Starting phenix.real_space_refine on Sun Jun 22 18:47:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ddw_27344/06_2025/8ddw_27344.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ddw_27344/06_2025/8ddw_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ddw_27344/06_2025/8ddw_27344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ddw_27344/06_2025/8ddw_27344.map" model { file = "/net/cci-nas-00/data/ceres_data/8ddw_27344/06_2025/8ddw_27344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ddw_27344/06_2025/8ddw_27344.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.16, per 1000 atoms: 0.62 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: 5.91 Conformation dependent library (CDL) restraints added in 3.4 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: 2.62 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: 8.75 Time building geometry restraints manager: 7.04 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: 5.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 56.660 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.240 ------------------------------------------------------------------------------- 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 : 11.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (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 TRP 0.009 0.001 TRP B 483 HIS 0.008 0.001 HIS D 633 PHE 0.013 0.001 PHE B 376 TYR 0.016 0.001 TYR A 380 ARG 0.003 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.18015 ( 1230) hydrogen bonds : angle 6.33003 ( 3641) covalent geometry : bond 0.00275 (26364) covalent geometry : angle 0.52867 (35584) *********************** 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 : 3.047 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: 0.6300 (m-70) cc_final: 0.5568 (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: 0.6105 (tp40) REVERT: A 296 LEU cc_start: -0.1325 (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: 0.8805 (pt) REVERT: A 489 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8391 (mt-10) REVERT: A 516 ARG cc_start: 0.8952 (mtp-110) cc_final: 0.8614 (mmp-170) REVERT: A 559 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: A 633 HIS cc_start: 0.5343 (OUTLIER) cc_final: 0.4928 (t70) REVERT: A 662 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 704 GLN cc_start: 0.9013 (tp40) cc_final: 0.8675 (tp40) REVERT: A 708 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8451 (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: 0.6447 (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: 0.4591 (m100) REVERT: A 1186 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.7996 (p) REVERT: A 1194 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8253 (m-70) REVERT: A 1204 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8720 (t80) REVERT: A 1230 MET cc_start: 0.7838 (ttm) cc_final: 0.7242 (ttm) 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: 0.6982 (mmm160) REVERT: B 275 GLN cc_start: -0.1222 (OUTLIER) cc_final: -0.1436 (tp-100) REVERT: B 291 HIS cc_start: 0.4914 (m-70) cc_final: 0.4200 (m-70) REVERT: B 350 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7494 (mp) REVERT: B 412 HIS cc_start: 0.2917 (OUTLIER) cc_final: 0.2547 (t70) REVERT: B 440 ILE cc_start: 0.8316 (mm) cc_final: 0.7994 (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: 0.7864 (mmpt) REVERT: B 469 VAL cc_start: 0.6950 (p) cc_final: 0.6719 (p) REVERT: B 471 ILE cc_start: 0.9262 (mm) cc_final: 0.9018 (pt) REVERT: B 492 MET cc_start: 0.7732 (tpp) cc_final: 0.6600 (tpp) REVERT: B 501 VAL cc_start: 0.7217 (t) cc_final: 0.6657 (t) REVERT: B 580 ARG cc_start: 0.6804 (ttt90) cc_final: 0.6173 (tpt170) REVERT: B 636 PHE cc_start: 0.7251 (m-80) cc_final: 0.6750 (m-10) REVERT: B 656 PHE cc_start: 0.8156 (t80) cc_final: 0.7609 (t80) REVERT: B 657 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: B 670 VAL cc_start: 0.8444 (t) cc_final: 0.8096 (t) REVERT: B 694 GLU cc_start: 0.8532 (mt-10) cc_final: 0.7986 (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: 0.6731 (t70) REVERT: B 748 ASP cc_start: 0.8915 (m-30) cc_final: 0.8631 (m-30) REVERT: B 752 HIS cc_start: 0.7021 (t-90) cc_final: 0.6807 (t-90) REVERT: B 754 CYS cc_start: 0.9161 (t) cc_final: 0.8869 (t) REVERT: B 756 GLN cc_start: 0.9268 (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: 0.8438 (mt) REVERT: B 1202 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 1213 ASN cc_start: 0.8536 (m-40) cc_final: 0.8260 (m-40) REVERT: B 1226 ARG cc_start: 0.8520 (mtt180) cc_final: 0.8254 (mtm-85) REVERT: C 158 VAL cc_start: 0.9360 (t) cc_final: 0.9150 (m) REVERT: C 186 ILE cc_start: 0.8059 (mt) cc_final: 0.7749 (mp) REVERT: C 248 ILE cc_start: 0.6914 (mt) cc_final: 0.6616 (tp) REVERT: C 291 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6534 (m170) REVERT: C 293 HIS cc_start: 0.7615 (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: 0.7916 (m) REVERT: C 414 PHE cc_start: 0.6763 (OUTLIER) cc_final: 0.6476 (m-80) REVERT: C 479 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7350 (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: 0.5988 (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: 0.7547 (p) REVERT: C 672 CYS cc_start: 0.8928 (t) cc_final: 0.8612 (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: 0.7399 (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: 0.8604 (pt) REVERT: D 261 ASN cc_start: 0.5803 (OUTLIER) cc_final: 0.5281 (m-40) REVERT: D 277 MET cc_start: 0.5539 (tmm) cc_final: 0.5267 (pmm) REVERT: D 278 SER cc_start: 0.4649 (t) cc_final: 0.3809 (m) REVERT: D 417 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5158 (mt) REVERT: D 431 ARG cc_start: 0.5347 (ptp-110) cc_final: 0.5031 (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: 0.8206 (p) REVERT: D 474 SER cc_start: 0.8548 (m) cc_final: 0.8342 (p) REVERT: D 506 LEU cc_start: 0.8903 (tp) cc_final: 0.8356 (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: 0.7668 (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: 0.8470 (mt) REVERT: D 642 MET cc_start: 0.8436 (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: 0.8154 (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: 0.7800 (mttt) REVERT: D 1195 ASP cc_start: 0.9179 (m-30) cc_final: 0.8955 (m-30) REVERT: D 1202 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7550 (pp20) REVERT: D 1235 GLU cc_start: 0.8873 (tp30) cc_final: 0.8671 (mm-30) REVERT: I 101 MET cc_start: 0.8686 (mmm) cc_final: 0.8200 (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: 0.5512 (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: 0.4785 (mt) outliers start: 233 outliers final: 49 residues processed: 1037 average time/residue: 0.4000 time to fit residues: 630.0472 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 : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 4.9990 chunk 242 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 129 optimal weight: 50.0000 chunk 250 optimal weight: 0.0980 chunk 97 optimal weight: 0.0870 chunk 152 optimal weight: 6.9990 chunk 186 optimal weight: 0.5980 chunk 290 optimal weight: 9.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 275 GLN A 288 ASN A 314 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 490 GLN A 510 ASN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 HIS ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 HIS A 712 GLN A 739 GLN A1116 ASN B 134 GLN B 198 GLN B 696 ASN B 697 HIS B1116 ASN B1194 HIS C 151 HIS C 189 HIS C 240 HIS C 275 GLN C 279 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS C 437 HIS C 539 HIS C 660 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN C 719 GLN C 746 HIS ** D 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS D 411 GLN ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 ASN D 719 GLN D 734 ASN D 739 GLN D1115 ASN D1199 GLN I 44 GLN ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 GLN ** I 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.118820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.089136 restraints weight = 164438.