Starting phenix.real_space_refine on Thu Mar 5 23:39:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ddw_27344/03_2026/8ddw_27344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddw_27344/03_2026/8ddw_27344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ddw_27344/03_2026/8ddw_27344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddw_27344/03_2026/8ddw_27344.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ddw_27344/03_2026/8ddw_27344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddw_27344/03_2026/8ddw_27344.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 175 5.16 5 C 16413 2.51 5 N 4530 2.21 5 O 4751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25869 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5576 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 20, 'TRANS': 674} Chain breaks: 5 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5576 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 20, 'TRANS': 674} Chain breaks: 5 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 5576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5576 Classifications: {'peptide': 695} Link IDs: {'PTRANS': 20, 'TRANS': 674} Chain breaks: 5 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 5765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 719, 5765 Classifications: {'peptide': 719} Link IDs: {'PTRANS': 23, 'TRANS': 695} Chain breaks: 5 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 2598 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} bond proxies already assigned to first conformer: 2631 Chain: "J" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Time building chain proxies: 6.08, per 1000 atoms: 0.24 Number of scatterers: 25869 At special positions: 0 Unit cell: (145.8, 190.08, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 175 16.00 O 4751 8.00 N 4530 7.00 C 16413 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: 1.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6134 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 14 sheets defined 55.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.674A pdb=" N LEU A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.930A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.802A pdb=" N HIS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 307 through 322 removed outlier: 4.320A pdb=" N LEU A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 322 " --> pdb=" O HIS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.700A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.648A pdb=" N LYS A 401 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 439 through 451 Processing helix chain 'A' and resid 455 through 467 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.683A pdb=" N ALA A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 500 through 510 Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.613A pdb=" N ILE A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.744A pdb=" N ASN A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 649 removed outlier: 4.100A pdb=" N GLU A 640 " --> pdb=" O PHE A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 4.006A pdb=" N GLN A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 685 Processing helix chain 'A' and resid 689 through 717 removed outlier: 3.589A pdb=" N GLN A 693 " --> pdb=" O ASP A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 removed outlier: 3.527A pdb=" N LEU A 725 " --> pdb=" O ALA A 721 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 727 " --> pdb=" O LYS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 removed outlier: 3.789A pdb=" N SER A 733 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 746 through 751 Processing helix chain 'A' and resid 752 through 761 removed outlier: 3.700A pdb=" N MET A 757 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 758 " --> pdb=" O CYS A 754 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1006 removed outlier: 3.568A pdb=" N TYR A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A1001 " --> pdb=" O GLY A 997 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A1002 " --> pdb=" O PRO A 998 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1003 " --> pdb=" O TYR A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1117 removed outlier: 3.608A pdb=" N THR A1117 " --> pdb=" O VAL A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1142 removed outlier: 4.668A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1215 Processing helix chain 'A' and resid 1215 through 1240 removed outlier: 3.965A pdb=" N ARG A1240 " --> pdb=" O GLU A1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.561A pdb=" N LEU B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 removed outlier: 4.101A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 242 removed outlier: 4.002A pdb=" N SER B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.622A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.730A pdb=" N LYS B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.966A pdb=" N LYS B 423 " --> pdb=" O GLU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.607A pdb=" N LEU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 467 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.598A pdb=" N ALA B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 499 removed outlier: 3.753A pdb=" N VAL B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 536 through 545 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.658A pdb=" N ILE B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 636 through 648 removed outlier: 4.313A pdb=" N GLU B 640 " --> pdb=" O PHE B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.938A pdb=" N GLN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 685 Processing helix chain 'B' and resid 689 through 717 removed outlier: 4.320A pdb=" N GLN B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 729 through 733 removed outlier: 4.163A pdb=" N SER B 733 " --> pdb=" O LYS B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 745 Processing helix chain 'B' and resid 746 through 752 Processing helix chain 'B' and resid 752 through 762 removed outlier: 3.752A pdb=" N LEU B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 761 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET B 762 " --> pdb=" O LEU B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1007 Processing helix chain 'B' and resid 1110 through 1117 Processing helix chain 'B' and resid 1118 through 1142 removed outlier: 4.520A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1214 Processing helix chain 'B' and resid 1215 through 1240 removed outlier: 3.864A pdb=" N ARG B1240 " --> pdb=" O GLU B1236 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.666A pdb=" N UNK F 5 " --> pdb=" O UNK F 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 175 removed outlier: 3.836A pdb=" N LEU C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 216 removed outlier: 3.738A pdb=" N VAL C 204 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 244 removed outlier: 4.161A pdb=" N SER C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS C 243 " --> pdb=" O ASP C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 344 through 355 Processing helix chain 'C' and resid 369 through 379 removed outlier: 4.106A pdb=" N LYS C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 413 through 423 removed outlier: 4.230A pdb=" N LYS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 451 removed outlier: 3.752A pdb=" N LEU C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 467 Processing helix chain 'C' and resid 468 through 476 removed outlier: 3.733A pdb=" N ALA C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 497 removed outlier: 3.767A pdb=" N GLN C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 510 Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 556 through 569 Processing helix chain 'C' and resid 574 through 577 Processing helix chain 'C' and resid 578 through 587 removed outlier: 3.776A pdb=" N ASN C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 649 removed outlier: 4.102A pdb=" N GLU C 640 " --> pdb=" O PHE C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 659 removed outlier: 3.552A pdb=" N GLN C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 685 Processing helix chain 'C' and resid 689 through 717 Processing helix chain 'C' and resid 718 through 724 Processing helix chain 'C' and resid 729 through 733 removed outlier: 3.962A pdb=" N SER C 733 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing helix chain 'C' and resid 736 through 745 Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 752 through 760 removed outlier: 4.322A pdb=" N LEU C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1007 removed outlier: 3.920A pdb=" N TYR C 999 " --> pdb=" O TYR C 995 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET C1001 " --> pdb=" O GLY C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1116 Processing helix chain 'C' and resid 1118 through 1142 removed outlier: 4.535A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1186 through 1215 removed outlier: 3.609A pdb=" N SER C1215 " --> pdb=" O ARG C1211 " (cutoff:3.500A) Processing helix chain 'C' and resid 1215 through 1240 removed outlier: 3.557A pdb=" N ARG C1240 " --> pdb=" O GLU C1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 removed outlier: 3.877A pdb=" N LEU D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 216 removed outlier: 4.177A pdb=" N PHE D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'D' and resid 308 through 322 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 365 through 368 removed outlier: 3.871A pdb=" N GLY D 368 " --> pdb=" O ASP D 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 365 through 368' Processing helix chain 'D' and resid 369 through 379 removed outlier: 4.237A pdb=" N LYS D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.943A pdb=" N GLU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 451 removed outlier: 3.533A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 467 Processing helix chain 'D' and resid 468 through 475 Processing helix chain 'D' and resid 486 through 499 Processing helix chain 'D' and resid 500 through 510 Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 578 through 588 Processing helix chain 'D' and resid 596 through 601 removed outlier: 3.920A pdb=" N LEU D 600 " --> pdb=" O ALA D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 648 removed outlier: 3.750A pdb=" N GLU D 640 " --> pdb=" O PHE D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 659 Processing helix chain 'D' and resid 663 through 685 removed outlier: 3.529A pdb=" N ASN D 685 " --> pdb=" O GLU D 681 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 717 removed outlier: 4.254A pdb=" N GLN D 693 " --> pdb=" O ASP D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 725 removed outlier: 3.873A pdb=" N LEU D 725 " --> pdb=" O ALA D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 736 through 745 Processing helix chain 'D' and resid 746 through 752 Processing helix chain 'D' and resid 752 through 761 removed outlier: 3.914A pdb=" N ASP D 761 " --> pdb=" O MET D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1005 removed outlier: 4.008A pdb=" N TYR D 999 " --> pdb=" O TYR D 995 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET D1001 " --> pdb=" O GLY D 997 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D1003 " --> pdb=" O TYR D 999 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D1005 " --> pdb=" O MET D1001 " (cutoff:3.500A) Processing helix chain 'D' and resid 1109 through 1117 Processing helix chain 'D' and resid 1118 through 1142 removed outlier: 4.890A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1186 