: 3.646A pdb=" N GLY B 536 " --> pdb=" O MET B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 589 through 593 removed outlier: 3.837A pdb=" N GLY B 593 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 616 removed outlier: 3.842A pdb=" N LEU B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 629 Processing helix chain 'B' and resid 636 through 657 removed outlier: 3.909A pdb=" N SER B 645 " --> pdb=" O ARG B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 674 No H-bonds generated for 'chain 'B' and resid 672 through 674' Processing helix chain 'B' and resid 675 through 694 Processing helix chain 'B' and resid 704 through 711 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 737 Processing helix chain 'B' and resid 747 through 751 Processing helix chain 'B' and resid 789 through 808 Processing helix chain 'B' and resid 811 through 824 Processing helix chain 'B' and resid 827 through 836 Processing helix chain 'B' and resid 838 through 854 removed outlier: 3.980A pdb=" N GLN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 874 through 880 Processing helix chain 'B' and resid 889 through 903 removed outlier: 3.906A pdb=" N GLY B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 939 Processing helix chain 'B' and resid 943 through 960 Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 992 through 996 removed outlier: 4.022A pdb=" N PHE B 996 " --> pdb=" O PRO B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1002 No H-bonds generated for 'chain 'B' and resid 1000 through 1002' Processing helix chain 'B' and resid 1014 through 1020 Processing helix chain 'B' and resid 1023 through 1032 removed outlier: 3.840A pdb=" N TRP B1027 " --> pdb=" O TYR B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1052 Processing helix chain 'B' and resid 1052 through 1068 removed outlier: 3.682A pdb=" N ALA B1068 " --> pdb=" O ALA B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1081 removed outlier: 3.718A pdb=" N TYR B1081 " --> pdb=" O ASN B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1127 Processing helix chain 'B' and resid 1155 through 1159 Processing helix chain 'B' and resid 1176 through 1190 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 47 removed outlier: 6.567A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.411A pdb=" N ALA A 341 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE A 385 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.950A pdb=" N VAL A 595 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU A 868 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N THR A 597 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 870 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS A 599 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY A 702 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N THR A 732 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 744 through 745 Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 962 through 963 removed outlier: 4.020A pdb=" N ASN A1042 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 997 through 998 removed outlier: 3.519A pdb=" N TYR A 983 " --> pdb=" O VAL A1008 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1086 through 1088 removed outlier: 3.993A pdb=" N ILE A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE A1131 " --> pdb=" O ILE A1162 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE A1164 " --> pdb=" O PHE A1131 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TYR A1133 " --> pdb=" O ILE A1164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1137 through 1138 removed outlier: 3.626A pdb=" N GLY A1138 " --> pdb=" O ILE A1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 43 through 47 removed outlier: 6.568A pdb=" N LEU B 88 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU B 242 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR B 90 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AB6, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AB8, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.350A pdb=" N ALA B 341 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE B 385 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 343 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N SER B 387 " --> pdb=" O ASN B 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 595 through 601 removed outlier: 6.718A pdb=" N VAL B 595 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LEU B 868 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N THR B 597 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 870 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LYS B 599 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 774 " --> pdb=" O PHE B 869 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASP B 871 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU B 776 " --> pdb=" O ASP B 871 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 702 " --> pdb=" O PHE B 730 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N THR B 732 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 744 through 745 Processing sheet with id=AC2, first strand: chain 'B' and resid 755 through 757 Processing sheet with id=AC3, first strand: chain 'B' and resid 962 through 963 removed outlier: 3.713A pdb=" N ASN B1042 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 997 through 998 Processing sheet with id=AC5, first strand: chain 'B' and resid 1071 through 1074 removed outlier: 3.525A pdb=" N VAL B1134 " --> pdb=" O ASP B1100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1137 through 1138 removed outlier: 3.788A pdb=" N GLY B1138 " --> pdb=" O ILE B1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 1004 hydrogen bonds defined for protein. 