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.090903 restraints weight = 122586.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.092330 restraints weight = 98213.488| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26364 Z= 0.140 Angle : 0.633 10.619 35584 Z= 0.331 Chirality : 0.042 0.208 3993 Planarity : 0.004 0.052 4551 Dihedral : 4.722 27.061 3504 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 0.18 % Allowed : 4.37 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.15), residues: 3148 helix: 1.34 (0.13), residues: 1662 sheet: -0.17 (0.28), residues: 345 loop : -1.74 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 219 HIS 0.016 0.002 HIS I 142 PHE 0.032 0.002 PHE B 376 TYR 0.026 0.002 TYR D 479 ARG 0.015 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 1230) hydrogen bonds : angle 4.82023 ( 3641) covalent geometry : bond 0.00290 (26364) covalent geometry : angle 0.63297 (35584) *********************** 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 649 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 644 time to evaluate : 3.027 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: A 143 THR cc_start: 0.7557 (m) cc_final: 0.7105 (t) REVERT: A 156 MET cc_start: 0.8474 (mmt) cc_final: 0.7805 (mmp) REVERT: A 175 LYS cc_start: 0.7715 (tttt) cc_final: 0.7317 (mtpt) REVERT: A 197 LEU cc_start: 0.7407 (mt) cc_final: 0.7154 (mt) REVERT: A 244 SER cc_start: 0.8779 (t) cc_final: 0.8385 (m) REVERT: A 414 PHE cc_start: 0.6489 (t80) cc_final: 0.6111 (t80) REVERT: A 418 MET cc_start: 0.7566 (tpt) cc_final: 0.7243 (tpt) REVERT: A 471 ILE cc_start: 0.8906 (mm) cc_final: 0.8037 (pt) REVERT: A 489 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8383 (mt-10) REVERT: A 492 MET cc_start: 0.8612 (tpp) cc_final: 0.8285 (tpp) REVERT: A 524 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7402 (tp30) REVERT: A 704 GLN cc_start: 0.8712 (tp40) cc_final: 0.7859 (tp40) REVERT: A 712 GLN cc_start: 0.6999 (tp-100) cc_final: 0.6657 (tm-30) REVERT: A 729 LEU cc_start: 0.9025 (mt) cc_final: 0.8752 (mp) REVERT: A 1195 ASP cc_start: 0.8565 (m-30) cc_final: 0.8320 (m-30) REVERT: B 144 ILE cc_start: 0.8369 (mm) cc_final: 0.7881 (tp) REVERT: B 281 MET cc_start: 0.4996 (mtm) cc_final: 0.4740 (ptp) REVERT: B 418 MET cc_start: 0.3082 (mmm) cc_final: 0.2766 (tmm) REVERT: B 492 MET cc_start: 0.7957 (tpp) cc_final: 0.6893 (tpp) REVERT: B 580 ARG cc_start: 0.7053 (ttt90) cc_final: 0.6598 (tpt170) REVERT: B 687 MET cc_start: 0.7515 (tpp) cc_final: 0.7233 (tpp) REVERT: B 752 HIS cc_start: 0.7509 (t-90) cc_final: 0.6659 (t-90) REVERT: B 754 CYS cc_start: 0.8691 (t) cc_final: 0.8404 (t) REVERT: B 1179 TYR cc_start: 0.8563 (t80) cc_final: 0.8000 (t80) REVERT: B 1182 LYS cc_start: 0.7690 (mttp) cc_final: 0.7300 (mmmt) REVERT: B 1202 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8204 (tm-30) REVERT: B 1203 GLU cc_start: 0.8067 (tp30) cc_final: 0.7843 (pt0) REVERT: B 1230 MET cc_start: 0.8544 (mtp) cc_final: 0.8209 (mtp) REVERT: C 156 MET cc_start: 0.7574 (mtp) cc_final: 0.6271 (mtm) REVERT: C 158 VAL cc_start: 0.9106 (t) cc_final: 0.8894 (m) REVERT: C 290 MET cc_start: 0.7126 (mmp) cc_final: 0.6735 (mmp) REVERT: C 494 ASP cc_start: 0.7355 (m-30) cc_final: 0.6748 (m-30) REVERT: C 672 CYS cc_start: 0.8575 (t) cc_final: 0.8363 (t) REVERT: C 675 CYS cc_start: 0.7607 (m) cc_final: 0.7046 (m) REVERT: C 694 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8286 (tt0) REVERT: C 758 LEU cc_start: 0.8419 (tp) cc_final: 0.7656 (tp) REVERT: C 1230 MET cc_start: 0.8896 (mtp) cc_final: 0.8570 (mtm) REVERT: D 156 MET cc_start: 0.8512 (mmt) cc_final: 0.7334 (mpp) REVERT: D 173 MET cc_start: 0.8971 (mtm) cc_final: 0.8631 (mtp) REVERT: D 181 LEU cc_start: 0.9143 (mt) cc_final: 0.8659 (pt) REVERT: D 196 GLU cc_start: 0.7981 (tt0) cc_final: 0.7537 (tp30) REVERT: D 221 PHE cc_start: 0.8542 (m-80) cc_final: 0.8338 (m-80) REVERT: D 281 MET cc_start: 0.5553 (ptt) cc_final: 0.5049 (mmp) REVERT: D 290 MET cc_start: 0.7888 (mmm) cc_final: 0.7683 (mmm) REVERT: D 350 LEU cc_start: 0.9107 (mm) cc_final: 0.8403 (pp) REVERT: D 418 MET cc_start: 0.5947 (mmm) cc_final: 0.5708 (mmm) REVERT: D 419 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8037 (mm-30) REVERT: D 462 LEU cc_start: 0.8974 (mt) cc_final: 0.8742 (mt) REVERT: D 494 ASP cc_start: 0.8211 (m-30) cc_final: 0.7811 (t0) REVERT: D 502 ASP cc_start: 0.8712 (p0) cc_final: 0.8362 (m-30) REVERT: D 506 LEU cc_start: 0.8853 (tp) cc_final: 0.8393 (tp) REVERT: D 540 LEU cc_start: 0.8812 (mt) cc_final: 0.8477 (mt) REVERT: D 564 ILE cc_start: 0.9630 (mt) cc_final: 0.9355 (mt) REVERT: D 578 ARG cc_start: 0.8728 (mmt-90) cc_final: 0.8473 (mmm160) REVERT: D 642 MET cc_start: 0.8553 (ttt) cc_final: 0.8088 (mtp) REVERT: D 689 ASP cc_start: 0.8655 (m-30) cc_final: 0.7969 (m-30) REVERT: D 690 ASP cc_start: 0.8262 (p0) cc_final: 0.7905 (p0) REVERT: D 722 MET cc_start: 0.6443 (ttm) cc_final: 0.5113 (ttm) REVERT: D 1130 LYS cc_start: 0.7857 (mttt) cc_final: 0.7624 (mttt) REVERT: D 1199 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8320 (mm-40) REVERT: D 1202 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8333 (tm-30) REVERT: I 101 MET cc_start: 0.8402 (mmm) cc_final: 0.8150 (mmm) REVERT: I 186 ASP cc_start: 0.9295 (m-30) cc_final: 0.9066 (t0) REVERT: I 188 MET cc_start: 0.7261 (mmp) cc_final: 0.6775 (mpp) REVERT: I 217 MET cc_start: 0.2251 (tpt) cc_final: 0.1545 (ttt) REVERT: I 312 ASP cc_start: 0.7738 (p0) cc_final: 0.7270 (p0) outliers start: 5 outliers final: 1 residues processed: 646 average time/residue: 0.3706 time to fit residues: 370.9845 Evaluate side-chains 465 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 463 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 97 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 251 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 151 optimal weight: 0.0030 chunk 140 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN A 531 HIS ** 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 712 GLN A1115 ASN A1199 GLN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS B 716 GLN ** B1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 GLN C 232 HIS ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 HIS C 322 GLN C 330 GLN C 475 GLN C 660 HIS C 696 ASN ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1242 HIS D 378 HIS D 539 HIS D 548 ASN ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1116 ASN I 110 ASN I 225 HIS I 268 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.110129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.080568 restraints weight = 158755.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.082396 restraints weight = 117481.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.083790 restraints weight = 95043.812| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26364 Z= 0.202 Angle : 0.705 11.264 35584 Z= 0.372 Chirality : 0.044 0.180 3993 Planarity : 0.005 0.054 4551 Dihedral : 4.894 26.695 3504 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.79 % Rotamer: Outliers : 0.11 % Allowed : 4.