through 1214 Processing helix chain 'D' and resid 1215 through 1240 removed outlier: 4.000A pdb=" N ARG D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 26 removed outlier: 3.814A pdb=" N GLN I 9 " --> pdb=" O ASP I 5 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN I 17 " --> pdb=" O GLN I 13 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 removed outlier: 3.642A pdb=" N ILE I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 29 through 34' Processing helix chain 'J' and resid 9 through 24 removed outlier: 3.652A pdb=" N ARG J 13 " --> pdb=" O ILE J 9 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN J 24 " --> pdb=" O LYS J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 39 removed outlier: 3.638A pdb=" N ALA J 35 " --> pdb=" O SER J 31 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 137 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 275 removed outlier: 4.046A pdb=" N VAL A 270 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR A 143 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 272 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 155 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A 294 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N MET A 156 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU A 296 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 158 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP A 298 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 160 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N THR A 250 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE A 295 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY A 252 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA A 297 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA A 254 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 220 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE A 253 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR A 222 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 186 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU A 185 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU A 337 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 187 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS A 364 " --> pdb=" O ILE A 338 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL A 361 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE A 430 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 363 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 270 through 275 removed outlier: 3.818A pdb=" N VAL B 270 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 143 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 145 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 157 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE B 294 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N MET B 156 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU B 296 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 158 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP B 298 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 160 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR B 250 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 295 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY B 252 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 297 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA B 254 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 186 " --> pdb=" O PHE B 221 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 185 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU B 337 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER B 187 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL B 339 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS B 189 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N VAL B 362 " --> pdb=" O VAL B 334 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 336 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N CYS B 364 " --> pdb=" O ALA B 336 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE B 338 " --> pdb=" O CYS B 364 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 361 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE B 430 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 363 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 273 through 275 removed outlier: 8.553A pdb=" N TYR C 274 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU C 145 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 155 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE C 294 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N MET C 156 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 296 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N VAL C 158 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP C 298 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL C 160 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLY C 300 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ASN C 299 " --> pdb=" O TRP C 256 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE C 251 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE C 220 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE C 253 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 222 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 185 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU C 337 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER C 187 " --> pdb=" O LEU C 337 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N VAL C 362 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA C 336 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N CYS C 364 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE C 338 " --> pdb=" O CYS C 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.793A pdb=" N SER D 136 " --> pdb=" O UNK H 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 271 through 275 removed outlier: 8.094A pdb=" N ARG D 272 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR D 143 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR D 274 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLU D 145 " --> pdb=" O TYR D 274 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR D 157 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 155 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE D 294 " --> pdb=" O LYS D 154 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N MET D 156 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU D 296 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL D 158 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP D 298 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL D 160 " --> pdb=" O ASP D 298 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE D 220 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 253 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR D 222 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU D 185 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU D 337 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER D 187 " --> pdb=" O LEU D 337 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL D 361 " --> pdb=" O THR D 428 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 46 through 50 removed outlier: 6.367A pdb=" N ILE I 338 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR I 50 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU I 336 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL I 327 " --> pdb=" O TRP I 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 58 through 63 removed outlier: 7.293A pdb=" N ALA I 73 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N MET I 61 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL I 71 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP I 63 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU I 69 " --> pdb=" O TRP I 63 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE I 80 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N SER I 74 " --> pdb=" O LYS I 78 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS I 78 " --> pdb=" O SER I 74 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS I 91 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP I 83 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LYS I 89 " --> pdb=" O ASP I 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 100 through 105 removed outlier: 3.835A pdb=" N GLY I 115 " --> pdb=" O THR I 102 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N CYS I 121 " --> pdb=" O GLU I 138 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU I 138 " --> pdb=" O CYS I 121 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE I 123 " --> pdb=" O SER I 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 146 through 151 removed outlier: 4.000A pdb=" N CYS I 148 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER I 161 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR I 165 " --> pdb=" O SER I 161 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU I 168 " --> pdb=" O THR I 178 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR I 178 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP I 170 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN I 176 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 187 through 192 removed outlier: 4.004A pdb=" N SER I 201 " --> pdb=" O LYS I 209 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS I 209 " --> pdb=" O SER I 201 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA I 203 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N SER I 207 " --> pdb=" O ALA I 203 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA I 208 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR I 221 " --> pdb=" O ALA I 208 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU I 210 " --> pdb=" O ARG I 219 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET I 217 " --> pdb=" O ASP I 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 231 through 234 removed outlier: 3.854A pdb=" N PHE I 241 " --> pdb=" O PHE I 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE I 253 " --> pdb=" O PHE I 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 273 through 277 Processing sheet with id=AB5, first strand: chain 'I' and resid 294 through 295 removed outlier: 4.045A pdb=" N CYS I 294 " --> pdb=" O LEU I 308 " (cutoff:3.500A) 1230 hydrogen bonds defined for protein. 