2859 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: 18.08 Time building geometry restraints manager: 7.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.33: 4670 1.33 - 1.51: 7543 1.51 - 1.69: 7524 1.69 - 1.87: 76 1.87 - 2.05: 2 Bond restraints: 19815 Sorted by residual: bond pdb=" C4 AGS B1301 " pdb=" C5 AGS B1301 " ideal model delta sigma weight residual 1.386 1.459 -0.073 1.00e-02 1.00e+04 5.26e+01 bond pdb=" C5 AGS B1301 " pdb=" N7 AGS B1301 " ideal model delta sigma weight residual 1.387 1.318 0.069 1.00e-02 1.00e+04 4.81e+01 bond pdb=" C4 AGS A1301 " pdb=" N9 AGS A1301 " ideal model delta sigma weight residual 1.374 1.306 0.068 1.00e-02 1.00e+04 4.64e+01 bond pdb=" C ARG A 830 " pdb=" O ARG A 830 " ideal model delta sigma weight residual 1.237 1.149 0.087 1.31e-02 5.83e+03 4.42e+01 bond pdb=" C5 AGS A1301 " pdb=" N7 AGS A1301 " ideal model delta sigma weight residual 1.387 1.321 0.066 1.00e-02 1.00e+04 4.39e+01 ... (remaining 19810 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 26753 3.76 - 7.52: 96 7.52 - 11.29: 16 11.29 - 15.05: 2 15.05 - 18.81: 2 Bond angle restraints: 26869 Sorted by residual: angle pdb=" C5 AGS B1301 " pdb=" C4 AGS B1301 " pdb=" N3 AGS B1301 " ideal model delta sigma weight residual 126.80 119.35 7.45 7.41e-01 1.82e+00 1.01e+02 angle pdb=" C5 AGS A1301 " pdb=" C4 AGS A1301 " pdb=" N3 AGS A1301 " ideal model delta sigma weight residual 126.80 119.41 7.39 7.41e-01 1.82e+00 9.95e+01 angle pdb=" N GLY B 476 " pdb=" CA GLY B 476 " pdb=" C GLY B 476 " ideal model delta sigma weight residual 114.66 105.23 9.43 1.24e+00 6.50e-01 5.78e+01 angle pdb=" C4 AGS A1301 " pdb=" C5 AGS A1301 " pdb=" N7 AGS A1301 " ideal model delta sigma weight residual 110.73 107.40 3.33 4.52e-01 4.89e+00 5.41e+01 angle pdb=" N3 AGS B1301 " pdb=" C4 AGS B1301 " pdb=" N9 AGS B1301 " ideal model delta sigma weight residual 127.16 134.69 -7.53 1.06e+00 8.92e-01 5.06e+01 ... (remaining 26864 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.50: 10913 28.50 - 57.00: 887 57.00 - 85.50: 87 85.50 - 114.00: 8 114.00 - 142.50: 2 Dihedral angle restraints: 11897 sinusoidal: 5005 harmonic: 6892 Sorted by residual: dihedral pdb=" CA PHE B 520 " pdb=" C PHE B 520 " pdb=" N LEU B 521 " pdb=" CA LEU B 521 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" O1A AGS A1301 " pdb=" O3A AGS A1301 " pdb=" PA AGS A1301 " pdb=" PB AGS A1301 " ideal model delta sinusoidal sigma weight residual -67.73 74.77 -142.50 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" O1A AGS B1301 " pdb=" O3A AGS B1301 " pdb=" PA AGS B1301 " pdb=" PB AGS B1301 " ideal model delta sinusoidal sigma weight residual -67.73 61.99 -129.72 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 11894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2606 0.059 - 0.117: 327 0.117 - 0.175: 26 0.175 - 0.234: 2 0.234 - 0.292: 2 Chirality restraints: 2963 Sorted by residual: chirality pdb=" CA LEU B 477 " pdb=" N LEU B 477 " pdb=" C LEU B 477 " pdb=" CB LEU B 477 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" PB AGS A1301 " pdb=" O2B AGS A1301 " pdb=" O3A AGS A1301 " pdb=" O3B AGS A1301 " both_signs ideal model delta sigma weight residual True 3.18 -2.93 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" PB AGS B1301 " pdb=" O2B AGS B1301 " pdb=" O3A AGS B1301 " pdb=" O3B AGS B1301 " both_signs ideal model delta sigma weight residual True 3.18 2.97 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2960 not shown) Planarity restraints: 3410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 475 " 0.573 9.50e-02 1.11e+02 2.57e-01 4.05e+01 pdb=" NE ARG B 475 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG B 475 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 475 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 475 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 478 " -0.417 9.50e-02 1.11e+02 1.87e-01 2.14e+01 pdb=" NE ARG B 478 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 478 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 478 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 478 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 829 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.31e+01 pdb=" C GLU A 829 " 0.063 2.00e-02 2.50e+03 pdb=" O GLU A 829 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG A 830 " -0.022 2.00e-02 2.50e+03 ... (remaining 3407 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 178 2.60 - 3.18: 15785 3.18 - 3.75: 30150 3.75 - 4.33: 43777 4.33 - 4.90: 71780 Nonbonded interactions: 161670 Sorted by model distance: nonbonded pdb=" O3G AGS B1301 " pdb="MG MG B1302 " model vdw 2.030 2.170 nonbonded pdb=" OG1 THR B 979 " pdb=" O TYR B 982 " model vdw 2.058 3.040 nonbonded pdb=" O3G AGS A1301 " pdb="MG MG A1302 " model vdw 2.078 2.170 nonbonded pdb=" OD1 ASP A 770 " pdb=" OG1 THR A 859 " model vdw 2.089 3.040 nonbonded pdb=" O CYS A1013 " pdb=" OH TYR A1103 " model vdw 2.126 3.040 ... (remaining 161665 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 77 or resid 83 through 390 or resid 398 through \ 436 or resid 441 through 1190 or resid 1301 through 1302)) selection = (chain 'B' and (resid 1 through 478 or resid 485 through 1190 or resid 1301 thro \ ugh 1302)) } ncs_group { reference = (chain 'C' and resid 3 through 11) selection = (chain 'D' and resid 2 through 10) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 52.320 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: 0.030 Extract box with map and model: 5.650 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 63.900 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.120 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: 0.020 Load rotamer database and sin/cos tables:77.