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3148 helix: 0.85 (0.13), residues: 1677 sheet: -0.31 (0.30), residues: 309 loop : -1.68 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D1129 HIS 0.010 0.002 HIS I 142 PHE 0.027 0.002 PHE C 414 TYR 0.021 0.002 TYR C1134 ARG 0.015 0.001 ARG C 580 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 1230) hydrogen bonds : angle 4.88940 ( 3641) covalent geometry : bond 0.00434 (26364) covalent geometry : angle 0.70470 (35584) *********************** 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 593 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 590 time to evaluate : 2.821 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: A 135 LEU cc_start: 0.8454 (tp) cc_final: 0.7778 (pt) REVERT: A 143 THR cc_start: 0.6892 (m) cc_final: 0.6339 (t) REVERT: A 301 THR cc_start: 0.7443 (p) cc_final: 0.7173 (p) REVERT: A 378 HIS cc_start: 0.7800 (t-90) cc_final: 0.7384 (t70) REVERT: A 421 MET cc_start: 0.7630 (mmp) cc_final: 0.7381 (mmp) REVERT: A 471 ILE cc_start: 0.9030 (mm) cc_final: 0.8635 (pt) REVERT: A 492 MET cc_start: 0.8863 (tpp) cc_final: 0.8434 (tpt) REVERT: A 524 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7596 (tp30) REVERT: A 687 MET cc_start: 0.8548 (mmp) cc_final: 0.7894 (mmm) REVERT: A 704 GLN cc_start: 0.9180 (tp40) cc_final: 0.8573 (tp40) REVERT: A 727 TYR cc_start: 0.7624 (p90) cc_final: 0.7268 (p90) REVERT: A 728 GLU cc_start: 0.7885 (tt0) cc_final: 0.7358 (pm20) REVERT: A 729 LEU cc_start: 0.9046 (mt) cc_final: 0.8700 (mp) REVERT: A 1202 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8467 (pp20) REVERT: A 1213 ASN cc_start: 0.8695 (m-40) cc_final: 0.8321 (p0) REVERT: B 185 LEU cc_start: 0.7767 (tp) cc_final: 0.7369 (tp) REVERT: B 277 MET cc_start: 0.4648 (tmm) cc_final: 0.4248 (tmm) REVERT: B 418 MET cc_start: 0.4636 (mmm) cc_final: 0.4080 (tmm) REVERT: B 492 MET cc_start: 0.8158 (tpp) cc_final: 0.7195 (tpp) REVERT: B 523 LEU cc_start: 0.8906 (mt) cc_final: 0.8647 (mt) REVERT: B 545 LYS cc_start: 0.9106 (tptm) cc_final: 0.8541 (ptmt) REVERT: B 580 ARG cc_start: 0.7512 (ttt90) cc_final: 0.6980 (tpt170) REVERT: B 687 MET cc_start: 0.8210 (tpp) cc_final: 0.7992 (tpp) REVERT: B 720 LEU cc_start: 0.8870 (mt) cc_final: 0.8463 (tp) REVERT: B 754 CYS cc_start: 0.9221 (t) cc_final: 0.8894 (t) REVERT: B 1202 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8533 (tm-30) REVERT: C 183 LYS cc_start: 0.7384 (mttt) cc_final: 0.7181 (mmtt) REVERT: C 211 LYS cc_start: 0.7708 (tttp) cc_final: 0.7486 (tttp) REVERT: C 560 ILE cc_start: 0.8347 (mm) cc_final: 0.7911 (mm) REVERT: C 694 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8258 (tt0) REVERT: C 757 MET cc_start: 0.8671 (tmm) cc_final: 0.8450 (tpt) REVERT: C 1230 MET cc_start: 0.9182 (mtp) cc_final: 0.8923 (mtm) REVERT: D 156 MET cc_start: 0.8441 (mmt) cc_final: 0.8205 (mpp) REVERT: D 173 MET cc_start: 0.8874 (mtm) cc_final: 0.8627 (mtp) REVERT: D 181 LEU cc_start: 0.9251 (mt) cc_final: 0.8680 (pt) REVERT: D 277 MET cc_start: 0.5665 (pmm) cc_final: 0.5373 (pmm) REVERT: D 290 MET cc_start: 0.8092 (mmm) cc_final: 0.7806 (mmm) REVERT: D 418 MET cc_start: 0.6100 (mmm) cc_final: 0.5668 (mmm) REVERT: D 419 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8183 (mm-30) REVERT: D 462 LEU cc_start: 0.9144 (mt) cc_final: 0.8755 (mt) REVERT: D 474 SER cc_start: 0.8242 (m) cc_final: 0.7906 (p) REVERT: D 476 ILE cc_start: 0.8122 (tp) cc_final: 0.7677 (tp) REVERT: D 494 ASP cc_start: 0.8566 (m-30) cc_final: 0.8251 (t0) REVERT: D 642 MET cc_start: 0.8983 (ttt) cc_final: 0.8456 (mtp) REVERT: D 1199 GLN cc_start: 0.8990 (pt0) cc_final: 0.8137 (pp30) REVERT: D 1232 MET cc_start: 0.8857 (mtp) cc_final: 0.8413 (mtp) REVERT: I 186 ASP cc_start: 0.9162 (m-30) cc_final: 0.8837 (t0) REVERT: I 188 MET cc_start: 0.6790 (mmp) cc_final: 0.6432 (mmm) REVERT: I 217 MET cc_start: 0.2617 (tpt) cc_final: 0.1928 (ttt) outliers start: 3 outliers final: 1 residues processed: 592 average time/residue: 0.3642 time to fit residues: 337.8265 Evaluate side-chains 438 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 437 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 245 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 275 optimal weight: 0.7980 chunk 315 optimal weight: 0.1980 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 296 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 HIS A 232 HIS ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 GLN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 HIS B 659 GLN B1194 HIS C 151 HIS C 232 HIS C 288 ASN C 291 HIS ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 660 HIS ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN C 746 HIS D 322 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 HIS I 110 ASN I 268 ASN ** J 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.109775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.083840 restraints weight = 133218.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.086569 restraints weight = 107341.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.087030 restraints weight = 75428.187| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3594 r_free = 0.3594 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.6749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26364 Z= 0.129 Angle : 0.582 8.827 35584 Z= 0.306 Chirality : 0.041 0.210 3993 Planarity : 0.004 0.054 4551 Dihedral : 4.530 25.594 3504 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 0.04 % Allowed : 2.37 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3148 helix: 1.15 (0.13), residues: 1651 sheet: -0.38 (0.30), residues: 325 loop : -1.44 (0.18), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 658 HIS 0.009 0.001 HIS B 240 PHE 0.018 0.001 PHE I 278 TYR 0.017 0.001 TYR B1134 ARG 0.008 0.000 ARG B1233 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1230) hydrogen bonds : angle 4.45066 ( 3641) covalent geometry : bond 0.00274 (26364) covalent geometry : angle 0.58155 (35584) *********************** 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 559 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 558 time to evaluate : 2.939 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: 0.8440 (tp) cc_final: 0.7750 (pt) REVERT: A 173 MET cc_start: 0.8029 (mpp) cc_final: 0.7697 (ptp) REVERT: A 378 HIS cc_start: 0.7741 (t-90) cc_final: 0.7483 (t70) REVERT: A 418 MET cc_start: 0.7551 (tpt) cc_final: 0.7009 (tpp) REVERT: A 432 MET cc_start: 0.6437 (mmm) cc_final: 0.6212 (mtp) REVERT: A 471 ILE cc_start: 0.9022 (mm) cc_final: 0.8537 (pt) REVERT: A 492 MET cc_start: 0.8895 (tpp) cc_final: 0.8503 (tpp) REVERT: A 524 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7626 (mm-30) REVERT: A 704 GLN cc_start: 0.8783 (tp40) cc_final: 0.7958 (tp40) REVERT: A 708 GLU cc_start: 0.8789 (mt-10) cc_final: 0.7996 (mt-10) REVERT: A 729 LEU cc_start: 0.8838 (mt) cc_final: 0.8573 (mp) REVERT: B 144 ILE cc_start: 0.8578 (mm) cc_final: 0.8021 (tp) REVERT: B 185 LEU cc_start: 0.7785 (tp) cc_final: 0.7354 (tp) REVERT: B 193 GLN cc_start: 0.8454 (tp40) cc_final: 0.7374 (tm-30) REVERT: B 418 MET cc_start: 0.4630 (mmm) cc_final: 0.4296 (tmm) REVERT: B 492 MET cc_start: 0.8107 (tpp) cc_final: 0.7198 (tpp) REVERT: B 500 ARG cc_start: 0.5446 (mmt-90) cc_final: 0.4987 (mmt-90) REVERT: B 523 LEU cc_start: 0.8741 (mt) cc_final: 0.8513 (mt) REVERT: B 548 ASN cc_start: 0.7589 (m-40) cc_final: 0.7327 (t0) REVERT: B 580 ARG cc_start: 0.7606 (ttt90) cc_final: 0.7074 (tpt170) REVERT: B 659 GLN cc_start: 0.9098 (pt0) cc_final: 0.8622 (mt0) REVERT: B 712 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8593 (tp40) REVERT: C 141 PHE cc_start: 0.6263 (p90) cc_final: 0.6062 (p90) REVERT: C 177 TRP cc_start: 0.6866 (m-10) cc_final: 0.6559 (m-10) REVERT: C 211 LYS cc_start: 0.7750 (tttp) cc_final: 0.7493 (tttp) REVERT: C 235 ASP cc_start: 0.9152 (m-30) cc_final: 0.8941 (m-30) REVERT: C 509 GLU cc_start: 0.9222 (mt-10) cc_final: 0.9007 (mm-30) REVERT: C 548 ASN cc_start: 0.5972 (m110) cc_final: 0.4854 (p0) REVERT: C 568 MET cc_start: 0.6851 (mtm) cc_final: 0.6587 (mtm) REVERT: C 665 MET cc_start: 0.8484 (tmm) cc_final: 0.7993 (tpp) REVERT: C 672 CYS cc_start: 0.9186 (t) cc_final: 0.8892 (t) REVERT: C 675 CYS cc_start: 0.7803 (m) cc_final: 0.7467 (m) REVERT: C 694 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8363 (tt0) REVERT: C 757 MET cc_start: 0.8632 (tmm) cc_final: 0.8273 (tmm) REVERT: C 1183 LEU cc_start: 0.7047 (mp) cc_final: 0.6801 (mt) REVERT: D 181 LEU cc_start: 0.9218 (mt) cc_final: 0.8671 (pt) REVERT: D 277 MET cc_start: 0.5701 (pmm) cc_final: 0.5442 (pmm) REVERT: D 418 MET cc_start: 0.6284 (mmm) cc_final: 0.5850 (mmm) REVERT: D 419 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8222 (mm-30) REVERT: D 462 LEU cc_start: 0.8943 (mt) cc_final: 0.8675 (mt) REVERT: D 540 LEU cc_start: 0.9047 (mt) cc_final: 0.8798 (mt) REVERT: D 565 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7228 (tp30) REVERT: D 595 LYS cc_start: 0.8577 (pptt) cc_final: 0.8221 (tmmt) REVERT: D 729 LEU cc_start: 0.8821 (mt) cc_final: 0.8596 (mt) REVERT: D 1129 TRP cc_start: 0.8528 (t60) cc_final: 0.8104 (t60) REVERT: D 1195 ASP cc_start: 0.9230 (m-30) cc_final: 0.8923 (m-30) REVERT: D 1199 GLN cc_start: 0.8933 (pt0) cc_final: 0.8462 (pp30) REVERT: I 89 LYS cc_start: 0.6390 (tmtt) cc_final: 0.6069 (tmtt) REVERT: I 110 ASN cc_start: 0.6608 (m-40) cc_final: 0.5850 (m110) REVERT: I 111 TYR cc_start: 0.7878 (m-80) cc_final: 0.7612 (m-80) REVERT: I 186 ASP cc_start: 0.9161 (m-30) cc_final: 0.8788 (m-30) REVERT: I 188 MET cc_start: 0.6882 (mmp) cc_final: 0.6496 (mmm) REVERT: I 217 MET cc_start: 0.2430 (tpt) cc_final: 0.1806 (ttt) outliers start: 1 outliers final: 0 residues processed: 559 average time/residue: 0.4302 time to fit residues: 378.7483 Evaluate side-chains 428 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 5.