3641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8353 1.34 - 1.45: 3435 1.45 - 1.57: 14279 1.57 - 1.69: 0 1.69 - 1.81: 297 Bond restraints: 26364 Sorted by residual: bond pdb=" CA PRO D 629 " pdb=" C PRO D 629 " ideal model delta sigma weight residual 1.526 1.492 0.034 8.50e-03 1.38e+04 1.62e+01 bond pdb=" CA ASN D 632 " pdb=" C ASN D 632 " ideal model delta sigma weight residual 1.526 1.479 0.047 1.29e-02 6.01e+03 1.33e+01 bond pdb=" N HIS D 633 " pdb=" CA HIS D 633 " ideal model delta sigma weight residual 1.458 1.419 0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" N PHE D 634 " pdb=" CA PHE D 634 " ideal model delta sigma weight residual 1.456 1.419 0.036 1.13e-02 7.83e+03 1.04e+01 bond pdb=" CA HIS D 633 " pdb=" C HIS D 633 " ideal model delta sigma weight residual 1.520 1.487 0.034 1.17e-02 7.31e+03 8.31e+00 ... (remaining 26359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 35346 2.33 - 4.66: 214 4.66 - 6.99: 20 6.99 - 9.32: 2 9.32 - 11.65: 2 Bond angle restraints: 35584 Sorted by residual: angle pdb=" N ASN D 632 " pdb=" CA ASN D 632 " pdb=" C ASN D 632 " ideal model delta sigma weight residual 111.54 99.89 11.65 1.36e+00 5.41e-01 7.34e+01 angle pdb=" N GLU D 630 " pdb=" CA GLU D 630 " pdb=" C GLU D 630 " ideal model delta sigma weight residual 110.80 100.69 10.11 2.13e+00 2.20e-01 2.25e+01 angle pdb=" C ASN D 632 " pdb=" N HIS D 633 " pdb=" CA HIS D 633 " ideal model delta sigma weight residual 122.77 117.10 5.67 1.41e+00 5.03e-01 1.62e+01 angle pdb=" N PRO A 357 " pdb=" CA PRO A 357 " pdb=" C PRO A 357 " ideal model delta sigma weight residual 110.70 105.88 4.82 1.22e+00 6.72e-01 1.56e+01 angle pdb=" C ASP I 195 " pdb=" N THR I 196 " pdb=" CA THR I 196 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 ... (remaining 35579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 14369 17.45 - 34.89: 1084 34.89 - 52.34: 315 52.34 - 69.79: 90 69.79 - 87.23: 18 Dihedral angle restraints: 15876 sinusoidal: 6409 harmonic: 9467 Sorted by residual: dihedral pdb=" CA PRO J 55 " pdb=" C PRO J 55 " pdb=" N ALA J 56 " pdb=" CA ALA J 56 " ideal model delta harmonic sigma weight residual 180.00 -154.65 -25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE I 151 " pdb=" C PHE I 151 " pdb=" N LEU I 152 " pdb=" CA LEU I 152 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 15873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3378 0.054 - 0.107: 553 0.107 - 0.161: 60 0.161 - 0.214: 1 0.214 - 0.268: 1 Chirality restraints: 3993 Sorted by residual: chirality pdb=" CA HIS D 633 " pdb=" N HIS D 633 " pdb=" C HIS D 633 " pdb=" CB HIS D 633 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ILE D 631 " pdb=" N ILE D 631 " pdb=" C ILE D 631 " pdb=" CB ILE D 631 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE I 120 " pdb=" N ILE I 120 " pdb=" C ILE I 120 " pdb=" CB ILE I 120 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 3990 not shown) Planarity restraints: 4551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 634 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO D 635 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO D 635 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO D 635 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 357 " 0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 358 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN J 59 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO J 60 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO J 60 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO J 60 " -0.027 5.00e-02 4.00e+02 ... (remaining 4548 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1339 2.72 - 3.27: 27630 3.27 - 3.81: 44530 3.81 - 4.36: 51123 4.36 - 4.90: 83189 Nonbonded interactions: 207811 Sorted by model distance: nonbonded pdb=" OG SER C 556 " pdb=" OD1 ASP C 559 " model vdw 2.179 3.040 nonbonded pdb=" OH TYR I 264 " pdb=" O ALA I 299 " model vdw 2.185 3.040 nonbonded pdb=" OE2 GLU C 565 " pdb=" OG1 THR C 577 " model vdw 2.187 3.040 nonbonded pdb=" O ILE A 248 " pdb=" OG SER A 292 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 402 " pdb=" OE1 GLN C 409 " model vdw 2.216 3.040 ... (remaining 207806 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' selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 129 through 588 or resid 632 through 1009 or resid 1109 th \ rough 1243)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.160 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.520 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6186 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26364 Z= 0.147 Angle : 0.529 11.653 35584 Z= 0.298 Chirality : 0.038 0.268 3993 Planarity : 0.004 0.106 4551 Dihedral : 14.465 87.234 9742 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 8.35 % Allowed : 10.33 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3148 helix: 1.52 (0.13), residues: 1602 sheet: -0.66 (0.28), residues: 359 loop : -1.67 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 272 TYR 0.016 0.001 TYR A 380 PHE 0.013 0.001 PHE B 376 TRP 0.009 0.001 TRP B 483 HIS 0.008 0.001 HIS D 633 Details of bonding type rmsd covalent geometry : bond 0.00275 (26364) covalent geometry : angle 0.52867 (35584) hydrogen bonds : bond 0.18015 ( 1230) hydrogen bonds : angle 6.33003 ( 3641) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1100 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 867 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 HIS cc_start: 0.6299 (m-70) cc_final: 0.5572 (m-70) REVERT: A 156 MET cc_start: 0.7836 (mmt) cc_final: 0.7514 (mtp) REVERT: A 275 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.6103 (tp40) REVERT: A 296 LEU cc_start: -0.1324 (OUTLIER) cc_final: -0.2171 (mt) REVERT: A 350 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8684 (tp) REVERT: A 407 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7893 (mmp-170) REVERT: A 417 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.4204 (pp) REVERT: A 471 ILE cc_start: 0.9024 (mm) cc_final: 0.8802 (pt) REVERT: A 489 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8389 (mt-10) REVERT: A 516 ARG cc_start: 0.8952 (mtp-110) cc_final: 0.8612 (mmp-170) REVERT: A 559 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: A 633 HIS cc_start: 0.5342 (OUTLIER) cc_final: 0.4926 (t70) REVERT: A 662 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: A 704 GLN cc_start: 0.9014 (tp40) cc_final: 0.8674 (tp40) REVERT: A 708 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8448 (mt-10) REVERT: A 709 LEU cc_start: 0.8785 (tp) cc_final: 0.8511 (tp) REVERT: A 712 GLN cc_start: 0.8107 (tp40) cc_final: 0.6437 (tm-30) REVERT: A 722 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8624 (mmm) REVERT: A 729 LEU cc_start: 0.9306 (mt) cc_final: 0.8962 (mt) REVERT: A 732 TRP cc_start: 0.6206 (m100) cc_final: 0.4592 (m100) REVERT: A 1186 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.7995 (p) REVERT: A 1194 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8252 (m-70) REVERT: A 1204 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (t80) REVERT: B 156 MET cc_start: 0.7783 (mmt) cc_final: 0.7386 (mmp) REVERT: B 171 HIS cc_start: 0.6503 (t-90) cc_final: 0.6268 (t70) REVERT: B 245 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6981 (mmm160) REVERT: B 275 GLN cc_start: -0.1222 (OUTLIER) cc_final: -0.1435 (tp-100) REVERT: B 291 HIS cc_start: 0.4913 (m-70) cc_final: 0.4200 (m-70) REVERT: B 350 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7494 (mp) REVERT: B 412 HIS cc_start: 0.2917 (OUTLIER) cc_final: 0.2548 (t70) REVERT: B 440 ILE cc_start: 0.8316 (mm) cc_final: 0.7993 (mp) REVERT: B 445 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6587 (mm) REVERT: B 450 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7863 (mmpt) REVERT: B 469 VAL cc_start: 0.6950 (p) cc_final: 0.6722 (p) REVERT: B 471 ILE cc_start: 0.9262 (mm) cc_final: 0.9019 (pt) REVERT: B 492 MET cc_start: 0.7732 (tpp) cc_final: 0.6598 (tpp) REVERT: B 501 VAL cc_start: 0.7217 (t) cc_final: 0.6656 (t) REVERT: B 580 ARG cc_start: 0.6804 (ttt90) cc_final: 0.6173 (tpt170) REVERT: B 636 PHE cc_start: 0.7252 (m-80) cc_final: 0.6749 (m-10) REVERT: B 656 PHE cc_start: 0.8156 (t80) cc_final: 0.7605 (t80) REVERT: B 657 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7537 (m-10) REVERT: B 670 VAL cc_start: 0.8444 (t) cc_final: 0.8090 (t) REVERT: B 694 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7987 (tm-30) REVERT: B 720 LEU cc_start: 0.8819 (mt) cc_final: 0.8267 (tt) REVERT: B 722 MET cc_start: 0.8797 (mtm) cc_final: 0.8292 (mpp) REVERT: B 746 HIS cc_start: 0.7598 (t-90) cc_final: 0.7287 (t70) REVERT: B 748 ASP cc_start: 0.8915 (m-30) cc_final: 0.8682 (m-30) REVERT: B 752 HIS cc_start: 0.7021 (t-90) cc_final: 0.6805 (t-90) REVERT: B 754 CYS cc_start: 0.9161 (t) cc_final: 0.8867 (t) REVERT: B 756 GLN cc_start: 0.9269 (mm-40) cc_final: 0.9049 (mt0) REVERT: B 1182 LYS cc_start: 0.7533 (mttp) cc_final: 0.7133 (mmmm) REVERT: B 1190 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8437 (mt) REVERT: B 1202 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 1213 ASN cc_start: 0.8536 (m-40) cc_final: 0.8214 (m-40) REVERT: B 1226 ARG cc_start: 0.8520 (mtt180) cc_final: 0.8257 (mtm-85) REVERT: C 158 VAL cc_start: 0.9360 (t) cc_final: 0.9149 (m) REVERT: C 186 ILE cc_start: 0.8059 (mt) cc_final: 0.7750 (mp) REVERT: C 248 ILE cc_start: 0.6914 (mt) cc_final: 0.6617 (tp) REVERT: C 291 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6534 (m170) REVERT: C 293 HIS cc_start: 0.7614 (m90) cc_final: 0.7170 (m-70) REVERT: C 294 PHE cc_start: 0.5479 (OUTLIER) cc_final: 0.4926 (t80) REVERT: C 345 VAL cc_start: 0.8183 (p) cc_final: 0.7918 (m) REVERT: C 414 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6478 (m-80) REVERT: C 479 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: C 494 ASP cc_start: 0.7984 (m-30) cc_final: 0.7403 (m-30) REVERT: C 499 ASP cc_start: 0.6693 (t0) cc_final: 0.5992 (t0) REVERT: C 559 ASP cc_start: 0.4183 (OUTLIER) cc_final: 0.3957 (p0) REVERT: C 646 VAL cc_start: 0.7936 (t) cc_final: 0.7548 (p) REVERT: C 672 CYS cc_start: 0.8928 (t) cc_final: 0.8613 (t) REVERT: C 681 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: D 131 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7400 (mmmt) REVERT: D 179 LEU cc_start: 0.7711 (mt) cc_final: 0.7282 (mt) REVERT: D 181 LEU cc_start: 0.9057 (mt) cc_final: 0.8603 (pt) REVERT: D 261 ASN cc_start: 0.5803 (OUTLIER) cc_final: 0.5275 (m-40) REVERT: D 277 MET cc_start: 0.5539 (tmm) cc_final: 0.5264 (pmm) REVERT: D 278 SER cc_start: 0.4649 (t) cc_final: 0.3808 (m) REVERT: D 417 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5155 (mt) REVERT: D 431 ARG cc_start: 0.5347 (ptp-110) cc_final: 0.5030 (mtt180) REVERT: D 459 GLN cc_start: 0.8817 (mt0) cc_final: 0.8537 (mm-40) REVERT: D 469 VAL cc_start: 0.8465 (p) cc_final: 0.8207 (p) REVERT: D 474 SER cc_start: 0.8548 (m) cc_final: 0.8340 (p) REVERT: D 506 LEU cc_start: 0.8903 (tp) cc_final: 0.8357 (tp) REVERT: D 526 LEU cc_start: 0.8802 (mt) cc_final: 0.8463 (mt) REVERT: D 542 ARG cc_start: 0.8359 (ttp-110) cc_final: 0.7667 (ttp-110) REVERT: D 564 ILE cc_start: 0.9444 (mt) cc_final: 0.9146 (mt) REVERT: D 567 LEU cc_start: 0.8931 (mt) cc_final: 0.8469 (mt) REVERT: D 642 MET cc_start: 0.8435 (ttt) cc_final: 0.7746 (mtp) REVERT: D 689 ASP cc_start: 0.8185 (m-30) cc_final: 0.7856 (m-30) REVERT: D 690 ASP cc_start: 0.8438 (p0) cc_final: 0.8153 (p0) REVERT: D 711 ASP cc_start: 0.9244 (t0) cc_final: 0.8918 (p0) REVERT: D 724 LEU cc_start: 0.9455 (tp) cc_final: 0.9165 (tp) REVERT: D 727 TYR cc_start: 0.8188 (p90) cc_final: 0.7602 (t80) REVERT: D 740 LEU cc_start: 0.9147 (mt) cc_final: 0.8930 (mm) REVERT: D 1130 LYS cc_start: 0.8087 (mttt) cc_final: 0.7799 (mttt) REVERT: D 1195 ASP cc_start: 0.9179 (m-30) cc_final: 0.8954 (m-30) REVERT: D 1202 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7551 (pp20) REVERT: I 101 MET cc_start: 0.8686 (mmm) cc_final: 0.8201 (mmm) REVERT: I 145 TYR cc_start: 0.3088 (p90) cc_final: 0.2793 (p90) REVERT: I 178 THR cc_start: -0.4195 (OUTLIER) cc_final: -0.4584 (t) REVERT: I 187 VAL cc_start: 0.6235 (OUTLIER) cc_final: 0.5513 (p) REVERT: I 217 MET cc_start: 0.2206 (tpt) cc_final: 0.1814 (tmm) REVERT: I 232 ILE cc_start: 0.5496 (tt) cc_final: 0.4787 (mt) outliers start: 233 outliers final: 49 residues processed: 1037 average time/residue: 0.1766 time to fit residues: 281.6334 Evaluate side-chains 625 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 544 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN A 314 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 490 GLN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN A 697 HIS A 712 GLN A 739 GLN A1116 ASN B 134 GLN B 198 GLN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS B 659 GLN B 696 ASN ** B 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 716 GLN B1116 ASN ** B1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 178 GLN C 189 HIS C 232 HIS ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN C 378 HIS C 696 ASN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN C 719 GLN ** C 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 GLN C1242 HIS D 232 HIS D 411 GLN D 535 ASN D 548 ASN ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 ASN ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D1115 ASN D1242 HIS I 44 GLN ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 GLN J 44 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.112674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.083266 restraints weight = 154422.