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.004 0.106 19815 Z= 0.263 Angle : 0.693 18.809 26869 Z= 0.400 Chirality : 0.040 0.292 2963 Planarity : 0.008 0.257 3410 Dihedral : 19.127 142.501 7425 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.04 % Favored : 95.87 % Rotamer: Outliers : 2.12 % Allowed : 25.52 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2324 helix: -0.17 (0.14), residues: 1157 sheet: 0.11 (0.31), residues: 301 loop : -0.75 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 643 HIS 0.007 0.001 HIS A 178 PHE 0.013 0.001 PHE B 607 TYR 0.012 0.001 TYR B1081 ARG 0.010 0.001 ARG B 432 Details of bonding type rmsd hydrogen bonds : bond 0.15145 ( 1004) hydrogen bonds : angle 6.34096 ( 2859) covalent geometry : bond 0.00441 (19815) covalent geometry : angle 0.69311 (26869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 3.351 Fit side-chains revert: symmetry clash REVERT: A 162 GLU cc_start: 0.6816 (tt0) cc_final: 0.6558 (tt0) REVERT: A 375 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8480 (ptpt) REVERT: A 531 ASP cc_start: 0.8352 (m-30) cc_final: 0.8058 (m-30) REVERT: A 830 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7495 (mmm160) REVERT: B 1040 GLU cc_start: 0.5974 (mm-30) cc_final: 0.5535 (mm-30) outliers start: 44 outliers final: 35 residues processed: 249 average time/residue: 2.0972 time to fit residues: 589.4560 Evaluate side-chains 234 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 5.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 491 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 770 ASP Chi-restraints excluded: chain A residue 830 ARG Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 760 ASP Chi-restraints excluded: chain B residue 770 ASP Chi-restraints excluded: chain B residue 809 GLU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 901 SER Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1104 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 0.4980 chunk 184 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN A 166 GLN A 178 HIS A 486 ASN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 660 ASN A 676 GLN A 805 GLN A 833 GLN ** A1106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 65 GLN B 178 HIS B 496 HIS B 588 ASN B 592 ASN B 676 GLN B 741 ASN B 807 ASN B 939 ASN B 940 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.181681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117028 restraints weight = 20046.925| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.14 r_work: 0.3121 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19815 Z= 0.194 Angle : 0.570 6.878 26869 Z= 0.304 Chirality : 0.041 0.163 2963 Planarity : 0.004 0.046 3410 Dihedral : 11.231 154.764 2858 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 4.29 % Allowed : 22.48 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2324 helix: 1.31 (0.15), residues: 1168 sheet: 0.05 (0.31), residues: 302 loop : -0.67 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 643 HIS 0.008 0.001 HIS A 496 PHE 0.017 0.002 PHE B 607 TYR 0.010 0.002 TYR B 982 ARG 0.008 0.001 ARG B 478 Details of bonding type rmsd hydrogen bonds : bond 0.05825 ( 1004) hydrogen bonds : angle 4.67959 ( 2859) covalent geometry : bond 0.00457 (19815) covalent geometry : angle 0.56953 (26869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 201 time to evaluate : 2.175 Fit side-chains revert: symmetry clash REVERT: A 56 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8193 (m) REVERT: A 76 LYS cc_start: 0.6237 (mmtp) cc_final: 0.6037 (ttpp) REVERT: A 162 GLU cc_start: 0.7209 (tt0) cc_final: 0.6970 (tt0) REVERT: A 197 ARG cc_start: 0.8316 (ttm170) cc_final: 0.7788 (ttm170) REVERT: A 663 MET cc_start: 0.8175 (ttm) cc_final: 0.7836 (ttt) REVERT: A 833 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8578 (tt0) REVERT: A 952 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6441 (m-30) REVERT: A 954 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6694 (mtp85) REVERT: A 1170 ASP cc_start: 0.5349 (OUTLIER) cc_final: 0.4749 (p0) REVERT: B 314 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7990 (ttm-80) REVERT: B 445 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7734 (tt0) outliers start: 89 outliers final: 32 residues processed: 267 average time/residue: 1.6298 time to fit residues: 483.9900 Evaluate side-chains 229 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 915 LEU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 954 ARG Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 1035 CYS Chi-restraints excluded: chain B residue 1104 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 186 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 174 optimal weight: 0.1980 chunk 153 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 HIS ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN A 817 ASN A 833 GLN A1086 ASN ** A1106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 65 GLN B 178 HIS B 588 ASN B1022 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.120858 restraints weight = 19875.928| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.43 r_work: 0.3121 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19815 Z= 0.132 Angle : 0.497 5.802 26869 Z= 0.268 Chirality : 0.039 0.161 2963 Planarity : 0.003 0.044 3410 Dihedral : 10.774 155.766 2816 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.75 % Favored : 97.12 % Rotamer: Outliers : 3.80 % Allowed : 22.68 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2324 helix: 1.94 (0.15), residues: 1156 sheet: 0.04 (0.31), residues: 296 loop : -0.65 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 643 HIS 0.004 0.001 HIS A 496 PHE 0.017 0.001 PHE B 607 TYR 0.011 0.001 TYR A 582 ARG 0.007 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04779 ( 1004) hydrogen bonds : angle 4.39424 ( 2859) covalent geometry : bond 0.00297 (19815) covalent geometry : angle 0.49728 (26869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 209 time to evaluate : 2.021 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.5944 (mmtp) cc_final: 0.5639 (ttpp) REVERT: A 162 GLU cc_start: 0.7273 (tt0) cc_final: 0.7033 (tt0) REVERT: A 177 ARG cc_start: 0.7390 (mtt180) cc_final: 0.7172 (ptp-110) REVERT: A 197 ARG cc_start: 0.8347 (ttm170) cc_final: 0.8073 (tmm-80) REVERT: A 574 GLU cc_start: 0.6925 (tm-30) cc_final: 0.6717 (tm-30) REVERT: A 632 ILE cc_start: 0.6024 (OUTLIER) cc_final: 0.5742 (mp) REVERT: A 663 MET cc_start: 0.8185 (ttm) cc_final: 0.7858 (ttt) REVERT: A 720 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7433 (mt) REVERT: A 778 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7588 (tttt) REVERT: A 833 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: A 1170 ASP cc_start: 0.5436 (OUTLIER) cc_final: 0.4823 (p0) REVERT: B 5 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7862 (mt) REVERT: B 445 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7694 (tt0) REVERT: B 709 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6162 (ptp90) REVERT: B 751 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.4533 (mp0) REVERT: B 980 LYS cc_start: 0.7865 (tppt) cc_final: 0.7477 (tppp) REVERT: B 1039 LYS cc_start: 0.7375 (mmpt) cc_final: 0.7165 (mmmt) REVERT: B 1147 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5850 (pt) outliers start: 79 outliers final: 35 residues processed: 269 average time/residue: 1.4870 time to fit residues: 450.3653 Evaluate side-chains 237 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 809 GLU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 930 ILE Chi-restraints excluded: chain B residue 1147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 225 optimal weight: 0.3980 chunk 80 optimal weight: 0.9980 chunk 232 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN A 496 HIS A 588 ASN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 807 ASN A 833 GLN ** A1106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 ASN B 178 HIS B 588 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.182245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117716 restraints weight = 20126.709| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.94 r_work: 0.3126 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 19815 Z= 0.175 Angle : 0.530 6.238 26869 Z= 0.282 Chirality : 0.040 0.148 2963 Planarity : 0.004 0.042 3410 Dihedral : 10.794 154.900 2810 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.10 % Favored : 96.77 % Rotamer: Outliers : 4.33 % Allowed : 22.44 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.17), residues: 2324 helix: 1.98 (0.15), residues: 1166 sheet: 0.03 (0.31), residues: 302 loop : -0.59 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 643 HIS 0.006 0.001 HIS A 496 PHE 0.018 0.001 PHE B 607 TYR 0.010 0.001 TYR B 982 ARG 0.007 0.000 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 1004) hydrogen bonds : angle 4.32563 ( 2859) covalent geometry : bond 0.00411 (19815) covalent geometry : angle 0.53029 (26869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 202 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.6243 (mmtp) cc_final: 0.6024 (ttpp) REVERT: A 185 LYS cc_start: 0.6846 (mmmt) cc_final: 0.6201 (mmtp) REVERT: A 197 ARG cc_start: 0.8442 (ttm170) cc_final: 0.8195 (tmm-80) REVERT: A 590 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7397 (ttpp) REVERT: A 632 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5899 (mp) REVERT: A 663 MET cc_start: 0.8354 (ttm) cc_final: 0.8053 (ttt) REVERT: A 720 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7637 (mt) REVERT: A 778 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7795 (tttt) REVERT: A 1170 ASP cc_start: 0.5567 (OUTLIER) cc_final: 0.4894 (p0) REVERT: B 306 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8438 (m-30) REVERT: B 445 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: B 709 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6363 (ptp90) REVERT: B 751 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.4747 (mp0) REVERT: B 969 ARG cc_start: 0.7742 (mmm160) cc_final: 0.7392 (mmt-90) REVERT: B 980 LYS cc_start: 0.8042 (tppt) cc_final: 0.7623 (tppp) REVERT: B 1147 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5905 (pt) outliers start: 90 outliers final: 40 residues processed: 267 average time/residue: 1.4412 time to fit residues: 430.6416 Evaluate side-chains 242 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 778 LYS Chi-restraints excluded: chain A residue 826 MET Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 283 SER Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 809 GLU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 952 ASP Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 95 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 227 optimal weight: 0.7980 chunk 183 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 147 optimal weight: 0.0370 chunk 19 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN A1086 ASN