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 95 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 292 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 314 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN B 680 HIS C 132 HIS C 151 HIS C 194 ASN ** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN C 716 GLN C 731 ASN ** C 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 696 ASN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 734 ASN D1127 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.104933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.075047 restraints weight = 135038.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.076607 restraints weight = 103433.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.077309 restraints weight = 85622.769| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 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 = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.8265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 26364 Z= 0.217 Angle : 0.696 10.997 35584 Z= 0.366 Chirality : 0.044 0.170 3993 Planarity : 0.005 0.054 4551 Dihedral : 4.834 26.372 3504 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3148 helix: 0.83 (0.13), residues: 1676 sheet: -0.42 (0.30), residues: 312 loop : -1.64 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP I 297 HIS 0.015 0.002 HIS D 412 PHE 0.054 0.003 PHE B 636 TYR 0.032 0.002 TYR B1134 ARG 0.009 0.001 ARG B1226 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 1230) hydrogen bonds : angle 4.75433 ( 3641) covalent geometry : bond 0.00464 (26364) covalent geometry : angle 0.69640 (35584) *********************** 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 539 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 536 time to evaluate : 3.198 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 135 LEU cc_start: 0.8747 (tp) cc_final: 0.8268 (pt) REVERT: A 168 LEU cc_start: 0.8970 (tp) cc_final: 0.8683 (tp) REVERT: A 181 LEU cc_start: 0.8026 (mt) cc_final: 0.7213 (pt) REVERT: A 237 LEU cc_start: 0.9326 (mt) cc_final: 0.9066 (mp) REVERT: A 292 SER cc_start: 0.8330 (m) cc_final: 0.7827 (t) REVERT: A 338 ILE cc_start: 0.9059 (mm) cc_final: 0.8805 (mm) REVERT: A 418 MET cc_start: 0.7417 (tpt) cc_final: 0.6909 (tpt) REVERT: A 432 MET cc_start: 0.6593 (mmm) cc_final: 0.6374 (ttt) REVERT: A 442 LEU cc_start: 0.9533 (mt) cc_final: 0.9303 (pp) REVERT: A 471 ILE cc_start: 0.9199 (mm) cc_final: 0.8698 (pt) REVERT: A 492 MET cc_start: 0.8949 (tpp) cc_final: 0.8574 (tpp) REVERT: A 687 MET cc_start: 0.8742 (mmp) cc_final: 0.8318 (mmm) REVERT: A 704 GLN cc_start: 0.8875 (tp40) cc_final: 0.8565 (tp-100) REVERT: A 728 GLU cc_start: 0.7541 (tt0) cc_final: 0.7206 (pm20) REVERT: B 144 ILE cc_start: 0.8568 (mm) cc_final: 0.8030 (tp) REVERT: B 243 LYS cc_start: 0.8500 (mppt) cc_final: 0.8107 (ptpp) REVERT: B 317 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6719 (tptt) REVERT: B 407 ARG cc_start: 0.8826 (ttp-170) cc_final: 0.8134 (mtt90) REVERT: B 418 MET cc_start: 0.5207 (mmm) cc_final: 0.4945 (tmm) REVERT: B 442 LEU cc_start: 0.8175 (mp) cc_final: 0.7582 (tp) REVERT: B 492 MET cc_start: 0.8271 (tpp) cc_final: 0.7501 (tpp) REVERT: B 523 LEU cc_start: 0.8864 (mt) cc_final: 0.8530 (mt) REVERT: B 545 LYS cc_start: 0.9068 (tppt) cc_final: 0.8861 (tppt) REVERT: B 580 ARG cc_start: 0.7778 (ttt90) cc_final: 0.7259 (tpt170) REVERT: B 659 GLN cc_start: 0.9238 (pt0) cc_final: 0.8937 (mt0) REVERT: B 665 MET cc_start: 0.8796 (tpp) cc_final: 0.8275 (ttm) REVERT: B 712 GLN cc_start: 0.9042 (tp-100) cc_final: 0.8716 (tp40) REVERT: B 1202 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8758 (tm-30) REVERT: B 1203 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9135 (tm-30) REVERT: C 141 PHE cc_start: 0.6226 (p90) cc_final: 0.5936 (p90) REVERT: C 194 ASN cc_start: 0.7267 (OUTLIER) cc_final: 0.7018 (t0) REVERT: C 235 ASP cc_start: 0.9184 (m-30) cc_final: 0.8792 (t0) REVERT: C 277 MET cc_start: 0.6569 (pmm) cc_final: 0.5902 (pmm) REVERT: C 418 MET cc_start: 0.6816 (tmm) cc_final: 0.6374 (tmm) REVERT: C 421 MET cc_start: 0.2877 (mmm) cc_final: 0.2042 (mmt) REVERT: C 498 LEU cc_start: 0.7378 (mt) cc_final: 0.6969 (mt) REVERT: C 526 LEU cc_start: 0.8547 (mt) cc_final: 0.8261 (mt) REVERT: C 665 MET cc_start: 0.8724 (tmm) cc_final: 0.7761 (tpp) REVERT: C 672 CYS cc_start: 0.9362 (t) cc_final: 0.9013 (t) REVERT: C 732 TRP cc_start: 0.8478 (m100) cc_final: 0.8202 (m100) REVERT: C 757 MET cc_start: 0.8718 (tmm) cc_final: 0.8251 (tmm) REVERT: C 1199 GLN cc_start: 0.8455 (tt0) cc_final: 0.7921 (mm-40) REVERT: C 1203 GLU cc_start: 0.8307 (pp20) cc_final: 0.7697 (tp30) REVERT: C 1225 GLU cc_start: 0.8825 (mp0) cc_final: 0.8568 (mp0) REVERT: D 156 MET cc_start: 0.8237 (mpp) cc_final: 0.7874 (mpp) REVERT: D 181 LEU cc_start: 0.9295 (mt) cc_final: 0.8797 (pt) REVERT: D 277 MET cc_start: 0.5587 (pmm) cc_final: 0.5352 (pmm) REVERT: D 418 MET cc_start: 0.6513 (mmm) cc_final: 0.5981 (mmm) REVERT: D 419 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8281 (mm-30) REVERT: D 462 LEU cc_start: 0.9021 (mt) cc_final: 0.8767 (mt) REVERT: D 538 TYR cc_start: 0.8119 (t80) cc_final: 0.7708 (t80) REVERT: D 557 LEU cc_start: 0.8653 (mt) cc_final: 0.8434 (mt) REVERT: D 565 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7749 (tp30) REVERT: D 653 MET cc_start: 0.8817 (mmt) cc_final: 0.8494 (mmt) REVERT: D 708 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7800 (mt-10) REVERT: D 1129 TRP cc_start: 0.8215 (t60) cc_final: 0.7841 (t60) REVERT: D 1195 ASP cc_start: 0.9240 (m-30) cc_final: 0.8779 (m-30) REVERT: D 1199 GLN cc_start: 0.9015 (pt0) cc_final: 0.8580 (pp30) REVERT: I 89 LYS cc_start: 0.5948 (tmtt) cc_final: 0.5500 (tmtt) REVERT: I 110 ASN cc_start: 0.6531 (m-40) cc_final: 0.6123 (m110) REVERT: I 186 ASP cc_start: 0.9163 (m-30) cc_final: 0.8900 (m-30) REVERT: I 188 MET cc_start: 0.6800 (mmp) cc_final: 0.6477 (mmm) REVERT: I 217 MET cc_start: 0.2608 (tpt) cc_final: 0.1817 (ttt) REVERT: J 38 MET cc_start: 0.4829 (mpp) cc_final: 0.3629 (ppp) outliers start: 3 outliers final: 1 residues processed: 538 average time/residue: 0.3869 time to fit residues: 324.9146 Evaluate side-chains 418 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 416 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 159 optimal weight: 0.0570 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 235 optimal weight: 0.4980 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 698 ASN C 704 GLN C 746 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS D 291 HIS D 459 GLN ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 HIS I 340 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.103572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.073688 restraints weight = 171033.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.075693 restraints weight = 119499.