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.085008 restraints weight = 116115.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.086325 restraints weight = 94382.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.087099 restraints weight = 80510.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.087916 restraints weight = 71442.135| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26364 Z= 0.214 Angle : 0.761 9.700 35584 Z= 0.399 Chirality : 0.046 0.224 3993 Planarity : 0.006 0.112 4551 Dihedral : 5.193 27.363 3504 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 0.25 % Allowed : 5.41 % Favored : 94.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.15), residues: 3148 helix: 0.77 (0.12), residues: 1674 sheet: -0.77 (0.28), residues: 361 loop : -1.78 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 700 TYR 0.035 0.003 TYR D 479 PHE 0.044 0.003 PHE B 376 TRP 0.061 0.003 TRP B 219 HIS 0.015 0.002 HIS I 142 Details of bonding type rmsd covalent geometry : bond 0.00448 (26364) covalent geometry : angle 0.76088 (35584) hydrogen bonds : bond 0.04572 ( 1230) hydrogen bonds : angle 5.05410 ( 3641) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 652 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8416 (tp) cc_final: 0.7750 (pt) REVERT: A 197 LEU cc_start: 0.7849 (mt) cc_final: 0.7602 (mt) REVERT: A 418 MET cc_start: 0.7517 (tpt) cc_final: 0.7156 (tpt) REVERT: A 471 ILE cc_start: 0.9075 (mm) cc_final: 0.8742 (pt) REVERT: A 492 MET cc_start: 0.8731 (tpp) cc_final: 0.8421 (tpp) REVERT: A 524 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7517 (mm-30) REVERT: A 683 SER cc_start: 0.8724 (t) cc_final: 0.8509 (p) REVERT: A 687 MET cc_start: 0.8421 (mmp) cc_final: 0.8122 (mmm) REVERT: A 728 GLU cc_start: 0.7809 (tt0) cc_final: 0.7217 (pm20) REVERT: A 729 LEU cc_start: 0.9016 (mt) cc_final: 0.8655 (mp) REVERT: A 755 SER cc_start: 0.7119 (m) cc_final: 0.6892 (t) REVERT: A 1195 ASP cc_start: 0.8564 (m-30) cc_final: 0.8310 (m-30) REVERT: A 1206 ARG cc_start: 0.8055 (ptp-110) cc_final: 0.7790 (ptp-170) REVERT: A 1218 GLU cc_start: 0.8197 (tp30) cc_final: 0.7836 (tp30) REVERT: B 144 ILE cc_start: 0.8261 (mm) cc_final: 0.7889 (tp) REVERT: B 171 HIS cc_start: 0.6291 (t-90) cc_final: 0.6090 (t70) REVERT: B 407 ARG cc_start: 0.8764 (ttp-170) cc_final: 0.8201 (mpt180) REVERT: B 418 MET cc_start: 0.4097 (mmm) cc_final: 0.3724 (tmm) REVERT: B 492 MET cc_start: 0.8167 (tpp) cc_final: 0.7106 (tpp) REVERT: B 545 LYS cc_start: 0.9108 (tptm) cc_final: 0.8537 (ptmt) REVERT: B 580 ARG cc_start: 0.7509 (ttt90) cc_final: 0.6999 (tpt170) REVERT: B 656 PHE cc_start: 0.8556 (t80) cc_final: 0.8140 (t80) REVERT: B 659 GLN cc_start: 0.8928 (pt0) cc_final: 0.8479 (mt0) REVERT: B 687 MET cc_start: 0.8216 (tpp) cc_final: 0.7915 (tpp) REVERT: B 720 LEU cc_start: 0.8884 (mt) cc_final: 0.8369 (tt) REVERT: B 752 HIS cc_start: 0.7435 (t-90) cc_final: 0.6379 (t-90) REVERT: B 754 CYS cc_start: 0.8792 (t) cc_final: 0.8282 (t) REVERT: B 1179 TYR cc_start: 0.8552 (t80) cc_final: 0.7715 (t80) REVERT: B 1202 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8476 (tm-30) REVERT: B 1230 MET cc_start: 0.8740 (mtp) cc_final: 0.8481 (mtp) REVERT: C 156 MET cc_start: 0.7761 (mtp) cc_final: 0.7359 (mtm) REVERT: C 183 LYS cc_start: 0.7269 (mttt) cc_final: 0.6982 (mmtt) REVERT: C 184 LEU cc_start: 0.8271 (tp) cc_final: 0.7863 (tp) REVERT: C 211 LYS cc_start: 0.7867 (tptt) cc_final: 0.7614 (tttp) REVERT: C 245 ARG cc_start: 0.6429 (tpm170) cc_final: 0.6146 (tpm170) REVERT: C 248 ILE cc_start: 0.7589 (mt) cc_final: 0.7306 (tp) REVERT: C 317 LYS cc_start: 0.8106 (mttm) cc_final: 0.7728 (tptt) REVERT: C 514 MET cc_start: 0.6761 (ttm) cc_final: 0.6514 (tpp) REVERT: C 516 ARG cc_start: 0.7966 (tpm170) cc_final: 0.7686 (tpm170) REVERT: C 672 CYS cc_start: 0.8781 (t) cc_final: 0.8568 (t) REVERT: C 675 CYS cc_start: 0.7977 (m) cc_final: 0.7412 (m) REVERT: C 694 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8248 (tt0) REVERT: C 708 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7722 (mt-10) REVERT: C 716 GLN cc_start: 0.7821 (tt0) cc_final: 0.7583 (tp-100) REVERT: C 742 VAL cc_start: 0.8954 (t) cc_final: 0.8741 (t) REVERT: C 757 MET cc_start: 0.8384 (tmm) cc_final: 0.8059 (tmm) REVERT: C 1230 MET cc_start: 0.9152 (mtp) cc_final: 0.8907 (mtm) REVERT: D 173 MET cc_start: 0.8903 (mtm) cc_final: 0.8672 (mtt) REVERT: D 181 LEU cc_start: 0.9220 (mt) cc_final: 0.8765 (pt) REVERT: D 290 MET cc_start: 0.8097 (mmm) cc_final: 0.7726 (mmm) REVERT: D 291 HIS cc_start: 0.8498 (m90) cc_final: 0.8285 (m170) REVERT: D 418 MET cc_start: 0.6123 (mmm) cc_final: 0.5512 (mmm) REVERT: D 419 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8079 (mm-30) REVERT: D 462 LEU cc_start: 0.9077 (mt) cc_final: 0.8660 (mt) REVERT: D 476 ILE cc_start: 0.8104 (tp) cc_final: 0.7786 (tp) REVERT: D 494 ASP cc_start: 0.8439 (m-30) cc_final: 0.8072 (t0) REVERT: D 540 LEU cc_start: 0.8761 (mt) cc_final: 0.8417 (mt) REVERT: D 565 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7039 (tp30) REVERT: D 642 MET cc_start: 0.8787 (ttt) cc_final: 0.8235 (mtp) REVERT: D 687 MET cc_start: 0.5614 (mmm) cc_final: 0.5142 (mmm) REVERT: D 689 ASP cc_start: 0.8876 (m-30) cc_final: 0.8636 (t0) REVERT: D 690 ASP cc_start: 0.8244 (p0) cc_final: 0.7664 (p0) REVERT: D 711 ASP cc_start: 0.8835 (t0) cc_final: 0.8587 (p0) REVERT: D 1199 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.7397 (pp30) REVERT: D 1202 GLU cc_start: 0.8611 (tm-30) cc_final: 0.7127 (tm-30) REVERT: D 1218 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7808 (mm-30) REVERT: D 1233 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8390 (tpp80) REVERT: D 1235 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8498 (mm-30) REVERT: I 61 MET cc_start: 0.4059 (ptm) cc_final: 0.3649 (ptm) REVERT: I 70 LEU cc_start: 0.7339 (tt) cc_final: 0.6975 (pp) REVERT: I 186 ASP cc_start: 0.9254 (m-30) cc_final: 0.8741 (t0) REVERT: I 188 MET cc_start: 0.7022 (mmp) cc_final: 0.6697 (mmm) REVERT: I 312 ASP cc_start: 0.7868 (p0) cc_final: 0.7384 (p0) REVERT: I 325 MET cc_start: 0.8273 (mtp) cc_final: 0.8027 (mpp) outliers start: 7 outliers final: 2 residues processed: 655 average time/residue: 0.1684 time to fit residues: 172.1027 Evaluate side-chains 463 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 460 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 235 optimal weight: 0.0070 chunk 118 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 303 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 278 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 HIS ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 HIS A 719 GLN A1115 ASN ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 HIS C 151 HIS C 203 GLN C 232 HIS C 240 HIS C 288 ASN C 291 HIS C 318 HIS C 322 GLN ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 HIS C 660 HIS C 746 HIS C1213 ASN C1242 HIS D 293 HIS D 459 GLN D 539 HIS D 734 ASN D1116 ASN ** I 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.112736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.081090 restraints weight = 190006.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.083402 restraints weight = 132529.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.084927 restraints weight = 102524.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.086385 restraints weight = 84764.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.087481 restraints weight = 74301.944| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.6082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26364 Z= 0.129 Angle : 0.579 8.110 35584 Z= 0.308 Chirality : 0.041 0.189 3993 Planarity : 0.004 0.053 4551 Dihedral : 4.585 25.898 3504 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 0.04 % Allowed : 3.51 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3148 helix: 1.21 (0.13), residues: 1673 sheet: -0.28 (0.30), residues: 312 loop : -1.72 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 700 TYR 0.017 0.001 TYR A1204 PHE 0.021 0.002 PHE C 636 TRP 0.032 0.001 TRP I 332 HIS 0.011 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00275 (26364) covalent geometry : angle 0.57929 (35584) hydrogen bonds : bond 0.03840 ( 1230) hydrogen bonds : angle 4.59587 ( 3641) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 583 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8476 (tp) cc_final: 0.7801 (pt) REVERT: A 432 MET cc_start: 0.6468 (mmm) cc_final: 0.6236 (mtp) REVERT: A 471 ILE cc_start: 0.8973 (mm) cc_final: 0.8588 (pt) REVERT: A 489 GLU cc_start: 0.8723 (tt0) cc_final: 0.8470 (pp20) REVERT: A 492 MET cc_start: 0.8737 (tpp) cc_final: 0.8347 (tpt) REVERT: A 500 ARG cc_start: 0.8267 (mmp80) cc_final: 0.7810 (mmt-90) REVERT: A 524 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7472 (mm-30) REVERT: A 687 MET cc_start: 0.8730 (mmp) cc_final: 0.8195 (mmm) REVERT: A 704 GLN cc_start: 0.8741 (tp40) cc_final: 0.8459 (tp40) REVERT: A 727 TYR cc_start: 0.7243 (p90) cc_final: 0.7007 (p90) REVERT: A 728 GLU cc_start: 0.6981 (tt0) cc_final: 0.6355 (pm20) REVERT: A 729 LEU cc_start: 0.8758 (mt) cc_final: 0.8386 (mp) REVERT: A 1218 GLU cc_start: 0.8474 (tp30) cc_final: 0.7950 (tp30) REVERT: A 1230 MET cc_start: 0.8693 (ttm) cc_final: 0.8454 (ttm) REVERT: B 144 ILE cc_start: 0.8406 (mm) cc_final: 0.7910 (tp) REVERT: B 407 ARG cc_start: 0.8757 (ttp-170) cc_final: 0.8184 (mtt90) REVERT: B 418 MET cc_start: 0.4370 (mmm) cc_final: 0.3947 (tmm) REVERT: B 492 MET cc_start: 0.8060 (tpp) cc_final: 0.7095 (tpp) REVERT: B 523 LEU cc_start: 0.8783 (mt) cc_final: 0.8536 (mt) REVERT: B 545 LYS cc_start: 0.9047 (tptm) cc_final: 0.8351 (ptmt) REVERT: B 548 ASN cc_start: 0.7524 (m-40) cc_final: 0.7111 (t0) REVERT: B 580 ARG cc_start: 0.7490 (ttt90) cc_final: 0.6989 (tpt170) REVERT: B 656 PHE cc_start: 0.8753 (t80) cc_final: 0.8473 (t80) REVERT: B 687 MET cc_start: 0.8178 (tpp) cc_final: 0.7947 (tpp) REVERT: B 688 VAL cc_start: 0.9092 (t) cc_final: 0.8839 (t) REVERT: B 720 LEU cc_start: 0.8965 (mt) cc_final: 0.8402 (tt) REVERT: B 740 LEU cc_start: 0.8805 (mm) cc_final: 0.8506 (mm) REVERT: B 1179 TYR cc_start: 0.8666 (t80) cc_final: 0.7584 (t80) REVERT: B 1182 LYS cc_start: 0.6963 (mttt) cc_final: 0.6601 (mmmt) REVERT: B 1202 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8367 (tm-30) REVERT: B 1203 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8922 (tm-30) REVERT: C 156 MET cc_start: 0.8000 (mtp) cc_final: 0.7642 (mtm) REVERT: C 211 LYS cc_start: 0.7825 (tptt) cc_final: 0.7515 (tttp) REVERT: C 248 ILE cc_start: 0.7735 (mt) cc_final: 0.7480 (tp) REVERT: C 526 LEU cc_start: 0.8368 (mt) cc_final: 0.8011 (mt) REVERT: C 694 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8233 (tt0) REVERT: C 742 VAL cc_start: 0.9015 (t) cc_final: 0.8735 (t) REVERT: C 757 MET cc_start: 0.8486 (tmm) cc_final: 0.7870 (tmm) REVERT: C 758 LEU cc_start: 0.8539 (tp) cc_final: 0.8338 (tp) REVERT: C 1230 MET cc_start: 0.9125 (mtp) cc_final: 0.8853 (mtm) REVERT: D 181 LEU cc_start: 0.9242 (mt) cc_final: 0.8699 (pt) REVERT: D 185 LEU cc_start: 0.9368 (tp) cc_final: 0.9059 (tp) REVERT: D 290 MET cc_start: 0.8192 (mmm) cc_final: 0.7901 (mmm) REVERT: D 291 HIS cc_start: 0.8657 (m90) cc_final: 0.8279 (m170) REVERT: D 418 MET cc_start: 0.6194 (mmm) cc_final: 0.5726 (mmm) REVERT: D 419 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8156 (mm-30) REVERT: D 462 LEU cc_start: 0.8912 (mt) cc_final: 0.8638 (mt) REVERT: D 474 SER cc_start: 0.8234 (m) cc_final: 0.8002 (t) REVERT: D 494 ASP cc_start: 0.8537 (m-30) cc_final: 0.8231 (t0) REVERT: D 565 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7120 (tp30) REVERT: D 747 ARG cc_start: 0.8813 (tpp80) cc_final: 0.8484 (tpp80) REVERT: D 1129 TRP cc_start: 0.8409 (t60) cc_final: 0.8155 (t60) REVERT: D 1195 ASP cc_start: 0.9264 (m-30) cc_final: 0.8751 (m-30) REVERT: D 1199 GLN cc_start: 0.8600 (pm20) cc_final: 0.7840 (pp30) REVERT: D 1202 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8149 (tm-30) REVERT: D 1232 MET cc_start: 0.8864 (mtp) cc_final: 0.8119 (mtp) REVERT: D 1235 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8141 (mp0) REVERT: I 188 MET cc_start: 0.6801 (mmp) cc_final: 0.6125 (mpp) outliers start: 1 outliers final: 0 residues processed: 584 average time/residue: 0.1636 time to fit residues: 151.3937 Evaluate side-chains 438 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 140 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 203 optimal weight: 0.0670 chunk 120 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 267 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 315 optimal weight: 6.