A1106 HIS B 178 HIS B 588 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.182925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.125650 restraints weight = 20189.730| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.26 r_work: 0.3141 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19815 Z= 0.112 Angle : 0.468 5.748 26869 Z= 0.253 Chirality : 0.038 0.141 2963 Planarity : 0.003 0.041 3410 Dihedral : 10.531 155.209 2809 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 3.23 % Allowed : 23.21 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2324 helix: 2.30 (0.15), residues: 1160 sheet: 0.04 (0.31), residues: 296 loop : -0.53 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 643 HIS 0.004 0.001 HIS A1106 PHE 0.015 0.001 PHE B 607 TYR 0.010 0.001 TYR A 582 ARG 0.009 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 1004) hydrogen bonds : angle 4.13526 ( 2859) covalent geometry : bond 0.00245 (19815) covalent geometry : angle 0.46787 (26869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 210 time to evaluate : 1.992 Fit side-chains REVERT: A 76 LYS cc_start: 0.6102 (mmtp) cc_final: 0.5875 (ttpp) REVERT: A 162 GLU cc_start: 0.6984 (tt0) cc_final: 0.6443 (tt0) REVERT: A 163 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6362 (ttp80) REVERT: A 197 ARG cc_start: 0.8496 (tmm160) cc_final: 0.8262 (tmm-80) REVERT: A 448 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8085 (t80) REVERT: A 590 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7500 (ttpp) REVERT: A 632 ILE cc_start: 0.6276 (OUTLIER) cc_final: 0.5929 (mp) REVERT: A 663 MET cc_start: 0.8313 (ttm) cc_final: 0.8010 (ttt) REVERT: A 824 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7227 (mpm) REVERT: A 965 PHE cc_start: 0.6416 (t80) cc_final: 0.6159 (t80) REVERT: A 1170 ASP cc_start: 0.5656 (OUTLIER) cc_final: 0.5023 (p0) REVERT: B 371 LYS cc_start: 0.8350 (mttm) cc_final: 0.8054 (mttm) REVERT: B 709 ARG cc_start: 0.6881 (OUTLIER) cc_final: 0.6364 (ptp90) REVERT: B 751 GLU cc_start: 0.6407 (OUTLIER) cc_final: 0.4850 (mp0) REVERT: B 949 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: B 980 LYS cc_start: 0.8094 (tppt) cc_final: 0.7642 (tppp) REVERT: B 1147 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5751 (pt) outliers start: 67 outliers final: 31 residues processed: 257 average time/residue: 1.5225 time to fit residues: 435.6219 Evaluate side-chains 236 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 952 ASP Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1086 ASN Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 809 GLU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 949 GLU Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1147 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 147 optimal weight: 0.3980 chunk 69 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 215 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN A1086 ASN B 588 ASN B 986 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.185503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127025 restraints weight = 19962.550| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.40 r_work: 0.3162 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19815 Z= 0.104 Angle : 0.460 6.087 26869 Z= 0.248 Chirality : 0.038 0.139 2963 Planarity : 0.003 0.041 3410 Dihedral : 10.383 154.467 2808 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Rotamer: Outliers : 3.71 % Allowed : 23.01 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2324 helix: 2.41 (0.15), residues: 1169 sheet: 0.05 (0.31), residues: 296 loop : -0.45 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 643 HIS 0.003 0.001 HIS A1106 PHE 0.014 0.001 PHE B 607 TYR 0.009 0.001 TYR A 582 ARG 0.011 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1004) hydrogen bonds : angle 4.03048 ( 2859) covalent geometry : bond 0.00225 (19815) covalent geometry : angle 0.45983 (26869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 209 time to evaluate : 2.052 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: A 76 LYS cc_start: 0.6152 (mmtp) cc_final: 0.5863 (ttpp) REVERT: A 162 GLU cc_start: 0.7098 (tt0) cc_final: 0.6284 (tm-30) REVERT: A 197 ARG cc_start: 0.8412 (tmm160) cc_final: 0.8167 (tmm-80) REVERT: A 202 ARG cc_start: 0.7503 (mtt90) cc_final: 0.7256 (mtt-85) REVERT: A 371 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7945 (mttm) REVERT: A 448 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.8093 (t80) REVERT: A 590 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7351 (ttpp) REVERT: A 632 ILE cc_start: 0.6318 (OUTLIER) cc_final: 0.5986 (mp) REVERT: A 824 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7287 (mpm) REVERT: A 913 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7095 (ttm170) REVERT: A 959 ARG cc_start: 0.6530 (ttm-80) cc_final: 0.6305 (mtm-85) REVERT: A 965 PHE cc_start: 0.6395 (t80) cc_final: 0.6102 (t80) REVERT: A 1170 ASP cc_start: 0.5678 (OUTLIER) cc_final: 0.5118 (p0) REVERT: B 126 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: B 265 SER cc_start: 0.8982 (t) cc_final: 0.8620 (m) REVERT: B 371 LYS cc_start: 0.8339 (mttm) cc_final: 0.8022 (mttm) REVERT: B 709 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6209 (ptp90) REVERT: B 751 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.4798 (mp0) REVERT: B 949 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6782 (tm-30) REVERT: B 980 LYS cc_start: 0.8149 (tppt) cc_final: 0.7680 (tppp) REVERT: B 1102 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6322 (tppp) REVERT: B 1147 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5730 (pt) outliers start: 77 outliers final: 31 residues processed: 265 average time/residue: 1.4656 time to fit residues: 436.9781 Evaluate side-chains 236 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 520 PHE Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 809 GLU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 949 GLU Chi-restraints excluded: chain B residue 1102 LYS Chi-restraints excluded: chain B residue 1147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 149 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 72 optimal weight: 0.0970 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN A 166 GLN A 288 GLN A 588 ASN ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN B 588 ASN B 822 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.181558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117264 restraints weight = 19805.768| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.91 r_work: 0.3108 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 19815 Z= 0.222 Angle : 0.564 7.250 26869 Z= 0.297 Chirality : 0.042 0.147 2963 Planarity : 0.004 0.041 3410 Dihedral : 10.592 152.055 2802 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.31 % Favored : 96.60 % Rotamer: Outliers : 4.14 % Allowed : 22.82 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.17), residues: 2324 helix: 2.04 (0.15), residues: 1169 sheet: 0.05 (0.32), residues: 294 loop : -0.61 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 643 HIS 0.005 0.001 HIS A 496 PHE 0.020 0.002 PHE B 607 TYR 0.012 0.002 TYR B 582 ARG 0.011 0.001 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.05459 ( 1004) hydrogen bonds : angle 4.24804 ( 2859) covalent geometry : bond 0.00532 (19815) covalent geometry : angle 0.56419 (26869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 188 time to evaluate : 2.116 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: A 76 LYS cc_start: 0.6090 (mmtp) cc_final: 0.5824 (ttpp) REVERT: A 162 GLU cc_start: 0.6981 (tt0) cc_final: 0.6282 (tm-30) REVERT: A 185 LYS cc_start: 0.6808 (mmmt) cc_final: 0.6142 (mmtp) REVERT: A 197 ARG cc_start: 0.8411 (tmm160) cc_final: 0.8095 (ttp-170) REVERT: A 590 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7434 (ttpp) REVERT: A 632 ILE cc_start: 0.6221 (OUTLIER) cc_final: 0.5948 (mp) REVERT: A 663 MET cc_start: 0.8369 (ttm) cc_final: 0.8074 (ttt) REVERT: A 824 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7294 (mpm) REVERT: A 913 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7236 (ttm170) REVERT: A 965 PHE cc_start: 0.6496 (t80) cc_final: 0.6192 (t80) REVERT: A 969 ARG cc_start: 0.7424 (mmt-90) cc_final: 0.7222 (mmt-90) REVERT: A 1105 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.6054 (ttpp) REVERT: A 1170 ASP cc_start: 0.5702 (OUTLIER) cc_final: 0.5082 (p0) REVERT: B 126 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: B 371 LYS cc_start: 0.8383 (mttm) cc_final: 0.8007 (mttm) REVERT: B 709 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6372 (ptp90) REVERT: B 751 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.4907 (mp0) REVERT: B 969 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7568 (mmt-90) REVERT: B 976 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8073 (mt0) REVERT: B 980 LYS cc_start: 0.8056 (tppt) cc_final: 0.7488 (tppp) REVERT: B 1147 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5740 (pt) outliers start: 86 outliers final: 43 residues processed: 255 average time/residue: 1.5254 time to fit residues: 433.8416 Evaluate side-chains 238 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 562 GLU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1104 TRP Chi-restraints excluded: chain A residue 1105 LYS Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 361 SER Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 809 GLU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 952 ASP Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 976 GLN Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 227 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN A 288 GLN A 637 GLN A 822 GLN B 588 ASN B 822 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.184213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.123454 restraints weight = 19873.281| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.26 r_work: 0.3137 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19815 Z= 0.114 Angle : 0.480 5.705 26869 Z= 0.260 Chirality : 0.038 0.142 2963 Planarity : 0.003 0.048 3410 Dihedral : 10.415 153.666 2802 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 3.08 % Allowed : 23.93 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2324 helix: 2.32 (0.15), residues: 1170 sheet: 0.06 (0.31), residues: 296 loop : -0.55 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 643 HIS 0.003 0.001 HIS A 496 PHE 0.023 0.001 PHE A 425 TYR 0.010 0.001 TYR A 582 ARG 0.011 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 1004) hydrogen bonds : angle 4.08631 ( 2859) covalent geometry : bond 0.00250 (19815) covalent geometry : angle 0.48040 (26869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 193 time to evaluate : 2.160 Fit side-chains REVERT: A 6 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6773 (mp0) REVERT: A 76 LYS cc_start: 0.6037 (mmtp) cc_final: 0.5784 (ttpp) REVERT: A 185 LYS cc_start: 0.6723 (mmmt) cc_final: 0.6084 (mmtp) REVERT: A 197 ARG cc_start: 0.8410 (tmm160) cc_final: 0.8156 (tmm-80) REVERT: A 448 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.8099 (t80) REVERT: A 590 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7396 (ttpp) REVERT: A 632 ILE cc_start: 0.6158 (OUTLIER) cc_final: 0.5849 (mp) REVERT: A 663 MET cc_start: 0.8286 (ttm) cc_final: 0.7975 (ttt) REVERT: A 824 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7210 (mpm) REVERT: A 833 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8676 (tt0) REVERT: A 913 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7098 (ttm170) REVERT: A 965 PHE cc_start: 0.6451 (t80) cc_final: 0.6101 (t80) REVERT: A 969 ARG cc_start: 0.7484 (mmt-90) cc_final: 0.7253 (mmt-90) REVERT: A 1104 TRP cc_start: 0.5577 (OUTLIER) cc_final: 0.3742 (p90) REVERT: A 1170 ASP cc_start: 0.5826 (OUTLIER) cc_final: 0.5278 (p0) REVERT: B 126 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: B 371 LYS cc_start: 0.8371 (mttm) cc_final: 0.8004 (mttm) REVERT: B 448 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8200 (t80) REVERT: B 693 PHE cc_start: 0.7099 (m-80) cc_final: 0.6638 (m-80) REVERT: B 709 ARG cc_start: 0.6858 (OUTLIER) cc_final: 0.6339 (ptp90) REVERT: B 751 GLU cc_start: 0.6380 (OUTLIER) cc_final: 0.4880 (mp0) REVERT: B 959 ARG cc_start: 0.6615 (mtm-85) cc_final: 0.6334 (mtm-85) REVERT: B 969 ARG cc_start: 0.7829 (mmm-85) cc_final: 0.7592 (mmt-90) REVERT: B 976 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: B 980 LYS cc_start: 0.8038 (tppt) cc_final: 0.7557 (tppp) REVERT: B 1006 ASP cc_start: 0.7993 (m-30) cc_final: 0.7773 (m-30) REVERT: B 1147 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5698 (pt) outliers start: 64 outliers final: 34 residues processed: 245 average time/residue: 1.4150 time to fit residues: 388.1312 Evaluate side-chains 242 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1104 TRP Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 448 PHE Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 809 GLU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 976 GLN Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 197 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN A 166 GLN A 822 GLN B 588 ASN B 822 GLN B 923 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.181166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121855 restraints weight = 19951.443| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.31 r_work: 0.3054 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 19815 Z= 0.240 Angle : 0.585 7.292 26869 Z= 0.307 Chirality : 0.043 0.147 2963 Planarity : 0.004 0.045 3410 Dihedral : 10.650 152.430 2802 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 3.56 % Allowed : 23.50 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2324 helix: 1.96 (0.15), residues: 1166 sheet: 0.01 (0.31), residues: 302 loop : -0.66 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 643 HIS 0.005 0.001 HIS A 496 PHE 0.021 0.002 PHE B 607 TYR 0.012 0.002 TYR B 582 ARG 0.009 0.001 ARG A 72 Details of bonding type rmsd hydrogen bonds : bond 0.05587 ( 1004) hydrogen bonds : angle 4.26505 ( 2859) covalent geometry : bond 0.00576 (19815) covalent geometry : angle 0.58539 (26869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 190 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: A 76 LYS cc_start: 0.6075 (mmtp) cc_final: 0.5863 (ttpp) REVERT: A 162 GLU cc_start: 0.6800 (tt0) cc_final: 0.6389 (tm-30) REVERT: A 185 LYS cc_start: 0.6899 (mmmt) cc_final: 0.6211 (mmtp) REVERT: A 283 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8583 (m) REVERT: A 288 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7636 (pt0) REVERT: A 590 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7443 (ttpp) REVERT: A 632 ILE cc_start: 0.6308 (OUTLIER) cc_final: 0.6045 (mp) REVERT: A 663 MET cc_start: 0.8351 (ttm) cc_final: 0.8049 (ttt) REVERT: A 718 LYS cc_start: 0.7923 (mtmp) cc_final: 0.7688 (mtmt) REVERT: A 824 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7214 (mpm) REVERT: A 833 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: A 913 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7191 (ttm170) REVERT: A 965 PHE cc_start: 0.6545 (t80) cc_final: 0.6189 (t80) REVERT: A 969 ARG cc_start: 0.7443 (mmt-90) cc_final: 0.7230 (mmt-90) REVERT: A 1105 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.6055 (ttpp) REVERT: A 1170 ASP cc_start: 0.5741 (OUTLIER) cc_final: 0.5122 (p0) REVERT: B 31 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7728 (ptpp) REVERT: B 126 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: B 371 LYS cc_start: 0.8347 (mttm) cc_final: 0.7980 (mttm) REVERT: B 693 PHE cc_start: 0.7274 (m-80) cc_final: 0.6795 (m-80) REVERT: B 709 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6359 (ptp90) REVERT: B 751 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.5031 (mp0) REVERT: B 969 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7515 (mmt-90) REVERT: B 980 LYS cc_start: 0.8004 (tppt) cc_final: 0.7544 (tppp) REVERT: B 1147 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5741 (pt) outliers start: 74 outliers final: 39 residues processed: 250 average time/residue: 1.4852 time to fit residues: 415.6417 Evaluate side-chains 238 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 880 GLU Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1104 TRP Chi-restraints excluded: chain A residue 1105 LYS Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 330 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 678 ILE Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 809 GLU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 952 ASP Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1104 TRP Chi-restraints excluded: chain B residue 1147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 