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.076766 restraints weight = 93600.035| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.9077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26364 Z= 0.150 Angle : 0.626 9.606 35584 Z= 0.328 Chirality : 0.042 0.219 3993 Planarity : 0.004 0.055 4551 Dihedral : 4.665 26.280 3504 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.10 % Rotamer: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3148 helix: 1.04 (0.13), residues: 1671 sheet: -0.58 (0.28), residues: 349 loop : -1.55 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 658 HIS 0.010 0.001 HIS D 240 PHE 0.014 0.002 PHE C 638 TYR 0.026 0.002 TYR A1204 ARG 0.007 0.001 ARG A 354 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 1230) hydrogen bonds : angle 4.56067 ( 3641) covalent geometry : bond 0.00323 (26364) covalent geometry : angle 0.62579 (35584) *********************** 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 551 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 550 time to evaluate : 2.900 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: A 135 LEU cc_start: 0.8791 (tp) cc_final: 0.8328 (pt) REVERT: A 167 ASP cc_start: 0.9000 (p0) cc_final: 0.8744 (p0) REVERT: A 181 LEU cc_start: 0.8153 (mt) cc_final: 0.7390 (pt) REVERT: A 237 LEU cc_start: 0.9456 (mt) cc_final: 0.9166 (mt) REVERT: A 248 ILE cc_start: 0.8918 (mm) cc_final: 0.8632 (mm) REVERT: A 292 SER cc_start: 0.8369 (m) cc_final: 0.7784 (p) REVERT: A 409 GLN cc_start: 0.7814 (mt0) cc_final: 0.7401 (mp10) REVERT: A 418 MET cc_start: 0.7385 (tpt) cc_final: 0.6908 (tpp) REVERT: A 471 ILE cc_start: 0.9190 (mm) cc_final: 0.8818 (pt) REVERT: A 492 MET cc_start: 0.8997 (tpp) cc_final: 0.8617 (tpp) REVERT: A 499 ASP cc_start: 0.8782 (t0) cc_final: 0.8534 (t0) REVERT: A 524 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7613 (tp30) REVERT: A 653 MET cc_start: 0.8637 (mtt) cc_final: 0.8170 (mtp) REVERT: A 687 MET cc_start: 0.8728 (mmp) cc_final: 0.8294 (mmm) REVERT: B 144 ILE cc_start: 0.8753 (mm) cc_final: 0.8207 (tp) REVERT: B 290 MET cc_start: 0.6401 (mmp) cc_final: 0.5300 (mmt) REVERT: B 407 ARG cc_start: 0.8774 (ttp-170) cc_final: 0.8073 (mtt90) REVERT: B 460 LEU cc_start: 0.8795 (tp) cc_final: 0.8558 (tt) REVERT: B 492 MET cc_start: 0.8486 (tpp) cc_final: 0.7881 (tpp) REVERT: B 523 LEU cc_start: 0.8731 (mt) cc_final: 0.8496 (mt) REVERT: B 540 LEU cc_start: 0.8387 (mt) cc_final: 0.7879 (pp) REVERT: B 580 ARG cc_start: 0.7921 (ttt90) cc_final: 0.7322 (tpt170) REVERT: B 653 MET cc_start: 0.9239 (mmt) cc_final: 0.9021 (mmt) REVERT: B 659 GLN cc_start: 0.9158 (pt0) cc_final: 0.8928 (mt0) REVERT: B 665 MET cc_start: 0.8790 (ttm) cc_final: 0.8490 (ttm) REVERT: B 688 VAL cc_start: 0.9395 (t) cc_final: 0.9087 (t) REVERT: B 711 ASP cc_start: 0.8591 (m-30) cc_final: 0.8053 (m-30) REVERT: B 712 GLN cc_start: 0.9059 (tp-100) cc_final: 0.8778 (tp40) REVERT: B 722 MET cc_start: 0.9093 (mmp) cc_final: 0.8800 (mmm) REVERT: B 1191 LYS cc_start: 0.8521 (mttt) cc_final: 0.7998 (mttt) REVERT: B 1203 GLU cc_start: 0.9534 (tm-30) cc_final: 0.9278 (tm-30) REVERT: C 235 ASP cc_start: 0.9184 (m-30) cc_final: 0.8757 (t0) REVERT: C 277 MET cc_start: 0.6558 (pmm) cc_final: 0.5726 (pmm) REVERT: C 290 MET cc_start: 0.8176 (mpp) cc_final: 0.7467 (mpp) REVERT: C 352 TYR cc_start: 0.8032 (m-80) cc_final: 0.7611 (m-80) REVERT: C 415 ILE cc_start: 0.7905 (pt) cc_final: 0.7585 (tt) REVERT: C 418 MET cc_start: 0.6731 (tmm) cc_final: 0.6370 (tmm) REVERT: C 421 MET cc_start: 0.2943 (mmm) cc_final: 0.2171 (mmt) REVERT: C 492 MET cc_start: 0.7548 (tpp) cc_final: 0.7262 (tpt) REVERT: C 526 LEU cc_start: 0.8468 (mt) cc_final: 0.8133 (mt) REVERT: C 560 ILE cc_start: 0.9169 (mm) cc_final: 0.8854 (tt) REVERT: C 564 ILE cc_start: 0.8982 (mt) cc_final: 0.8775 (mt) REVERT: C 575 ASN cc_start: 0.8892 (p0) cc_final: 0.8681 (p0) REVERT: C 665 MET cc_start: 0.8429 (tmm) cc_final: 0.8228 (tmm) REVERT: C 722 MET cc_start: 0.7770 (ppp) cc_final: 0.7474 (ppp) REVERT: C 757 MET cc_start: 0.8861 (tmm) cc_final: 0.8302 (tmm) REVERT: C 1209 ASP cc_start: 0.8908 (m-30) cc_final: 0.8469 (m-30) REVERT: D 156 MET cc_start: 0.8233 (mpp) cc_final: 0.7895 (mpp) REVERT: D 173 MET cc_start: 0.8869 (mtm) cc_final: 0.8598 (mtm) REVERT: D 181 LEU cc_start: 0.9254 (mt) cc_final: 0.8776 (pt) REVERT: D 183 LYS cc_start: 0.7904 (mttt) cc_final: 0.7681 (mmtm) REVERT: D 237 LEU cc_start: 0.9249 (mt) cc_final: 0.9009 (mt) REVERT: D 418 MET cc_start: 0.6522 (mmm) cc_final: 0.6059 (mmm) REVERT: D 462 LEU cc_start: 0.9058 (mt) cc_final: 0.8799 (mt) REVERT: D 557 LEU cc_start: 0.8682 (mt) cc_final: 0.8454 (mt) REVERT: D 565 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7856 (tp30) REVERT: D 585 TYR cc_start: 0.8743 (t80) cc_final: 0.7845 (t80) REVERT: D 589 PHE cc_start: 0.7039 (t80) cc_final: 0.6269 (t80) REVERT: D 687 MET cc_start: 0.4874 (ptm) cc_final: 0.3486 (ptm) REVERT: D 708 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7863 (mt-10) REVERT: D 1195 ASP cc_start: 0.9191 (m-30) cc_final: 0.8712 (m-30) REVERT: D 1199 GLN cc_start: 0.8903 (pt0) cc_final: 0.8170 (pp30) REVERT: D 1203 GLU cc_start: 0.8436 (pt0) cc_final: 0.8068 (mm-30) REVERT: I 186 ASP cc_start: 0.9167 (m-30) cc_final: 0.8915 (m-30) REVERT: I 188 MET cc_start: 0.6656 (mmp) cc_final: 0.6362 (mmm) REVERT: I 217 MET cc_start: 0.2595 (tpt) cc_final: 0.1764 (ttt) outliers start: 1 outliers final: 0 residues processed: 551 average time/residue: 0.3825 time to fit residues: 329.5965 Evaluate side-chains 415 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 67 optimal weight: 0.5980 chunk 206 optimal weight: 2.9990 chunk 161 optimal weight: 0.4980 chunk 167 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 ASN ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 HIS B 151 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN B1229 ASN C 151 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 GLN ** C 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 704 GLN C1115 ASN C1199 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN D 330 GLN ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN D1127 GLN I 183 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 = 0.3814 r_free = 0.3814 target = 0.102167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.071944 restraints weight = 181461.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.074497 restraints weight = 132129.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.075620 restraints weight = 97395.380| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.9937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26364 Z= 0.163 Angle : 0.655 11.800 35584 Z= 0.342 Chirality : 0.043 0.171 3993 Planarity : 0.004 0.081 4551 Dihedral : 4.740 27.059 3504 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.15), residues: 3148 helix: 0.97 (0.13), residues: 1680 sheet: -0.57 (0.29), residues: 347 loop : -1.53 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP I 297 HIS 0.009 0.001 HIS I 183 PHE 0.038 0.002 PHE C1184 TYR 0.032 0.002 TYR B1134 ARG 0.009 0.001 ARG C 245 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 1230) hydrogen bonds : angle 4.62837 ( 3641) covalent geometry : bond 0.00355 (26364) covalent geometry : angle 0.65455 (35584) *********************** 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 520 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 2.886 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: 0.8887 (tp) cc_final: 0.8550 (pt) REVERT: A 153 ASN cc_start: 0.8783 (m-40) cc_final: 0.8383 (m-40) REVERT: A 167 ASP cc_start: 0.8902 (p0) cc_final: 0.8677 (p0) REVERT: A 181 LEU cc_start: 0.8356 (mt) cc_final: 0.7660 (pt) REVERT: A 292 SER cc_start: 0.8456 (m) cc_final: 0.7880 (p) REVERT: A 338 ILE cc_start: 0.9223 (mm) cc_final: 0.8992 (mm) REVERT: A 409 GLN cc_start: 0.7786 (mt0) cc_final: 0.7393 (mp10) REVERT: A 418 MET cc_start: 0.7341 (tpt) cc_final: 0.6768 (tpp) REVERT: A 471 ILE cc_start: 0.9189 (mm) cc_final: 0.8796 (pt) REVERT: A 499 ASP cc_start: 0.8792 (t0) cc_final: 0.8590 (t0) REVERT: A 524 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7528 (mm-30) REVERT: A 687 MET cc_start: 0.8754 (mmp) cc_final: 0.8343 (mmm) REVERT: A 704 GLN cc_start: 0.9039 (tp40) cc_final: 0.7864 (tp-100) REVERT: A 727 TYR cc_start: 0.7301 (p90) cc_final: 0.6649 (p90) REVERT: A 1230 MET cc_start: 0.8253 (ttm) cc_final: 0.7869 (ttm) REVERT: B 144 ILE cc_start: 0.8822 (mm) cc_final: 0.8332 (tp) REVERT: B 184 LEU cc_start: 