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 GLN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN B 275 GLN B 318 HIS C 132 HIS C 151 HIS C 232 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS C 704 GLN ** C 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1199 GLN C1213 ASN D 322 GLN D 459 GLN D 734 ASN I 62 HIS I 225 HIS I 268 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.105631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.076446 restraints weight = 145384.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.079486 restraints weight = 114177.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.079600 restraints weight = 81801.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.080235 restraints weight = 68843.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.080354 restraints weight = 63661.074| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.7769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 26364 Z= 0.210 Angle : 0.716 13.588 35584 Z= 0.376 Chirality : 0.044 0.247 3993 Planarity : 0.005 0.054 4551 Dihedral : 4.905 28.992 3504 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.94 % Favored : 94.02 % Rotamer: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.15), residues: 3148 helix: 0.89 (0.13), residues: 1675 sheet: -0.54 (0.30), residues: 325 loop : -1.73 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 700 TYR 0.027 0.003 TYR C 572 PHE 0.025 0.002 PHE C 221 TRP 0.032 0.003 TRP B 219 HIS 0.018 0.002 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00453 (26364) covalent geometry : angle 0.71555 (35584) hydrogen bonds : bond 0.04495 ( 1230) hydrogen bonds : angle 4.84524 ( 3641) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 555 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8712 (tp) cc_final: 0.8225 (pt) REVERT: A 167 ASP cc_start: 0.8189 (p0) cc_final: 0.7570 (t70) REVERT: A 237 LEU cc_start: 0.9358 (mt) cc_final: 0.9049 (mt) REVERT: A 248 ILE cc_start: 0.8744 (mm) cc_final: 0.8442 (mm) REVERT: A 292 SER cc_start: 0.8163 (m) cc_final: 0.7751 (t) REVERT: A 338 ILE cc_start: 0.8940 (mm) cc_final: 0.8691 (mm) REVERT: A 418 MET cc_start: 0.7604 (tpt) cc_final: 0.7050 (tpt) REVERT: A 432 MET cc_start: 0.6744 (mmm) cc_final: 0.6436 (ttt) REVERT: A 471 ILE cc_start: 0.9200 (mm) cc_final: 0.8964 (mm) REVERT: A 492 MET cc_start: 0.8999 (tpp) cc_final: 0.8635 (tpp) REVERT: A 524 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7800 (mm-30) REVERT: A 525 GLU cc_start: 0.8561 (mp0) cc_final: 0.8260 (mp0) REVERT: A 727 TYR cc_start: 0.7818 (p90) cc_final: 0.7565 (p90) REVERT: A 728 GLU cc_start: 0.7955 (tt0) cc_final: 0.7110 (pm20) REVERT: A 729 LEU cc_start: 0.8835 (mt) cc_final: 0.8367 (mp) REVERT: A 746 HIS cc_start: 0.8925 (t-90) cc_final: 0.8669 (t-90) REVERT: B 144 ILE cc_start: 0.8649 (mm) cc_final: 0.8134 (tp) REVERT: B 243 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8129 (pttt) REVERT: B 376 PHE cc_start: 0.7604 (m-80) cc_final: 0.7206 (m-10) REVERT: B 407 ARG cc_start: 0.8783 (ttp-170) cc_final: 0.8114 (mtt90) REVERT: B 408 THR cc_start: 0.7759 (p) cc_final: 0.7550 (t) REVERT: B 442 LEU cc_start: 0.8040 (mp) cc_final: 0.7385 (tp) REVERT: B 492 MET cc_start: 0.8263 (tpp) cc_final: 0.7392 (tpp) REVERT: B 496 LEU cc_start: 0.7490 (mt) cc_final: 0.7225 (mt) REVERT: B 523 LEU cc_start: 0.8867 (mt) cc_final: 0.8616 (mt) REVERT: B 540 LEU cc_start: 0.8271 (mt) cc_final: 0.7798 (pp) REVERT: B 580 ARG cc_start: 0.7758 (ttt90) cc_final: 0.7198 (tpt170) REVERT: B 688 VAL cc_start: 0.9272 (t) cc_final: 0.8927 (t) REVERT: B 722 MET cc_start: 0.8782 (mpp) cc_final: 0.8390 (mpp) REVERT: B 1198 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8599 (mm-30) REVERT: B 1202 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8684 (tm-30) REVERT: B 1203 GLU cc_start: 0.9339 (tm-30) cc_final: 0.9094 (tm-30) REVERT: B 1214 SER cc_start: 0.8805 (p) cc_final: 0.8542 (p) REVERT: B 1230 MET cc_start: 0.8791 (mmm) cc_final: 0.8548 (tpp) REVERT: C 141 PHE cc_start: 0.6460 (p90) cc_final: 0.6192 (p90) REVERT: C 177 TRP cc_start: 0.7567 (m-10) cc_final: 0.6892 (m-10) REVERT: C 211 LYS cc_start: 0.7904 (tptt) cc_final: 0.7490 (tttp) REVERT: C 248 ILE cc_start: 0.8446 (mt) cc_final: 0.8225 (tp) REVERT: C 277 MET cc_start: 0.6309 (pmm) cc_final: 0.5815 (pmm) REVERT: C 317 LYS cc_start: 0.8419 (mttm) cc_final: 0.8039 (tptt) REVERT: C 418 MET cc_start: 0.6567 (tmm) cc_final: 0.6245 (tmm) REVERT: C 498 LEU cc_start: 0.7159 (mt) cc_final: 0.6823 (mt) REVERT: C 514 MET cc_start: 0.8220 (tpp) cc_final: 0.7984 (tpp) REVERT: C 526 LEU cc_start: 0.8552 (mt) cc_final: 0.8220 (mt) REVERT: C 560 ILE cc_start: 0.8851 (mm) cc_final: 0.8615 (mm) REVERT: C 665 MET cc_start: 0.8413 (tmm) cc_final: 0.7788 (tpp) REVERT: C 672 CYS cc_start: 0.9146 (t) cc_final: 0.8880 (t) REVERT: C 694 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8406 (tt0) REVERT: C 714 TYR cc_start: 0.8429 (t80) cc_final: 0.8169 (t80) REVERT: C 754 CYS cc_start: 0.9358 (t) cc_final: 0.9125 (t) REVERT: C 757 MET cc_start: 0.8639 (tmm) cc_final: 0.8158 (tmm) REVERT: C 758 LEU cc_start: 0.8694 (tp) cc_final: 0.8465 (tp) REVERT: C 1203 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8344 (tm-30) REVERT: D 181 LEU cc_start: 0.9340 (mt) cc_final: 0.8884 (pt) REVERT: D 290 MET cc_start: 0.8305 (mmm) cc_final: 0.8000 (mmm) REVERT: D 291 HIS cc_start: 0.8716 (m90) cc_final: 0.8202 (m170) REVERT: D 418 MET cc_start: 0.6382 (mmm) cc_final: 0.5990 (mmm) REVERT: D 419 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8327 (mm-30) REVERT: D 462 LEU cc_start: 0.8992 (mt) cc_final: 0.8740 (mt) REVERT: D 557 LEU cc_start: 0.8505 (mt) cc_final: 0.8243 (mt) REVERT: D 565 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7639 (tp30) REVERT: D 690 ASP cc_start: 0.8712 (p0) cc_final: 0.8489 (p0) REVERT: D 708 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8009 (mt-10) REVERT: D 1129 TRP cc_start: 0.8329 (t60) cc_final: 0.7980 (t60) REVERT: D 1235 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8236 (mt-10) REVERT: I 186 ASP cc_start: 0.9112 (m-30) cc_final: 0.8879 (m-30) REVERT: I 188 MET cc_start: 0.7047 (mmp) cc_final: 0.6627 (mmm) REVERT: I 217 MET cc_start: -0.0624 (tmm) cc_final: -0.0916 (tmm) outliers start: 2 outliers final: 0 residues processed: 557 average time/residue: 0.1661 time to fit residues: 145.7809 Evaluate side-chains 406 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 314 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 167 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 272 optimal weight: 30.0000 chunk 279 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 288 ASN A 318 HIS ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1199 GLN A1238 ASN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 712 GLN ** B1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS C 232 HIS C 299 ASN ** C 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1242 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 HIS D 459 GLN D 531 HIS D 696 ASN I 268 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.104770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.073750 restraints weight = 163583.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.075472 restraints weight = 117031.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.076624 restraints weight = 92391.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.077691 restraints weight = 78562.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.078390 restraints weight = 70334.836| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.8884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26364 Z= 0.172 Angle : 0.650 11.087 35584 Z= 0.343 Chirality : 0.043 0.183 3993 Planarity : 0.005 0.090 4551 Dihedral : 4.827 27.512 3504 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 0.18 % Allowed : 2.98 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.15), residues: 3148 helix: 0.94 (0.13), residues: 1672 sheet: -0.30 (0.30), residues: 297 loop : -1.70 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B1226 TYR 0.021 0.002 TYR A1204 PHE 0.022 0.002 PHE D 749 TRP 0.043 0.002 TRP C 658 HIS 0.012 0.002 HIS I 91 Details of bonding type rmsd covalent geometry : bond 0.00370 (26364) covalent geometry : angle 0.64992 (35584) hydrogen bonds : bond 0.04005 ( 1230) hydrogen bonds : angle 4.68815 ( 3641) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 545 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8771 (tp) cc_final: 0.8291 (pt) REVERT: A 153 ASN cc_start: 0.8573 (m-40) cc_final: 0.8303 (m-40) REVERT: A 181 LEU cc_start: 0.8184 (mt) cc_final: 0.7349 (pt) REVERT: A 237 LEU cc_start: 0.9478 (mt) cc_final: 0.9109 (mt) REVERT: A 292 SER cc_start: 0.8171 (m) cc_final: 0.7679 (t) REVERT: A 418 MET cc_start: 0.7625 (tpt) cc_final: 0.7126 (tpt) REVERT: A 471 ILE cc_start: 0.9164 (mm) cc_final: 0.8723 (pt) REVERT: A 492 MET cc_start: 0.9057 (tpp) cc_final: 0.8640 (tpp) REVERT: A 687 MET cc_start: 0.8763 (mmp) cc_final: 0.8376 (mmm) REVERT: A 694 GLU cc_start: 0.8394 (pt0) cc_final: 0.7883 (pp20) REVERT: A 695 LEU cc_start: 0.9202 (mt) cc_final: 0.8944 (mt) REVERT: A 708 GLU cc_start: 0.8132 (tt0) cc_final: 0.7795 (tm-30) REVERT: A 727 TYR cc_start: 0.7634 (p90) cc_final: 0.7032 (p90) REVERT: B 144 ILE cc_start: 0.8669 (mm) cc_final: 0.8230 (tp) REVERT: B 243 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8303 (pttt) REVERT: B 290 MET cc_start: 0.6254 (mmp) cc_final: 0.5155 (mmt) REVERT: B 376 PHE cc_start: 0.7496 (m-80) cc_final: 0.7036 (m-80) REVERT: B 407 ARG cc_start: 0.8877 (ttp-170) cc_final: 0.8161 (mtt90) REVERT: B 408 THR cc_start: 0.7677 (p) cc_final: 0.7466 (t) REVERT: B 418 MET cc_start: 0.6726 (tmm) cc_final: 0.5753 (tpp) REVERT: B 442 LEU cc_start: 0.8214 (mp) cc_final: 0.7672 (tp) REVERT: B 460 LEU cc_start: 0.8865 (tp) cc_final: 0.8598 (tt) REVERT: B 492 MET cc_start: 0.8338 (tpp) cc_final: 0.7649 (tpp) REVERT: B 523 LEU cc_start: 0.8746 (mt) cc_final: 0.8536 (mt) REVERT: B 540 LEU cc_start: 0.8306 (mt) cc_final: 0.7798 (pp) REVERT: B 545 LYS cc_start: 0.9039 (tppt) cc_final: 0.8832 (tppt) REVERT: B 554 ARG cc_start: 0.8717 (tpt170) cc_final: 0.8330 (mmm-85) REVERT: B 580 ARG cc_start: 0.7966 (ttt90) cc_final: 0.7406 (tpt170) REVERT: B 653 MET cc_start: 0.9219 (mmt) cc_final: 0.9017 (mmt) REVERT: B 688 VAL cc_start: 0.9466 (t) cc_final: 0.9262 (t) REVERT: B 711 ASP cc_start: 0.8722 (m-30) cc_final: 0.8169 (m-30) REVERT: B 712 GLN cc_start: 0.9129 (tp40) cc_final: 