22 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 195 optimal weight: 0.8980 chunk 173 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 GLN A 166 GLN A 747 ASN A 822 GLN B 588 ASN B 822 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.183601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118951 restraints weight = 19889.465| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.35 r_work: 0.3120 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19815 Z= 0.123 Angle : 0.496 8.070 26869 Z= 0.266 Chirality : 0.039 0.186 2963 Planarity : 0.003 0.042 3410 Dihedral : 10.486 153.642 2802 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.93 % Favored : 96.99 % Rotamer: Outliers : 2.74 % Allowed : 24.17 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2324 helix: 2.26 (0.15), residues: 1166 sheet: 0.02 (0.31), residues: 296 loop : -0.61 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 643 HIS 0.003 0.001 HIS B 496 PHE 0.016 0.001 PHE B 607 TYR 0.010 0.001 TYR A 582 ARG 0.010 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04380 ( 1004) hydrogen bonds : angle 4.10455 ( 2859) covalent geometry : bond 0.00274 (19815) covalent geometry : angle 0.49585 (26869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 193 time to evaluate : 1.985 Fit side-chains revert: symmetry clash REVERT: A 6 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: A 76 LYS cc_start: 0.5955 (mmtp) cc_final: 0.5701 (ttpp) REVERT: A 162 GLU cc_start: 0.7086 (tt0) cc_final: 0.6391 (tm-30) REVERT: A 185 LYS cc_start: 0.6656 (mmmt) cc_final: 0.6026 (mmtp) REVERT: A 197 ARG cc_start: 0.8300 (ttp80) cc_final: 0.8075 (ttp-170) REVERT: A 590 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7425 (ttpp) REVERT: A 632 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5740 (mp) REVERT: A 663 MET cc_start: 0.8245 (ttm) cc_final: 0.7943 (ttt) REVERT: A 718 LYS cc_start: 0.7604 (mtmp) cc_final: 0.7219 (mttt) REVERT: A 824 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7221 (mpm) REVERT: A 833 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: A 913 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7035 (ttm170) REVERT: A 965 PHE cc_start: 0.6471 (t80) cc_final: 0.6121 (t80) REVERT: A 969 ARG cc_start: 0.7360 (mmt-90) cc_final: 0.7127 (mmt-90) REVERT: A 1104 TRP cc_start: 0.5601 (OUTLIER) cc_final: 0.3791 (p90) REVERT: A 1170 ASP cc_start: 0.5675 (OUTLIER) cc_final: 0.5160 (p0) REVERT: B 37 ASN cc_start: 0.7324 (m-40) cc_final: 0.6952 (m110) REVERT: B 126 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: B 371 LYS cc_start: 0.8386 (mttm) cc_final: 0.8005 (mttm) REVERT: B 693 PHE cc_start: 0.7074 (m-80) cc_final: 0.6594 (m-80) REVERT: B 709 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6296 (ptp90) REVERT: B 751 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.4793 (mp0) REVERT: B 833 GLN cc_start: 0.8802 (tt0) cc_final: 0.8567 (tt0) REVERT: B 959 ARG cc_start: 0.6520 (mtm-85) cc_final: 0.6222 (mtm-85) REVERT: B 969 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7499 (mmt-90) REVERT: B 980 LYS cc_start: 0.7874 (tppt) cc_final: 0.7362 (tppp) REVERT: B 1147 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5701 (pt) outliers start: 57 outliers final: 34 residues processed: 239 average time/residue: 1.4568 time to fit residues: 389.1293 Evaluate side-chains 235 residues out of total 2079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 188 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 471 SER Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 824 MET Chi-restraints excluded: chain A residue 833 GLN Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 913 ARG Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1043 VAL Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain A residue 1104 TRP Chi-restraints excluded: chain A residue 1170 ASP Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 562 GLU Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 706 ASP Chi-restraints excluded: chain B residue 709 ARG Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 751 GLU Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 809 GLU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain B residue 872 SER Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 969 ARG Chi-restraints excluded: chain B residue 1047 ILE Chi-restraints excluded: chain B residue 1147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 153 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN A 817 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.183231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119621 restraints weight = 20067.614| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.44 r_work: 0.3103 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19815 Z= 0.143 Angle : 0.512 12.134 26869 Z= 0.272 Chirality : 0.039 0.141 2963 Planarity : 0.003 0.042 3410 Dihedral : 10.468 153.048 2802 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 2.79 % Allowed : 24.12 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2324 helix: 2.26 (0.15), residues: 1165 sheet: 0.03 (0.31), residues: 296 loop : -0.62 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 643 HIS 0.004 0.001 HIS A 496 PHE 0.017 0.001 PHE B 607 TYR 0.009 0.001 TYR B 582 ARG 0.010 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.04539 ( 1004) hydrogen bonds : angle 4.09231 ( 2859) covalent geometry : bond 0.00332 (19815) covalent geometry : angle 0.51153 (26869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18510.34 seconds wall clock time: 319 minutes 9.47 seconds (19149.47 seconds total)