0.9361 (tp) cc_final: 0.9095 (tp) REVERT: B 290 MET cc_start: 0.6542 (mmp) cc_final: 0.5629 (mmt) REVERT: B 376 PHE cc_start: 0.7863 (m-80) cc_final: 0.7274 (m-80) REVERT: B 407 ARG cc_start: 0.8799 (ttp-170) cc_final: 0.7973 (mtt90) REVERT: B 418 MET cc_start: 0.6302 (tmm) cc_final: 0.5865 (tpt) REVERT: B 442 LEU cc_start: 0.8161 (mp) cc_final: 0.7635 (tp) REVERT: B 492 MET cc_start: 0.8573 (tpp) cc_final: 0.7583 (tpp) REVERT: B 508 ILE cc_start: 0.9207 (mt) cc_final: 0.8992 (tp) REVERT: B 523 LEU cc_start: 0.8653 (mt) cc_final: 0.8453 (mt) REVERT: B 659 GLN cc_start: 0.9200 (pt0) cc_final: 0.8880 (mt0) REVERT: B 665 MET cc_start: 0.8962 (ttm) cc_final: 0.8572 (ttm) REVERT: B 711 ASP cc_start: 0.8567 (m-30) cc_final: 0.8094 (m-30) REVERT: B 712 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8863 (tp-100) REVERT: B 722 MET cc_start: 0.9080 (mmp) cc_final: 0.8760 (mmm) REVERT: B 749 PHE cc_start: 0.9141 (t80) cc_final: 0.8925 (t80) REVERT: B 1191 LYS cc_start: 0.8665 (mttt) cc_final: 0.8060 (mttp) REVERT: B 1203 GLU cc_start: 0.9552 (tm-30) cc_final: 0.9310 (tm-30) REVERT: C 177 TRP cc_start: 0.8199 (m-10) cc_final: 0.7891 (m-10) REVERT: C 235 ASP cc_start: 0.9212 (m-30) cc_final: 0.8889 (t0) REVERT: C 275 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7493 (mm-40) REVERT: C 277 MET cc_start: 0.6600 (pmm) cc_final: 0.5820 (pmm) REVERT: C 352 TYR cc_start: 0.8111 (m-80) cc_final: 0.7720 (m-80) REVERT: C 415 ILE cc_start: 0.7920 (pt) cc_final: 0.7633 (tt) REVERT: C 418 MET cc_start: 0.6480 (tmm) cc_final: 0.6164 (tmm) REVERT: C 468 ARG cc_start: 0.8246 (tpm170) cc_final: 0.7843 (tpm170) REVERT: C 526 LEU cc_start: 0.8660 (mt) cc_final: 0.8334 (mt) REVERT: C 578 ARG cc_start: 0.8399 (mmp-170) cc_final: 0.7871 (mmm160) REVERT: C 722 MET cc_start: 0.7944 (ppp) cc_final: 0.7631 (ppp) REVERT: C 725 LEU cc_start: 0.9319 (tt) cc_final: 0.9088 (tt) REVERT: C 757 MET cc_start: 0.8552 (tmm) cc_final: 0.8281 (tmm) REVERT: C 1195 ASP cc_start: 0.9019 (m-30) cc_final: 0.8650 (t0) REVERT: C 1209 ASP cc_start: 0.8869 (m-30) cc_final: 0.8401 (m-30) REVERT: C 1225 GLU cc_start: 0.8722 (mp0) cc_final: 0.8289 (mp0) REVERT: D 156 MET cc_start: 0.8331 (mpp) cc_final: 0.7955 (mpp) REVERT: D 181 LEU cc_start: 0.9322 (mt) cc_final: 0.8811 (pt) REVERT: D 183 LYS cc_start: 0.8030 (mttt) cc_final: 0.7823 (mmtm) REVERT: D 196 GLU cc_start: 0.7932 (pp20) cc_final: 0.7401 (tp30) REVERT: D 418 MET cc_start: 0.6588 (mmm) cc_final: 0.6272 (mmm) REVERT: D 565 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7919 (tp30) REVERT: D 576 TYR cc_start: 0.8699 (m-10) cc_final: 0.8497 (m-10) REVERT: D 687 MET cc_start: 0.5100 (ptm) cc_final: 0.3653 (ptm) REVERT: D 708 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 1195 ASP cc_start: 0.9170 (m-30) cc_final: 0.8636 (m-30) REVERT: D 1199 GLN cc_start: 0.9064 (pt0) cc_final: 0.8477 (pp30) REVERT: D 1203 GLU cc_start: 0.8474 (pt0) cc_final: 0.8128 (mm-30) REVERT: I 19 ARG cc_start: 0.7781 (tpt170) cc_final: 0.7462 (ptt-90) REVERT: I 186 ASP cc_start: 0.9250 (m-30) cc_final: 0.9044 (m-30) REVERT: I 188 MET cc_start: 0.6972 (mmp) cc_final: 0.6617 (mmm) REVERT: I 217 MET cc_start: 0.2662 (tpt) cc_final: 0.1783 (ttt) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.3753 time to fit residues: 308.2589 Evaluate side-chains 402 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 165 optimal weight: 1.9990 chunk 318 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 115 optimal weight: 0.6980 chunk 262 optimal weight: 6.9990 chunk 270 optimal weight: 0.9990 chunk 281 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 HIS ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 151 HIS C 171 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 HIS C 481 GLN ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1199 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS D 539 HIS ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN I 75 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.098648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.068745 restraints weight = 150925.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.070277 restraints weight = 112827.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071049 restraints weight = 92061.770| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 1.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 26364 Z= 0.199 Angle : 0.720 16.376 35584 Z= 0.374 Chirality : 0.044 0.167 3993 Planarity : 0.005 0.074 4551 Dihedral : 4.962 27.026 3504 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3148 helix: 0.68 (0.13), residues: 1676 sheet: -0.64 (0.29), residues: 342 loop : -1.66 (0.19), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 644 HIS 0.015 0.002 HIS C 171 PHE 0.022 0.002 PHE A 638 TYR 0.036 0.002 TYR B1134 ARG 0.008 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 1230) hydrogen bonds : angle 4.85362 ( 3641) covalent geometry : bond 0.00434 (26364) covalent geometry : angle 0.72023 (35584) *********************** 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 485 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 485 time to evaluate : 3.345 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: 0.8931 (tp) cc_final: 0.8668 (pt) REVERT: A 167 ASP cc_start: 0.9053 (p0) cc_final: 0.8790 (p0) REVERT: A 181 LEU cc_start: 0.8605 (mt) cc_final: 0.7987 (pt) REVERT: A 237 LEU cc_start: 0.9510 (mt) cc_final: 0.9299 (mt) REVERT: A 249 CYS cc_start: 0.8449 (t) cc_final: 0.8164 (t) REVERT: A 292 SER cc_start: 0.8489 (m) cc_final: 0.8211 (m) REVERT: A 338 ILE cc_start: 0.9371 (mm) cc_final: 0.9010 (tp) REVERT: A 409 GLN cc_start: 0.7939 (mt0) cc_final: 0.7470 (mp10) REVERT: A 418 MET cc_start: 0.7473 (tpt) cc_final: 0.6899 (tpp) REVERT: A 432 MET cc_start: 0.7135 (mtp) cc_final: 0.6921 (mtt) REVERT: A 499 ASP cc_start: 0.8872 (t0) cc_final: 0.8592 (t0) REVERT: A 524 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7473 (mm-30) REVERT: A 687 MET cc_start: 0.8682 (mmp) cc_final: 0.8321 (mmm) REVERT: A 704 GLN cc_start: 0.8957 (tp40) cc_final: 0.8586 (tp-100) REVERT: A 724 LEU cc_start: 0.9548 (tp) cc_final: 0.9144 (tp) REVERT: A 727 TYR cc_start: 0.7356 (p90) cc_final: 0.6801 (p90) REVERT: A 1210 ASP cc_start: 0.9301 (t0) cc_final: 0.9065 (t0) REVERT: A 1230 MET cc_start: 0.8630 (ttm) cc_final: 0.8301 (ttm) REVERT: B 184 LEU cc_start: 0.9532 (tp) cc_final: 0.9275 (tp) REVERT: B 290 MET cc_start: 0.7116 (mmp) cc_final: 0.6351 (tpp) REVERT: B 376 PHE cc_start: 0.8100 (m-80) cc_final: 0.7449 (m-80) REVERT: B 442 LEU cc_start: 0.8210 (mp) cc_final: 0.7583 (tp) REVERT: B 492 MET cc_start: 0.8728 (tpp) cc_final: 0.8274 (tpp) REVERT: B 538 TYR cc_start: 0.7579 (t80) cc_final: 0.7372 (t80) REVERT: B 659 GLN cc_start: 0.9233 (pt0) cc_final: 0.8751 (mt0) REVERT: B 675 CYS cc_start: 0.8829 (t) cc_final: 0.8272 (p) REVERT: B 722 MET cc_start: 0.9136 (mmp) cc_final: 0.8799 (mmm) REVERT: B 1191 LYS cc_start: 0.8739 (mttt) cc_final: 0.8216 (mttp) REVERT: B 1225 GLU cc_start: 0.8899 (pm20) cc_final: 0.8621 (pm20) REVERT: C 151 HIS cc_start: 0.3442 (t-90) cc_final: 0.3191 (t-170) REVERT: C 156 MET cc_start: 0.8102 (mtm) cc_final: 0.7857 (mtm) REVERT: C 177 TRP cc_start: 0.8194 (m-10) cc_final: 0.7761 (m-10) REVERT: C 276 THR cc_start: 0.7719 (t) cc_final: 0.7480 (t) REVERT: C 352 TYR cc_start: 0.8287 (m-80) cc_final: 0.7955 (m-80) REVERT: C 415 ILE cc_start: 0.7599 (pt) cc_final: 0.7287 (tt) REVERT: C 468 ARG cc_start: 0.8080 (tpm170) cc_final: 0.7712 (tpm170) REVERT: C 526 LEU cc_start: 0.8848 (mt) cc_final: 0.8573 (mt) REVERT: C 578 ARG cc_start: 0.8435 (mmp-170) cc_final: 0.8086 (mmm160) REVERT: C 665 MET cc_start: 0.8883 (tmm) cc_final: 0.8656 (tmm) REVERT: C 667 LYS cc_start: 0.9243 (mtmt) cc_final: 0.8901 (mttt) REVERT: C 719 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8994 (mm-40) REVERT: C 722 MET cc_start: 0.7941 (ppp) cc_final: 0.7655 (ppp) REVERT: C 725 LEU cc_start: 0.9319 (tt) cc_final: 0.9055 (tt) REVERT: C 758 LEU cc_start: 0.9185 (tt) cc_final: 0.8783 (tp) REVERT: C 1209 ASP cc_start: 0.8922 (m-30) cc_final: 