0.8737 (tp-100) REVERT: B 1189 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8922 (mp0) REVERT: B 1203 GLU cc_start: 0.9363 (tm-30) cc_final: 0.9131 (tm-30) REVERT: B 1218 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7981 (tm-30) REVERT: C 151 HIS cc_start: 0.3618 (OUTLIER) cc_final: 0.3172 (t-170) REVERT: C 156 MET cc_start: 0.8710 (mtm) cc_final: 0.8381 (mtm) REVERT: C 211 LYS cc_start: 0.8206 (tptt) cc_final: 0.7832 (tttp) REVERT: C 248 ILE cc_start: 0.8691 (mt) cc_final: 0.8428 (mm) REVERT: C 277 MET cc_start: 0.6361 (pmm) cc_final: 0.5780 (pmm) REVERT: C 415 ILE cc_start: 0.7614 (pt) cc_final: 0.7205 (tt) REVERT: C 418 MET cc_start: 0.6647 (tmm) cc_final: 0.6201 (tmm) REVERT: C 421 MET cc_start: 0.3107 (mmm) cc_final: 0.2252 (mmt) REVERT: C 468 ARG cc_start: 0.8281 (tpm170) cc_final: 0.7932 (tpm170) REVERT: C 514 MET cc_start: 0.8658 (tpp) cc_final: 0.8039 (tpp) REVERT: C 526 LEU cc_start: 0.8619 (mt) cc_final: 0.8250 (mt) REVERT: C 665 MET cc_start: 0.8495 (tmm) cc_final: 0.7763 (tpp) REVERT: C 757 MET cc_start: 0.8912 (tmm) cc_final: 0.8307 (tmm) REVERT: C 1179 TYR cc_start: 0.5402 (t80) cc_final: 0.5085 (t80) REVERT: C 1203 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8428 (tm-30) REVERT: D 181 LEU cc_start: 0.9312 (mt) cc_final: 0.8869 (pt) REVERT: D 291 HIS cc_start: 0.8755 (m90) cc_final: 0.8203 (m170) REVERT: D 418 MET cc_start: 0.6272 (mmm) cc_final: 0.5928 (mmm) REVERT: D 419 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8328 (mm-30) REVERT: D 518 LEU cc_start: 0.9487 (tp) cc_final: 0.9197 (tt) REVERT: D 585 TYR cc_start: 0.8630 (t80) cc_final: 0.7840 (t80) REVERT: D 589 PHE cc_start: 0.6977 (t80) cc_final: 0.6343 (t80) REVERT: D 653 MET cc_start: 0.8860 (mmt) cc_final: 0.8558 (mmt) REVERT: D 708 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7902 (mt-10) REVERT: D 754 CYS cc_start: 0.9085 (t) cc_final: 0.8622 (t) REVERT: D 1129 TRP cc_start: 0.8234 (t60) cc_final: 0.7907 (t60) REVERT: D 1195 ASP cc_start: 0.9169 (m-30) cc_final: 0.8965 (m-30) REVERT: D 1199 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.7975 (pp30) REVERT: D 1202 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7892 (tm-30) REVERT: D 1225 GLU cc_start: 0.8736 (pp20) cc_final: 0.8119 (pp20) REVERT: D 1235 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8321 (mp0) REVERT: I 186 ASP cc_start: 0.9086 (m-30) cc_final: 0.8840 (m-30) REVERT: I 188 MET cc_start: 0.6667 (mmp) cc_final: 0.6417 (mmm) outliers start: 5 outliers final: 0 residues processed: 549 average time/residue: 0.1719 time to fit residues: 149.3305 Evaluate side-chains 405 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 403 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 224 optimal weight: 0.0570 chunk 168 optimal weight: 0.9980 chunk 232 optimal weight: 0.9980 chunk 289 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 59 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS B1213 ASN B1229 ASN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS ** C 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 698 ASN ** C 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS I 183 HIS I 340 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.102900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073204 restraints weight = 131296.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.074370 restraints weight = 102777.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.075232 restraints weight = 86506.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075650 restraints weight = 77120.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.076196 restraints weight = 72030.865| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.9585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26364 Z= 0.150 Angle : 0.631 11.132 35584 Z= 0.331 Chirality : 0.042 0.259 3993 Planarity : 0.004 0.061 4551 Dihedral : 4.642 25.780 3504 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.47 % Favored : 94.50 % Rotamer: Outliers : 0.04 % Allowed : 2.62 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 3148 helix: 1.04 (0.13), residues: 1672 sheet: -0.41 (0.32), residues: 292 loop : -1.66 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 700 TYR 0.017 0.001 TYR C1134 PHE 0.020 0.002 PHE C 221 TRP 0.043 0.002 TRP I 297 HIS 0.012 0.001 HIS D 240 Details of bonding type rmsd covalent geometry : bond 0.00322 (26364) covalent geometry : angle 0.63052 (35584) hydrogen bonds : bond 0.03874 ( 1230) hydrogen bonds : angle 4.56174 ( 3641) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8736 (tp) cc_final: 0.8360 (pt) REVERT: A 181 LEU cc_start: 0.8324 (mt) cc_final: 0.7580 (pt) REVERT: A 292 SER cc_start: 0.8429 (m) cc_final: 0.7700 (t) REVERT: A 338 ILE cc_start: 0.9247 (mm) cc_final: 0.9025 (mm) REVERT: A 409 GLN cc_start: 0.7806 (mt0) cc_final: 0.7308 (mp10) REVERT: A 418 MET cc_start: 0.7455 (tpt) cc_final: 0.6925 (tpt) REVERT: A 471 ILE cc_start: 0.9185 (mm) cc_final: 0.8788 (pt) REVERT: A 492 MET cc_start: 0.8990 (tpp) cc_final: 0.8740 (tpt) REVERT: A 499 ASP cc_start: 0.8405 (t0) cc_final: 0.8169 (t0) REVERT: A 524 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7608 (mm-30) REVERT: A 687 MET cc_start: 0.8726 (mmp) cc_final: 0.8320 (mmm) REVERT: A 704 GLN cc_start: 0.9049 (tp40) cc_final: 0.7814 (tp-100) REVERT: A 708 GLU cc_start: 0.8738 (tt0) cc_final: 0.7866 (pt0) REVERT: A 727 TYR cc_start: 0.7520 (p90) cc_final: 0.7114 (p90) REVERT: A 746 HIS cc_start: 0.8869 (t-90) cc_final: 0.8466 (t-90) REVERT: B 144 ILE cc_start: 0.8778 (mm) cc_final: 0.8388 (tp) REVERT: B 184 LEU cc_start: 0.9143 (tp) cc_final: 0.8911 (tp) REVERT: B 242 SER cc_start: 0.8874 (m) cc_final: 0.8516 (m) REVERT: B 243 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8451 (pttt) REVERT: B 290 MET cc_start: 0.6495 (mmp) cc_final: 0.5581 (mmt) REVERT: B 317 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8337 (tptt) REVERT: B 376 PHE cc_start: 0.7694 (m-80) cc_final: 0.7139 (m-80) REVERT: B 407 ARG cc_start: 0.8839 (ttp-170) cc_final: 0.8088 (mtt90) REVERT: B 408 THR cc_start: 0.7933 (p) cc_final: 0.7726 (t) REVERT: B 492 MET cc_start: 0.8426 (tpp) cc_final: 0.7707 (tpp) REVERT: B 554 ARG cc_start: 0.8853 (tpt170) cc_final: 0.8465 (mmm-85) REVERT: B 580 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7497 (tpt170) REVERT: B 653 MET cc_start: 0.9124 (mmt) cc_final: 0.8875 (mmt) REVERT: B 665 MET cc_start: 0.8976 (ttm) cc_final: 0.8552 (ttm) REVERT: B 711 ASP cc_start: 0.8708 (m-30) cc_final: 0.8103 (m-30) REVERT: B 712 GLN cc_start: 0.9150 (tp40) cc_final: 0.8812 (tp-100) REVERT: B 1191 LYS cc_start: 0.8534 (mttp) cc_final: 0.7981 (mttp) REVERT: B 1198 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8733 (mm-30) REVERT: B 1203 GLU cc_start: 0.9394 (tm-30) cc_final: 0.9115 (tm-30) REVERT: B 1218 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8047 (tm-30) REVERT: C 143 THR cc_start: 0.7455 (p) cc_final: 0.6028 (t) REVERT: C 211 LYS cc_start: 0.8272 (tttp) cc_final: 0.7912 (tttp) REVERT: C 248 ILE cc_start: 0.8754 (mt) cc_final: 0.8500 (mm) REVERT: C 275 GLN cc_start: 0.7811 (mm110) cc_final: 0.7508 (mm-40) REVERT: C 277 MET cc_start: 0.6715 (pmm) cc_final: 0.6060 (pmm) REVERT: C 418 MET cc_start: 0.6536 (tmm) cc_final: 0.6189 (tmm) REVERT: C 421 MET cc_start: 0.3012 (mmm) cc_final: 0.2304 (mmt) REVERT: C 468 ARG cc_start: 0.8262 (tpm170) cc_final: 0.7957 (tpm170) REVERT: C 578 ARG cc_start: 0.8500 (mmp-170) cc_final: 0.7885 (mmm160) REVERT: C 665 MET cc_start: 0.8295 (tmm) cc_final: 0.7754 (tpp) REVERT: C 711 ASP cc_start: 0.9270 (t0) cc_final: 0.9069 (t70) REVERT: C 719 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8678 (mm110) REVERT: C 757 MET cc_start: 0.8939 (tmm) cc_final: 0.8282 (tmm) REVERT: C 1203 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8400 (tm-30) REVERT: C 1209 ASP cc_start: 0.8940 (m-30) cc_final: 0.8535 (m-30) REVERT: D 173 MET cc_start: 0.8905 (mtm) cc_final: 0.8683 (mtm) REVERT: D 181 LEU cc_start: 0.9320 (mt) cc_final: 0.8818 (pt) REVERT: D 183 LYS cc_start: 0.8000 (mttt) cc_final: 0.7795 (mmtm) REVERT: D 291 HIS cc_start: 0.8800 (m90) cc_final: 0.8251 (m170) REVERT: D 363 VAL cc_start: 0.8844 (m) cc_final: 0.8353 (p) REVERT: D 462 LEU cc_start: 0.9078 (mt) cc_final: 0.8806 (mt) REVERT: D 474 SER cc_start: 0.8241 (m) cc_final: 0.7888 (t) REVERT: D 565 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7808 (tp30) REVERT: D 642 MET cc_start: 0.9180 (ttp) cc_final: 0.8953 (tmm) REVERT: D 708 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7966 (mt-10) REVERT: D 758 LEU cc_start: 0.9428 (tt) cc_final: 0.9141 (tt) REVERT: D 1129 TRP cc_start: 0.8124 (t60) cc_final: 0.7848 (t60) REVERT: D 1195 ASP cc_start: 0.9166 (m-30) cc_final: 0.8815 (m-30) REVERT: D 1235 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8322 (mp0) REVERT: I 57 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7388 (ttpt) REVERT: I 61 MET cc_start: 0.4527 (ptm) cc_final: 0.4269 (ptm) REVERT: I 188 MET cc_start: 0.6904 (mmp) cc_final: 0.6527 (mmm) REVERT: J 38 MET cc_start: 0.4703 (mpp) cc_final: 0.2202 (tpt) outliers start: 1 outliers final: 0 residues processed: 530 average time/residue: 0.1585 time to fit residues: 134.8041 Evaluate side-chains 408 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 90 optimal weight: 5.9990 chunk 132 optimal weight: 0.0980 chunk 316 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 308 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 120 optimal weight: 0.1980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN B 459 GLN B 515 HIS ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 ASN C 151 HIS C 299 ASN C 438 GLN ** C 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 ASN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 698 ASN C 704 GLN C 746 HIS C 756 GLN C1115 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS D1115 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.101430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.071408 restraints weight = 210325.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.074183 restraints weight = 144800.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.075452 restraints weight = 105988.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.076569 restraints weight = 79561.