0.8442 (m-30) REVERT: D 156 MET cc_start: 0.8297 (mpp) cc_final: 0.7939 (mpp) REVERT: D 181 LEU cc_start: 0.9357 (mt) cc_final: 0.8920 (pt) REVERT: D 183 LYS cc_start: 0.8114 (mttt) cc_final: 0.7876 (mmtm) REVERT: D 418 MET cc_start: 0.6588 (mmm) cc_final: 0.6273 (mmm) REVERT: D 462 LEU cc_start: 0.9179 (mt) cc_final: 0.8911 (mt) REVERT: D 471 ILE cc_start: 0.9269 (pt) cc_final: 0.9019 (mp) REVERT: D 492 MET cc_start: 0.8594 (tpt) cc_final: 0.8166 (tpp) REVERT: D 518 LEU cc_start: 0.9504 (tp) cc_final: 0.9259 (tt) REVERT: D 737 CYS cc_start: 0.8916 (m) cc_final: 0.8331 (t) REVERT: D 1195 ASP cc_start: 0.9075 (m-30) cc_final: 0.8626 (m-30) REVERT: D 1197 GLU cc_start: 0.8821 (pp20) cc_final: 0.8503 (pt0) REVERT: D 1198 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8825 (mt-10) REVERT: D 1199 GLN cc_start: 0.9009 (pt0) cc_final: 0.8580 (pp30) REVERT: D 1203 GLU cc_start: 0.8472 (pt0) cc_final: 0.8201 (mm-30) REVERT: D 1225 GLU cc_start: 0.8792 (pp20) cc_final: 0.8494 (pp20) REVERT: I 16 ASN cc_start: 0.8409 (m110) cc_final: 0.7963 (m-40) REVERT: I 19 ARG cc_start: 0.8100 (tpt170) cc_final: 0.7884 (ptt180) REVERT: I 186 ASP cc_start: 0.9179 (m-30) cc_final: 0.8920 (m-30) REVERT: I 188 MET cc_start: 0.6965 (mmp) cc_final: 0.6584 (mmm) REVERT: I 217 MET cc_start: 0.2883 (tpt) cc_final: 0.1905 (ttt) REVERT: I 260 GLU cc_start: 0.6275 (mt-10) cc_final: 0.5896 (mm-30) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.3763 time to fit residues: 289.0023 Evaluate side-chains 383 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 130 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 chunk 290 optimal weight: 0.6980 chunk 305 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 150 optimal weight: 3.9990 chunk 317 optimal weight: 4.9990 chunk 241 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 HIS ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 659 GLN ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1199 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 459 GLN D1115 ASN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.099417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.070200 restraints weight = 171094.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.072239 restraints weight = 118462.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073765 restraints weight = 91615.515| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 1.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26364 Z= 0.131 Angle : 0.643 9.783 35584 Z= 0.332 Chirality : 0.042 0.188 3993 Planarity : 0.004 0.069 4551 Dihedral : 4.667 25.041 3504 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3148 helix: 0.94 (0.13), residues: 1667 sheet: -0.59 (0.31), residues: 294 loop : -1.52 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 297 HIS 0.009 0.001 HIS B 240 PHE 0.013 0.001 PHE A1131 TYR 0.029 0.001 TYR B1134 ARG 0.009 0.001 ARG B1226 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 1230) hydrogen bonds : angle 4.58689 ( 3641) covalent geometry : bond 0.00285 (26364) covalent geometry : angle 0.64308 (35584) *********************** 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 500 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 3.101 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: 0.8886 (tp) cc_final: 0.8617 (pt) REVERT: A 181 LEU cc_start: 0.8554 (mt) cc_final: 0.7901 (pt) REVERT: A 184 LEU cc_start: 0.9051 (tp) cc_final: 0.8824 (tp) REVERT: A 186 ILE cc_start: 0.9454 (mt) cc_final: 0.9225 (mm) REVERT: A 237 LEU cc_start: 0.9405 (mt) cc_final: 0.9200 (mt) REVERT: A 249 CYS cc_start: 0.8554 (t) cc_final: 0.8309 (t) REVERT: A 292 SER cc_start: 0.8504 (m) cc_final: 0.8205 (p) REVERT: A 409 GLN cc_start: 0.7920 (mt0) cc_final: 0.7511 (mp10) REVERT: A 418 MET cc_start: 0.7523 (tpt) cc_final: 0.6980 (tpp) REVERT: A 421 MET cc_start: 0.8590 (mmm) cc_final: 0.8113 (mpp) REVERT: A 471 ILE cc_start: 0.9151 (mm) cc_final: 0.8404 (pt) REVERT: A 524 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7421 (mm-30) REVERT: A 687 MET cc_start: 0.8764 (mmp) cc_final: 0.8364 (mmm) REVERT: A 704 GLN cc_start: 0.8992 (tp40) cc_final: 0.8524 (tp-100) REVERT: A 724 LEU cc_start: 0.9522 (tp) cc_final: 0.9176 (tp) REVERT: A 727 TYR cc_start: 0.7197 (p90) cc_final: 0.6706 (p90) REVERT: A 758 LEU cc_start: 0.7931 (tp) cc_final: 0.7527 (tp) REVERT: A 1225 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8408 (tp30) REVERT: A 1229 ASN cc_start: 0.7980 (m-40) cc_final: 0.7772 (m-40) REVERT: A 1230 MET cc_start: 0.8537 (ttm) cc_final: 0.7865 (ttm) REVERT: B 184 LEU cc_start: 0.9523 (tp) cc_final: 0.9255 (tp) REVERT: B 290 MET cc_start: 0.7161 (mmp) cc_final: 0.6513 (tpp) REVERT: B 376 PHE cc_start: 0.8127 (m-80) cc_final: 0.7386 (m-80) REVERT: B 407 ARG cc_start: 0.8908 (ttp-170) cc_final: 0.8073 (mtt90) REVERT: B 442 LEU cc_start: 0.8346 (mp) cc_final: 0.7768 (tp) REVERT: B 492 MET cc_start: 0.8702 (tpp) cc_final: 0.8340 (tpp) REVERT: B 538 TYR cc_start: 0.7520 (t80) cc_final: 0.7219 (t80) REVERT: B 665 MET cc_start: 0.9031 (ttm) cc_final: 0.8568 (ttm) REVERT: B 687 MET cc_start: 0.8970 (tpt) cc_final: 0.8141 (tpp) REVERT: B 689 ASP cc_start: 0.8780 (m-30) cc_final: 0.8184 (t0) REVERT: B 701 ASP cc_start: 0.8652 (m-30) cc_final: 0.8403 (m-30) REVERT: B 711 ASP cc_start: 0.9315 (t0) cc_final: 0.9110 (t0) REVERT: B 712 GLN cc_start: 0.9286 (tp-100) cc_final: 0.8769 (tm-30) REVERT: B 722 MET cc_start: 0.9141 (mmp) cc_final: 0.8795 (mmm) REVERT: B 749 PHE cc_start: 0.9223 (t80) cc_final: 0.9001 (t80) REVERT: B 1138 MET cc_start: 0.3846 (mmm) cc_final: 0.2724 (ttt) REVERT: B 1191 LYS cc_start: 0.8683 (mttt) cc_final: 0.8312 (mttt) REVERT: B 1225 GLU cc_start: 0.8930 (pm20) cc_final: 0.8662 (pm20) REVERT: C 239 ASP cc_start: 0.8007 (m-30) cc_final: 0.7777 (m-30) REVERT: C 275 GLN cc_start: 0.8050 (mm110) cc_final: 0.6424 (pm20) REVERT: C 352 TYR cc_start: 0.8141 (m-80) cc_final: 0.7884 (m-80) REVERT: C 468 ARG cc_start: 0.8146 (tpm170) cc_final: 0.7694 (tpm170) REVERT: C 523 LEU cc_start: 0.9025 (tp) cc_final: 0.8820 (tp) REVERT: C 526 LEU cc_start: 0.8829 (mt) cc_final: 0.8506 (mt) REVERT: C 578 ARG cc_start: 0.8484 (mmp-170) cc_final: 0.8083 (mmm160) REVERT: C 642 MET cc_start: 0.9014 (tpp) cc_final: 0.8708 (tpp) REVERT: C 665 MET cc_start: 0.8736 (tmm) cc_final: 0.8514 (tmm) REVERT: C 667 LYS cc_start: 0.9236 (mtmt) cc_final: 0.8876 (mtmt) REVERT: C 1192 LYS cc_start: 0.8728 (tttt) cc_final: 0.8447 (tmtt) REVERT: C 1195 ASP cc_start: 0.8870 (m-30) cc_final: 0.8628 (t0) REVERT: C 1202 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8276 (mt-10) REVERT: C 1203 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8342 (tp30) REVERT: D 156 MET cc_start: 0.8290 (mpp) cc_final: 0.7878 (mpp) REVERT: D 181 LEU cc_start: 0.9266 (mt) cc_final: 0.8864 (pt) REVERT: D 183 LYS cc_start: 0.8026 (mttt) cc_final: 0.7798 (mmtm) REVERT: D 196 GLU cc_start: 0.7941 (pp20) cc_final: 0.7185 (tp30) REVERT: D 291 HIS cc_start: 0.8825 (m-70) cc_final: 0.8600 (m170) REVERT: D 418 MET cc_start: 0.6355 (mmm) cc_final: 0.6050 (mmm) REVERT: D 462 LEU cc_start: 0.9154 (mt) cc_final: 0.8891 (mt) REVERT: D 471 ILE cc_start: 0.9222 (pt) cc_final: 0.8987 (mp) REVERT: D 514 MET cc_start: 0.8862 (tpp) cc_final: 0.8605 (tpp) REVERT: D 678 MET cc_start: 0.8247 (ttt) cc_final: 0.8028 (ttp) REVERT: D 700 ARG cc_start: 0.8480 (mmp80) cc_final: 0.8212 (mmp80) REVERT: D 708 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7841 (mt-10) REVERT: D 715 LYS cc_start: 0.9107 (tmmt) cc_final: 0.8813 (tppt) REVERT: D 722 MET cc_start: 0.6800 (mpp) cc_final: 0.6588 (mpp) REVERT: D 737 CYS cc_start: 0.9124 (m) cc_final: 0.8180 (t) REVERT: D 1195 ASP cc_start: 0.9002 (m-30) cc_final: 0.8507 (m-30) REVERT: D 1197 GLU cc_start: 0.8771 (pp20) cc_final: 0.8484 (pt0) REVERT: D 1199 GLN cc_start: 0.9027 (pt0) cc_final: 0.8640 (pp30) REVERT: D 1235 GLU cc_start: 0.7252 (pm20) cc_final: 0.7010 (pm20) REVERT: I 188 MET cc_start: 0.6778 (mmp) cc_final: 0.6389 (mmm) REVERT: I 217 MET cc_start: 0.3067 (tpt) cc_final: 0.2107 (ttt) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.3856 time to fit residues: 305.2139 Evaluate side-chains 399 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 167 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 288 optimal weight: 0.0170 chunk 207 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 539 HIS ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1194 HIS ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1199 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.099557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.068528 restraints weight = 205455.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.070675 restraints weight = 136164.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.072358 restraints weight = 102839.568| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 1.1601 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= 0.139 Angle : 0.652 13.274 35584 Z= 0.334 Chirality : 0.042 0.177 3993 Planarity : 0.004 0.068 4551 Dihedral : 4.607 24.177 3504 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3148 helix: 0.93 (0.13), residues: 1677 sheet: -0.54 (0.29), residues: 343 loop : -1.52 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP I 332 HIS 0.010 0.001 HIS A 171 PHE 0.014 0.001 PHE A1131 TYR 0.026 0.001 TYR A1204 ARG 0.007 0.001 ARG A 473 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 1230) hydrogen bonds : angle 4.59972 ( 3641) covalent geometry : bond 0.00304 (26364) covalent geometry : angle 0.65166 (35584) ********************** 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 477 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 2.844 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: A 135 LEU cc_start: 0.8855 (tp) cc_final: 0.8618 (pt) REVERT: A 181 LEU cc_start: 0.8623 (mt) cc_final: 0.8041 (pt) REVERT: A 184 LEU cc_start: 0.9019 (tp) cc_final: 0.8807 (tp) REVERT: A 186 ILE cc_start: 0.9480 (mt) cc_final: 0.9226 (mm) REVERT: A 249 CYS cc_start: 0.8572 (t) cc_final: 0.8362 (t) REVERT: A 290 MET cc_start: 0.8875 (mpp) cc_final: 0.8289 (mpp) REVERT: A 316 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 338 ILE cc_start: 0.9348 (mm) cc_final: 0.8996 (tp) REVERT: A 409 GLN cc_start: 0.8018 (mt0) cc_final: 0.7567 (mp10) REVERT: A 418 MET cc_start: 0.7487 (tpt) cc_final: 0.6636 (tpp) REVERT: A 421 MET cc_start: 0.8611 (mmm) cc_final: 0.8143 (mpp) REVERT: A 471 ILE cc_start: 0.9144 (mm) cc_final: 0.8901 (pt) REVERT: A 524 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7473 (mm-30) REVERT: A 687 MET cc_start: 0.8731 (mmp) cc_final: 0.8350 (mmm) REVERT: A 724 LEU cc_start: 0.9504 (tp) cc_final: 0.9166 (tp) REVERT: A 727 TYR cc_start: 0.7295 (p90) cc_final: 0.6727 (p90) REVERT: A 1198 GLU cc_start: 0.8662 (mp0) cc_final: 0.8279 (mp0) REVERT: A 1225 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8407 (tp30) REVERT: A 1229 ASN cc_start: 0.7944 (m-40) cc_final: 0.7691 (m-40) REVERT: A 1230 MET cc_start: 0.8657 (ttm) cc_final: 0.8310 (ttm) REVERT: B 184 LEU cc_start: 0.9523 (tp) cc_final: 0.9221 (tp) REVERT: B 245 ARG cc_start: 0.7703 (mmm-85) cc_final: 0.7370 (mmm-85) REVERT: B 290 MET cc_start: 0.7267 (mmp) cc_final: 0.6693 (tpt) REVERT: B 376 PHE cc_start: 0.8192 (m-80) cc_final: 0.7422 (m-80) REVERT: B 407 ARG cc_start: 0.8793 (ttp-170) cc_final: 0.8014 (mtt90) REVERT: B 442 LEU cc_start: 0.8336 (mp) cc_final: 0.7763 (tp) REVERT: B 538 TYR cc_start: 0.7777 (t80) cc_final: 0.7481 (t80) REVERT: B 665 MET cc_start: 0.9145 (ttm) cc_final: 0.8742 (ttm) REVERT: B 687 MET cc_start: 0.8992 (tpt) cc_final: 0.8250 (tpp) REVERT: B 701 ASP cc_start: 0.8658 (m-30) cc_final: 0.8395 (m-30) REVERT: B 711 ASP cc_start: 0.9313 (t0) cc_final: 0.9106 (t0) REVERT: B 712 GLN cc_start: 0.9240 (tp-100) cc_final: 0.8816 (tm-30) REVERT: B 722 MET cc_start: 0.9098 (mmp) cc_final: 0.8809 (mmm) REVERT: B 749 PHE cc_start: 0.9217 (t80) cc_final: 0.8998 (t80) REVERT: B 1191 LYS cc_start: 0.8745 (mttt) cc_final: 0.8441 (mttt) REVERT: B 1203 GLU cc_start: 0.9671 (tm-30) cc_final: 0.9426 (tm-30) REVERT: B 1225 GLU cc_start: 0.8924 (pm20) cc_final: 0.8491 (pm20) REVERT: C 275 GLN cc_start: 0.8001 (mm110) cc_final: 0.6408 (pm20) REVERT: C 320 SER cc_start: 0.9410 (t) cc_final: 0.9165 (p) REVERT: C 352 TYR cc_start: 0.8096 (m-80) cc_final: 0.7864 (m-80) REVERT: C 526 LEU cc_start: 0.8932 (mt) cc_final: 0.8632 (mt) REVERT: C 578 ARG cc_start: 0.8610 (mmp-170) cc_final: 0.8283 (mmm160) REVERT: C 665 MET cc_start: 0.8781 (tmm) cc_final: 0.8533 (tmm) REVERT: C 667 LYS cc_start: 0.9263 (mtmt) cc_final: 0.8901 (mttt) REVERT: C 1192 LYS cc_start: 0.8739 (tttt) cc_final: 0.8455 (tmtt) REVERT: C 1195 ASP cc_start: 0.8912 (m-30) cc_final: 0.8664 (t0) REVERT: C 1202 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8454 (mt-10) REVERT: C 1203 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8438 (tp30) REVERT: D 156 MET cc_start: 0.8323 (mpp) cc_final: 0.7858 (mpp) REVERT: D 173 MET cc_start: 0.9022 (mtm) cc_final: 0.8759 (mtm) REVERT: D 181 LEU cc_start: 0.9308 (mt) cc_final: 0.8891 (pt) REVERT: D 183 LYS cc_start: 0.8028 (mttt) cc_final: 0.7821 (mmtm) REVERT: D 196 GLU cc_start: 0.7904 (pp20) cc_final: 0.7177 (tp30) REVERT: D 291 HIS cc_start: 0.8825 (m-70) cc_final: 0.8599 (m-70) REVERT: D 418 MET cc_start: 0.6460 (mmm) cc_final: 0.6175 (mmm) REVERT: D 462 LEU cc_start: 0.9174 (mt) cc_final: 0.8910 (mt) REVERT: D 471 ILE cc_start: 0.9215 (pt) cc_final: 0.8971 (mp) REVERT: D 492 MET cc_start: 0.8632 (tpp) cc_final: 0.8423 (tpp) REVERT: D 700 ARG cc_start: 0.8481 (mmp80) cc_final: 0.8163 (mmp80) REVERT: D 708 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7803 (mt-10) REVERT: D 715 LYS cc_start: 0.9119 (tmmt) cc_final: 0.8836 (tppt) REVERT: D 722 MET cc_start: 0.6696 (mpp) cc_final: 0.6343 (mpp) REVERT: D 737 CYS cc_start: 0.9092 (m) cc_final: 0.8175 (t) REVERT: D 758 LEU cc_start: 0.9511 (tt) cc_final: 0.9302 (pp) REVERT: D 1195 ASP cc_start: 0.9078 (m-30) cc_final: 0.8646 (m-30) REVERT: D 1197 GLU cc_start: 0.8771 (pp20) cc_final: 0.8409 (pt0) REVERT: D 1199 GLN cc_start: 0.8997 (pt0) cc_final: 0.8657 (pp30) REVERT: I 16 ASN cc_start: 0.8460 (m110) cc_final: 0.8191 (m110) REVERT: I 133 VAL cc_start: 0.1309 (t) cc_final: 0.0854 (t) REVERT: I 188 MET cc_start: 0.6845 (mmp) cc_final: 0.6287 (mmm) REVERT: I 217 MET cc_start: 0.2880 (tpt) cc_final: 0.2163 (ttt) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.3833 time to fit residues: 288.3808 Evaluate side-chains 382 residues out of total 2785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 165 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 275 optimal weight: 0.9980 chunk 174 optimal weight: 0.6980 chunk 168 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 152 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 HIS ** A1199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 697 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1199 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.100126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.070685 restraints weight = 143209.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072379 restraints weight = 105231.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.073594 restraints weight = 85076.783| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 1.1731 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= 0.125 Angle : 0.653 11.246 35584 Z= 0.332 Chirality : 0.042 0.222 3993 Planarity : 0.004 0.066 4551 Dihedral : 4.520 23.791 3504 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3148 helix: 0.99 (0.13), residues: 1678 sheet: -0.49 (0.29), residues: 334 loop : -1.50 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 483 HIS 0.007 0.001 HIS B 240 PHE 0.013 0.001 PHE D 146 TYR 0.027 0.001 TYR A1204 ARG 0.022 0.001 ARG B1226 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 1230) hydrogen bonds : angle 4.50541 ( 3641) covalent geometry : bond 0.00272 (26364) covalent geometry : angle 0.65284 (35584) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12351.30 seconds wall clock time: 218 minutes 50.45 seconds (13130.45 seconds total)