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.076914 restraints weight = 66323.298| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.9941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26364 Z= 0.136 Angle : 0.614 9.542 35584 Z= 0.322 Chirality : 0.042 0.201 3993 Planarity : 0.004 0.052 4551 Dihedral : 4.550 26.680 3504 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 0.07 % Allowed : 1.86 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3148 helix: 1.10 (0.13), residues: 1672 sheet: -0.37 (0.30), residues: 316 loop : -1.61 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 700 TYR 0.026 0.001 TYR C 572 PHE 0.019 0.001 PHE I 235 TRP 0.048 0.002 TRP I 297 HIS 0.010 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00295 (26364) covalent geometry : angle 0.61405 (35584) hydrogen bonds : bond 0.03713 ( 1230) hydrogen bonds : angle 4.51221 ( 3641) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 512 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8845 (tp) cc_final: 0.8465 (pt) REVERT: A 175 LYS cc_start: 0.7752 (mtpt) cc_final: 0.7458 (pttm) REVERT: A 181 LEU cc_start: 0.8379 (mt) cc_final: 0.7701 (pt) REVERT: A 292 SER cc_start: 0.8444 (m) cc_final: 0.7937 (t) REVERT: A 338 ILE cc_start: 0.9321 (mm) cc_final: 0.9108 (mm) REVERT: A 409 GLN cc_start: 0.7747 (mt0) cc_final: 0.7306 (mp10) REVERT: A 418 MET cc_start: 0.7339 (tpt) cc_final: 0.6780 (tpt) REVERT: A 471 ILE cc_start: 0.9159 (mm) cc_final: 0.8783 (pt) REVERT: A 499 ASP cc_start: 0.8497 (t0) cc_final: 0.8281 (t0) REVERT: A 524 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7700 (mm-30) REVERT: A 665 MET cc_start: 0.8970 (ttm) cc_final: 0.8770 (ttp) REVERT: A 687 MET cc_start: 0.8700 (mmp) cc_final: 0.8314 (mmm) REVERT: A 724 LEU cc_start: 0.9482 (tp) cc_final: 0.9187 (tp) REVERT: A 727 TYR cc_start: 0.7552 (p90) cc_final: 0.7211 (p90) REVERT: A 1232 MET cc_start: 0.8864 (mmp) cc_final: 0.8589 (mmp) REVERT: B 184 LEU cc_start: 0.9355 (tp) cc_final: 0.9090 (tp) REVERT: B 242 SER cc_start: 0.8886 (m) cc_final: 0.8539 (m) REVERT: B 243 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8517 (pttt) REVERT: B 290 MET cc_start: 0.6512 (mmp) cc_final: 0.5626 (mmt) REVERT: B 376 PHE cc_start: 0.7712 (m-80) cc_final: 0.7120 (m-80) REVERT: B 407 ARG cc_start: 0.8857 (ttp-170) cc_final: 0.8047 (mtt90) REVERT: B 408 THR cc_start: 0.7910 (p) cc_final: 0.7710 (t) REVERT: B 418 MET cc_start: 0.6217 (tmm) cc_final: 0.5472 (tpp) REVERT: B 442 LEU cc_start: 0.8637 (mt) cc_final: 0.8261 (tp) REVERT: B 492 MET cc_start: 0.8286 (tpp) cc_final: 0.7762 (tpp) REVERT: B 514 MET cc_start: 0.8585 (mmp) cc_final: 0.8371 (mmp) REVERT: B 554 ARG cc_start: 0.8901 (tpt170) cc_final: 0.8695 (mmm-85) REVERT: B 665 MET cc_start: 0.9085 (ttm) cc_final: 0.8626 (ttm) REVERT: B 675 CYS cc_start: 0.8769 (t) cc_final: 0.8242 (p) REVERT: B 711 ASP cc_start: 0.8699 (m-30) cc_final: 0.8116 (m-30) REVERT: B 712 GLN cc_start: 0.9173 (tp40) cc_final: 0.8838 (tp-100) REVERT: B 749 PHE cc_start: 0.9117 (t80) cc_final: 0.8828 (t80) REVERT: B 1203 GLU cc_start: 0.9367 (tm-30) cc_final: 0.9129 (tm-30) REVERT: B 1218 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8045 (tm-30) REVERT: C 248 ILE cc_start: 0.8820 (mt) cc_final: 0.8514 (mm) REVERT: C 277 MET cc_start: 0.6571 (pmm) cc_final: 0.5723 (pmm) REVERT: C 418 MET cc_start: 0.6637 (tmm) cc_final: 0.6311 (tmm) REVERT: C 421 MET cc_start: 0.3093 (mmm) cc_final: 0.2362 (mmt) REVERT: C 468 ARG cc_start: 0.8251 (tpm170) cc_final: 0.7891 (tpm170) REVERT: C 514 MET cc_start: 0.8819 (tpp) cc_final: 0.8240 (tpp) REVERT: C 526 LEU cc_start: 0.8677 (mt) cc_final: 0.8327 (mt) REVERT: C 578 ARG cc_start: 0.8388 (mmp-170) cc_final: 0.7881 (mmm160) REVERT: C 722 MET cc_start: 0.8364 (ptt) cc_final: 0.7689 (ppp) REVERT: C 757 MET cc_start: 0.8618 (tmm) cc_final: 0.8176 (tmm) REVERT: C 1203 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8307 (tp30) REVERT: C 1209 ASP cc_start: 0.8896 (m-30) cc_final: 0.8475 (m-30) REVERT: D 181 LEU cc_start: 0.9323 (mt) cc_final: 0.8818 (pt) REVERT: D 183 LYS cc_start: 0.8027 (mttt) cc_final: 0.7790 (mmtm) REVERT: D 363 VAL cc_start: 0.8806 (m) cc_final: 0.8339 (p) REVERT: D 418 MET cc_start: 0.6340 (mmm) cc_final: 0.6063 (mmm) REVERT: D 462 LEU cc_start: 0.9095 (mt) cc_final: 0.8833 (mt) REVERT: D 565 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7787 (tp30) REVERT: D 649 LYS cc_start: 0.9126 (ptmm) cc_final: 0.8920 (ptmm) REVERT: D 708 GLU cc_start: 0.8523 (mt-10) cc_final: 0.7993 (mt-10) REVERT: D 737 CYS cc_start: 0.8876 (m) cc_final: 0.8280 (t) REVERT: D 758 LEU cc_start: 0.9452 (tt) cc_final: 0.9174 (pp) REVERT: D 1129 TRP cc_start: 0.8347 (t60) cc_final: 0.7977 (t60) REVERT: D 1202 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8126 (tm-30) REVERT: D 1232 MET cc_start: 0.9001 (mtp) cc_final: 0.8762 (ttm) REVERT: D 1235 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8239 (mt-10) REVERT: I 61 MET cc_start: 0.4608 (ptm) cc_final: 0.4335 (ptm) REVERT: I 188 MET cc_start: 0.6997 (mmp) cc_final: 0.6612 (mmm) outliers start: 2 outliers final: 1 residues processed: 514 average time/residue: 0.1656 time to fit residues: 135.5382 Evaluate side-chains 398 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 87 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 298 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.070543 restraints weight = 163728.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.072445 restraints weight = 116241.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.073643 restraints weight = 91838.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074765 restraints weight = 78450.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.075202 restraints weight = 69841.716| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 1.0442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26364 Z= 0.143 Angle : 0.639 9.313 35584 Z= 0.333 Chirality : 0.042 0.184 3993 Planarity : 0.004 0.052 4551 Dihedral : 4.563 26.208 3504 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Rotamer: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.15), residues: 3148 helix: 1.05 (0.13), residues: 1677 sheet: -0.39 (0.30), residues: 318 loop : -1.64 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 700 TYR 0.016 0.001 TYR A1134 PHE 0.031 0.002 PHE C1184 TRP 0.036 0.002 TRP C 644 HIS 0.006 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00312 (26364) covalent geometry : angle 0.63904 (35584) hydrogen bonds : bond 0.03802 ( 1230) hydrogen bonds : angle 4.54140 ( 3641) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 511 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8863 (tp) cc_final: 0.8508 (pt) REVERT: A 175 LYS cc_start: 0.7765 (mtpt) cc_final: 0.7471 (pttm) REVERT: A 181 LEU cc_start: 0.8480 (mt) cc_final: 0.7840 (pt) REVERT: A 249 CYS cc_start: 0.8473 (t) cc_final: 0.8003 (t) REVERT: A 290 MET cc_start: 0.8848 (mpp) cc_final: 0.7864 (mpp) REVERT: A 292 SER cc_start: 0.8497 (m) cc_final: 0.7923 (t) REVERT: A 338 ILE cc_start: 0.9349 (mm) cc_final: 0.9038 (tp) REVERT: A 409 GLN cc_start: 0.7747 (mt0) cc_final: 0.7300 (mp10) REVERT: A 418 MET cc_start: 0.7411 (tpt) cc_final: 0.6831 (tpt) REVERT: A 471 ILE cc_start: 0.9160 (mm) cc_final: 0.8824 (pt) REVERT: A 499 ASP cc_start: 0.8515 (t0) cc_final: 0.8290 (t0) REVERT: A 524 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7597 (mm-30) REVERT: A 687 MET cc_start: 0.8766 (mmp) cc_final: 0.8374 (mmm) REVERT: A 694 GLU cc_start: 0.8315 (pt0) cc_final: 0.7735 (pp20) REVERT: A 695 LEU cc_start: 0.9249 (mt) cc_final: 0.9023 (mt) REVERT: A 704 GLN cc_start: 0.9072 (tp40) cc_final: 0.8419 (tp-100) REVERT: A 758 LEU cc_start: 0.7460 (tp) cc_final: 0.7233 (tp) REVERT: A 1229 ASN cc_start: 0.8428 (m-40) cc_final: 0.8152 (m-40) REVERT: A 1232 MET cc_start: 0.8896 (mmp) cc_final: 0.8607 (mmp) REVERT: B 184 LEU cc_start: 0.9441 (tp) cc_final: 0.9202 (tp) REVERT: B 242 SER cc_start: 0.8925 (m) cc_final: 0.8599 (m) REVERT: B 243 LYS cc_start: 0.8744 (mmtm) cc_final: 0.8519 (pttt) REVERT: B 290 MET cc_start: 0.6745 (mmp) cc_final: 0.5985 (mmt) REVERT: B 376 PHE cc_start: 0.7836 (m-80) cc_final: 0.7191 (m-80) REVERT: B 407 ARG cc_start: 0.8845 (ttp-170) cc_final: 0.8031 (mtt90) REVERT: B 418 MET cc_start: 0.6568 (tmm) cc_final: 0.5901 (tpt) REVERT: B 442 LEU cc_start: 0.8602 (mt) cc_final: 0.8229 (tp) REVERT: B 492 MET cc_start: 0.8314 (tpp) cc_final: 0.7774 (tpp) REVERT: B 554 ARG cc_start: 0.8955 (tpt170) cc_final: 0.8037 (tpt90) REVERT: B 665 MET cc_start: 0.9178 (ttm) cc_final: 0.8718 (ttm) REVERT: B 675 CYS cc_start: 0.8753 (t) cc_final: 0.8273 (p) REVERT: B 711 ASP cc_start: 0.8565 (m-30) cc_final: 0.8018 (m-30) REVERT: B 712 GLN cc_start: 0.9187 (tp40) cc_final: 0.8880 (tp-100) REVERT: B 722 MET cc_start: 0.8712 (mpp) cc_final: 0.8322 (mpp) REVERT: B 749 PHE cc_start: 0.9132 (t80) cc_final: 0.8883 (t80) REVERT: B 1203 GLU cc_start: 0.9417 (tm-30) cc_final: 0.9180 (tm-30) REVERT: B 1218 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8040 (tm-30) REVERT: C 248 ILE cc_start: 0.8831 (mt) cc_final: 0.8451 (tp) REVERT: C 275 GLN cc_start: 0.7955 (mm110) cc_final: 0.6464 (pm20) REVERT: C 418 MET cc_start: 0.6618 (tmm) cc_final: 0.6309 (tmm) REVERT: C 421 MET cc_start: 0.3246 (mmm) cc_final: 0.2549 (mmt) REVERT: C 468 ARG cc_start: 0.8190 (tpm170) cc_final: 0.7849 (tpm170) REVERT: C 514 MET cc_start: 0.8813 (tpp) cc_final: 0.8084 (tpp) REVERT: C 526 LEU cc_start: 0.8719 (mt) cc_final: 0.8346 (mt) REVERT: C 578 ARG cc_start: 0.8500 (mmp-170) cc_final: 0.7970 (mmm160) REVERT: C 667 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8871 (mttt) REVERT: C 691 ILE cc_start: 0.7620 (mt) cc_final: 0.7120 (mt) REVERT: C 722 MET cc_start: 0.8447 (ptt) cc_final: 0.7877 (ppp) REVERT: C 757 MET cc_start: 0.8588 (tmm) cc_final: 0.8160 (tmm) REVERT: C 1202 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8214 (mt-10) REVERT: C 1203 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8404 (tp30) REVERT: C 1209 ASP cc_start: 0.8907 (m-30) cc_final: 0.8681 (m-30) REVERT: C 1225 GLU cc_start: 0.8755 (mp0) cc_final: 0.8446 (mp0) REVERT: D 181 LEU cc_start: 0.9307 (mt) cc_final: 0.8877 (pt) REVERT: D 183 LYS cc_start: 0.8069 (mttt) cc_final: 0.7820 (mmtm) REVERT: D 198 GLN cc_start: 0.8991 (mp10) cc_final: 0.8374 (tm-30) REVERT: D 363 VAL cc_start: 0.8844 (m) cc_final: 0.8395 (p) REVERT: D 418 MET cc_start: 0.6303 (mmm) cc_final: 0.6059 (mmm) REVERT: D 441 ASP cc_start: 0.8465 (t70) cc_final: 0.7905 (t0) REVERT: D 462 LEU cc_start: 0.9125 (mt) cc_final: 0.8831 (mt) REVERT: D 536 THR cc_start: 0.9102 (p) cc_final: 0.8811 (p) REVERT: D 565 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7894 (tp30) REVERT: D 708 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7944 (mt-10) REVERT: D 737 CYS cc_start: 0.9036 (m) cc_final: 0.8278 (t) REVERT: D 1129 TRP cc_start: 0.8051 (t60) cc_final: 0.7640 (t60) REVERT: D 1195 ASP cc_start: 0.9128 (m-30) cc_final: 0.8706 (m-30) REVERT: D 1197 GLU cc_start: 0.8693 (pp20) cc_final: 0.8419 (pt0) REVERT: D 1232 MET cc_start: 0.8836 (mtp) cc_final: 0.8455 (ttm) REVERT: D 1235 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8322 (mp0) REVERT: I 61 MET cc_start: 0.4507 (ptm) cc_final: 0.4265 (ptm) REVERT: I 188 MET cc_start: 0.6694 (mmp) cc_final: 0.6394 (mmm) REVERT: J 38 MET cc_start: 0.4735 (mpp) cc_final: 0.2004 (tpt) outliers start: 1 outliers final: 0 residues processed: 511 average time/residue: 0.1607 time to fit residues: 130.9238 Evaluate side-chains 407 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 168 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 236 optimal weight: 5.9990 chunk 272 optimal weight: 50.0000 chunk 212 optimal weight: 10.0000 chunk 309 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 HIS A 153 ASN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 ASN ** A1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 151 HIS C 262 GLN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS D 739 GLN D1115 ASN ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.093659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.065423 restraints weight = 153337.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.067134 restraints weight = 111434.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.067723 restraints weight = 81687.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.068206 restraints weight = 75668.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.068222 restraints weight = 72866.191| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 1.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 26364 Z= 0.298 Angle : 0.908 11.555 35584 Z= 0.474 Chirality : 0.050 0.240 3993 Planarity : 0.006 0.089 4551 Dihedral : 5.959 28.152 3504 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.42 % Favored : 91.54 % Rotamer: Outliers : 0.04 % Allowed : 1.58 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3148 helix: 0.03 (0.12), residues: 1666 sheet: -0.85 (0.28), residues: 352 loop : -2.07 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 272 TYR 0.039 0.003 TYR B 527 PHE 0.028 0.003 PHE D 162 TRP 0.059 0.004 TRP B 644 HIS 0.014 0.003 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00637 (26364) covalent geometry : angle 0.90807 (35584) hydrogen bonds : bond 0.05426 ( 1230) hydrogen bonds : angle 5.51303 ( 3641) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 HIS cc_start: 0.7286 (t-170) cc_final: 0.6987 (t-90) REVERT: A 175 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7518 (pttm) REVERT: A 181 LEU cc_start: 0.8814 (mt) cc_final: 0.8475 (pt) REVERT: A 290 MET cc_start: 0.8826 (mpp) cc_final: 0.8275 (mpp) REVERT: A 316 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8026 (mt-10) REVERT: A 418 MET cc_start: 0.7646 (tpt) cc_final: 0.6927 (tpt) REVERT: A 499 ASP cc_start: 0.8813 (t0) cc_final: 0.8539 (t0) REVERT: A 514 MET cc_start: 0.8918 (mmm) cc_final: 0.8706 (mmm) REVERT: A 524 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7562 (tp30) REVERT: A 525 GLU cc_start: 0.9066 (pm20) cc_final: 0.8714 (pm20) REVERT: A 694 GLU cc_start: 0.8647 (pt0) cc_final: 0.8407 (pp20) REVERT: A 722 MET cc_start: 0.8723 (mmt) cc_final: 0.8367 (mmt) REVERT: A 1209 ASP cc_start: 0.8557 (m-30) cc_final: 0.8341 (p0) REVERT: A 1210 ASP cc_start: 0.9368 (t0) cc_final: 0.9144 (t70) REVERT: A 1232 MET cc_start: 0.9069 (mmp) cc_final: 0.8713 (mmp) REVERT: B 184 LEU cc_start: 0.9557 (tp) cc_final: 0.9242 (tp) REVERT: B 243 LYS cc_start: 0.8703 (mmtm) cc_final: 0.8421 (pttt) REVERT: B 290 MET cc_start: 0.7323 (mmp) cc_final: 0.6790 (tpt) REVERT: B 316 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8434 (pt0) REVERT: B 317 LYS cc_start: 0.9039 (ptpp) cc_final: 0.8718 (pttt) REVERT: B 376 PHE cc_start: 0.8351 (m-80) cc_final: 0.7631 (m-80) REVERT: B 418 MET cc_start: 0.7140 (tmm) cc_final: 0.6506 (tpt) REVERT: B 421 MET cc_start: 0.2469 (mmt) cc_final: 0.2139 (mmt) REVERT: B 442 LEU cc_start: 0.8547 (mt) cc_final: 0.8108 (tp) REVERT: B 514 MET cc_start: 0.8547 (mmp) cc_final: 0.8199 (mmp) REVERT: B 538 TYR cc_start: 0.8045 (t80) cc_final: 0.7691 (t80) REVERT: B 554 ARG cc_start: 0.8964 (tpt170) cc_final: 0.8453 (tpt90) REVERT: B 555 ILE cc_start: 0.8656 (mp) cc_final: 0.8414 (mp) REVERT: B 557 LEU cc_start: 0.9219 (mt) cc_final: 0.8921 (tp) REVERT: B 665 MET cc_start: 0.9239 (ttm) cc_final: 0.8980 (ttm) REVERT: B 690 ASP cc_start: 0.8884 (m-30) cc_final: 0.8567 (t0) REVERT: B 711 ASP cc_start: 0.8862 (m-30) cc_final: 0.8361 (m-30) REVERT: B 712 GLN cc_start: 0.9191 (tp40) cc_final: 0.8891 (tp-100) REVERT: B 722 MET cc_start: 0.8743 (mpp) cc_final: 0.8438 (mpp) REVERT: B 1191 LYS cc_start: 0.8690 (mttp) cc_final: 0.8366 (pttt) REVERT: B 1203 GLU cc_start: 0.9631 (tm-30) cc_final: 0.9297 (tm-30) REVERT: C 248 ILE cc_start: 0.8545 (mt) cc_final: 0.8219 (tp) REVERT: C 418 MET cc_start: 0.6907 (tmm) cc_final: 0.6608 (tmm) REVERT: C 421 MET cc_start: 0.4247 (mmm) cc_final: 0.3710 (mmp) REVERT: C 462 LEU cc_start: 0.9249 (mt) cc_final: 0.8919 (tp) REVERT: C 526 LEU cc_start: 0.8921 (mt) cc_final: 0.8641 (mt) REVERT: C 642 MET cc_start: 0.8923 (tpp) cc_final: 0.8627 (tpp) REVERT: C 722 MET cc_start: 0.8727 (ptt) cc_final: 0.8130 (ptt) REVERT: C 1202 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8682 (mt-10) REVERT: C 1203 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8688 (tp30) REVERT: D 156 MET cc_start: 0.8367 (mpp) cc_final: 0.8041 (mpp) REVERT: D 181 LEU cc_start: 0.9362 (mt) cc_final: 0.8928 (pt) REVERT: D 441 ASP cc_start: 0.8834 (t70) cc_final: 0.8050 (t0) REVERT: D 462 LEU cc_start: 0.9190 (mt) cc_final: 0.8885 (mt) REVERT: D 696 ASN cc_start: 0.8937 (m-40) cc_final: 0.8572 (t0) REVERT: D 700 ARG cc_start: 0.8456 (mmp80) cc_final: 0.8152 (mmp80) REVERT: D 745 LYS cc_start: 0.9052 (mttm) cc_final: 0.8603 (ptmm) REVERT: D 1197 GLU cc_start: 0.8716 (pp20) cc_final: 0.8318 (pt0) REVERT: I 16 ASN cc_start: 0.9012 (p0) cc_final: 0.8732 (p0) REVERT: I 188 MET cc_start: 0.6983 (mmp) cc_final: 0.6717 (mmm) REVERT: I 289 TYR cc_start: 0.4141 (m-80) cc_final: 0.3370 (m-80) outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.1699 time to fit residues: 126.2503 Evaluate side-chains 350 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 74 optimal weight: 0.0370 chunk 177 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 236 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A1229 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 288 ASN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN D1115 ASN D1127 GLN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.095747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.066135 restraints weight = 170648.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.067771 restraints weight = 117625.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.069045 restraints weight = 91475.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.070019 restraints weight = 77393.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.070486 restraints weight = 69018.172| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 1.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26364 Z= 0.170 Angle : 0.730 12.648 35584 Z= 0.378 Chirality : 0.045 0.288 3993 Planarity : 0.005 0.095 4551 Dihedral : 5.290 29.174 3504 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 3148 helix: 0.46 (0.12), residues: 1663 sheet: -0.71 (0.29), residues: 333 loop : -1.77 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C1226 TYR 0.035 0.002 TYR A1204 PHE 0.015 0.002 PHE C1184 TRP 0.051 0.003 TRP B 644 HIS 0.017 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00373 (26364) covalent geometry : angle 0.73030 (35584) hydrogen bonds : bond 0.04429 ( 1230) hydrogen bonds : angle 5.02573 ( 3641) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 HIS cc_start: 0.7504 (t-170) cc_final: 0.7068 (t-90) REVERT: A 172 LEU cc_start: 0.9318 (tp) cc_final: 0.9072 (mt) REVERT: A 175 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7566 (pttm) REVERT: A 181 LEU cc_start: 0.8826 (mt) cc_final: 0.8301 (pt) REVERT: A 249 CYS cc_start: 0.8465 (t) cc_final: 0.8230 (t) REVERT: A 290 MET cc_start: 0.8934 (mpp) cc_final: 0.8146 (mpp) REVERT: A 292 SER cc_start: 0.8500 (m) cc_final: 0.8058 (t) REVERT: A 316 GLU cc_start: 0.8757 (mt-10) cc_final: 0.7902 (mt-10) REVERT: A 418 MET cc_start: 0.7605 (tpt) cc_final: 0.6770 (tpt) REVERT: A 471 ILE cc_start: 0.9279 (mm) cc_final: 0.9042 (pt) REVERT: A 499 ASP cc_start: 0.8397 (t0) cc_final: 0.8041 (t0) REVERT: A 524 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7366 (tp30) REVERT: A 525 GLU cc_start: 0.8760 (pm20) cc_final: 0.8458 (pm20) REVERT: A 694 GLU cc_start: 0.8435 (pt0) cc_final: 0.8230 (pp20) REVERT: A 708 GLU cc_start: 0.8414 (pt0) cc_final: 0.7756 (pt0) REVERT: A 1182 LYS cc_start: 0.7679 (mttp) cc_final: 0.7463 (mmtm) REVERT: A 1198 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8316 (pp20) REVERT: A 1210 ASP cc_start: 0.9345 (t0) cc_final: 0.9116 (t0) REVERT: B 184 LEU cc_start: 0.9511 (tp) cc_final: 0.9219 (tp) REVERT: B 290 MET cc_start: 0.7333 (mmp) cc_final: 0.6958 (tpt) REVERT: B 316 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8496 (pt0) REVERT: B 317 LYS cc_start: 0.9075 (ptpp) cc_final: 0.8810 (ptpp) REVERT: B 376 PHE cc_start: 0.8419 (m-80) cc_final: 0.7814 (m-80) REVERT: B 407 ARG cc_start: 0.8752 (ttp-170) cc_final: 0.8027 (mtt90) REVERT: B 442 LEU cc_start: 0.8751 (mt) cc_final: 0.8315 (tp) REVERT: B 498 LEU cc_start: 0.8094 (mt) cc_final: 0.7861 (mt) REVERT: B 502 ASP cc_start: 0.9138 (m-30) cc_final: 0.8785 (p0) REVERT: B 514 MET cc_start: 0.8751 (mmp) cc_final: 0.8426 (mmp) REVERT: B 538 TYR cc_start: 0.8083 (t80) cc_final: 0.7697 (t80) REVERT: B 554 ARG cc_start: 0.9047 (tpt170) cc_final: 0.8500 (tpt90) REVERT: B 557 LEU cc_start: 0.9075 (mt) cc_final: 0.8767 (tp) REVERT: B 687 MET cc_start: 0.9278 (tpp) cc_final: 0.8664 (tpp) REVERT: B 701 ASP cc_start: 0.8615 (m-30) cc_final: 0.8326 (m-30) REVERT: B 712 GLN cc_start: 0.9205 (tp40) cc_final: 0.8761 (tm-30) REVERT: B 722 MET cc_start: 0.8824 (mpp) cc_final: 0.8526 (mpp) REVERT: B 1191 LYS cc_start: 0.8712 (mttp) cc_final: 0.8499 (pttt) REVERT: B 1225 GLU cc_start: 0.8828 (pm20) cc_final: 0.8601 (pm20) REVERT: C 156 MET cc_start: 0.8667 (mmm) cc_final: 0.8360 (mmm) REVERT: C 235 ASP cc_start: 0.9293 (m-30) cc_final: 0.8609 (t70) REVERT: C 238 LYS cc_start: 0.7869 (mppt) cc_final: 0.7569 (mmtm) REVERT: C 239 ASP cc_start: 0.8529 (t0) cc_final: 0.8119 (m-30) REVERT: C 248 ILE cc_start: 0.8547 (mt) cc_final: 0.8247 (tp) REVERT: C 421 MET cc_start: 0.4136 (mmm) cc_final: 0.3645 (mmt) REVERT: C 432 MET cc_start: 0.8330 (mpp) cc_final: 0.7566 (tpt) REVERT: C 462 LEU cc_start: 0.9179 (mt) cc_final: 0.8835 (tp) REVERT: C 526 LEU cc_start: 0.9048 (mt) cc_final: 0.8749 (mt) REVERT: C 640 GLU cc_start: 0.8892 (mp0) cc_final: 0.8680 (pm20) REVERT: C 642 MET cc_start: 0.8789 (tpp) cc_final: 0.8581 (tpp) REVERT: C 687 MET cc_start: 0.8210 (tpp) cc_final: 0.7820 (tpt) REVERT: C 722 MET cc_start: 0.8702 (ptt) cc_final: 0.8220 (ptt) REVERT: C 1202 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8668 (mt-10) REVERT: D 154 LYS cc_start: 0.8500 (mppt) cc_final: 0.8116 (mmtm) REVERT: D 156 MET cc_start: 0.8463 (mpp) cc_final: 0.8010 (mpp) REVERT: D 181 LEU cc_start: 0.9414 (mt) cc_final: 0.8973 (pt) REVERT: D 291 HIS cc_start: 0.8716 (m90) cc_final: 0.8331 (m-70) REVERT: D 441 ASP cc_start: 0.8696 (t70) cc_final: 0.7968 (t0) REVERT: D 462 LEU cc_start: 0.9196 (mt) cc_final: 0.8912 (mt) REVERT: D 678 MET cc_start: 0.8766 (ttp) cc_final: 0.8513 (ttp) REVERT: D 696 ASN cc_start: 0.8887 (m-40) cc_final: 0.8574 (t0) REVERT: D 700 ARG cc_start: 0.8458 (mmp80) cc_final: 0.8208 (mmp80) REVERT: D 745 LYS cc_start: 0.9219 (mttm) cc_final: 0.8718 (ptmm) REVERT: D 1191 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8753 (pttp) REVERT: D 1197 GLU cc_start: 0.8666 (pp20) cc_final: 0.8421 (pt0) REVERT: D 1235 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8377 (mp0) REVERT: I 145 TYR cc_start: 0.4641 (p90) cc_final: 0.4110 (p90) REVERT: I 289 TYR cc_start: 0.4548 (m-80) cc_final: 0.4103 (m-80) outliers start: 0 outliers final: 0 residues processed: 481 average time/residue: 0.1656 time to fit residues: 126.1222 Evaluate side-chains 376 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 252 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 303 optimal weight: 0.9980 chunk 57 optimal weight: 0.0370 chunk 119 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 GLN B 262 GLN ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN D1115 ASN I 75 GLN ** I 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS I 268 ASN J 18 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.097228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065857 restraints weight = 183724.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067969 restraints weight = 124217.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.069577 restraints weight = 95553.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.070240 restraints weight = 79590.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070824 restraints weight = 71372.305| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 1.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26364 Z= 0.139 Angle : 0.701 13.694 35584 Z= 0.359 Chirality : 0.043 0.208 3993 Planarity : 0.004 0.056 4551 Dihedral : 4.968 25.670 3504 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3148 helix: 0.66 (0.13), residues: 1658 sheet: -0.56 (0.29), residues: 328 loop : -1.68 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1226 TYR 0.034 0.001 TYR A1204 PHE 0.017 0.002 PHE C 581 TRP 0.043 0.002 TRP I 332 HIS 0.014 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00305 (26364) covalent geometry : angle 0.70135 (35584) hydrogen bonds : bond 0.04101 ( 1230) hydrogen bonds : angle 4.81089 ( 3641) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5311.06 seconds wall clock time: 92 minutes 11.47 seconds (5531.47 seconds total)