Starting phenix.real_space_refine on Thu Feb 5 20:45:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dd9_46761/02_2026/9dd9_46761.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dd9_46761/02_2026/9dd9_46761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dd9_46761/02_2026/9dd9_46761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dd9_46761/02_2026/9dd9_46761.map" model { file = "/net/cci-nas-00/data/ceres_data/9dd9_46761/02_2026/9dd9_46761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dd9_46761/02_2026/9dd9_46761.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.010 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 96 5.16 5 C 12423 2.51 5 N 3387 2.21 5 O 3804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19710 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4654 Classifications: {'peptide': 576} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 547} Chain breaks: 2 Chain: "H" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, I, J, M, N, F, K, G, O Time building chain proxies: 4.98, per 1000 atoms: 0.25 Number of scatterers: 19710 At special positions: 0 Unit cell: (141.93, 151.06, 177.62, 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 96 16.00 O 3804 8.00 N 3387 7.00 C 12423 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.04 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.04 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.06 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.04 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.06 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.06 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 7 " " MAN D 4 " - " MAN D 5 " " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA K 3 " - " MAN K 7 " " MAN K 4 " - " MAN K 5 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 6 " " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 901 " - " ASN A 430 " " NAG A 902 " - " ASN A 674 " " NAG B 901 " - " ASN B 430 " " NAG B 902 " - " ASN B 674 " " NAG C 901 " - " ASN C 430 " " NAG C 902 " - " ASN C 674 " " NAG D 1 " - " ASN A 141 " " NAG E 1 " - " ASN A 398 " " NAG F 1 " - " ASN B 141 " " NAG G 1 " - " ASN B 398 " " NAG K 1 " - " ASN C 141 " " NAG O 1 " - " ASN C 398 " Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 864.6 milliseconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 42 sheets defined 19.4% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 200 through 205 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.664A pdb=" N LYS A 415 " --> pdb=" O ASP A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 546 removed outlier: 3.509A pdb=" N GLN A 507 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Proline residue: A 516 - end of helix removed outlier: 4.289A pdb=" N THR A 537 " --> pdb=" O ASN A 533 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 544 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 660 through 664 removed outlier: 3.939A pdb=" N ILE A 664 " --> pdb=" O ARG A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 698 removed outlier: 4.092A pdb=" N GLY A 698 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 Processing helix chain 'A' and resid 711 through 717 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 411 through 429 removed outlier: 3.664A pdb=" N LYS B 415 " --> pdb=" O ASP B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 546 removed outlier: 3.509A pdb=" N GLN B 507 " --> pdb=" O PHE B 503 " (cutoff:3.500A) Proline residue: B 516 - end of helix removed outlier: 4.290A pdb=" N THR B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 538 " --> pdb=" O HIS B 534 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 541 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS B 544 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 545 " --> pdb=" O GLU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.938A pdb=" N ILE B 664 " --> pdb=" O ARG B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 698 removed outlier: 4.093A pdb=" N GLY B 698 " --> pdb=" O ILE B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 711 Processing helix chain 'B' and resid 711 through 717 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.664A pdb=" N LYS C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 546 removed outlier: 3.508A pdb=" N GLN C 507 " --> pdb=" O PHE C 503 " (cutoff:3.500A) Proline residue: C 516 - end of helix removed outlier: 4.290A pdb=" N THR C 537 " --> pdb=" O ASN C 533 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU C 541 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS C 544 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 660 through 664 removed outlier: 3.939A pdb=" N ILE C 664 " --> pdb=" O ARG C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 698 removed outlier: 4.091A pdb=" N GLY C 698 " --> pdb=" O ILE C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 711 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.928A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.926A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.926A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 574 through 576 removed outlier: 6.548A pdb=" N TYR A 114 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 568 through 569 removed outlier: 3.801A pdb=" N THR B 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 145 through 152 removed outlier: 6.991A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 366 through 372 current: chain 'A' and resid 448 through 457 Processing sheet with id=AA4, first strand: chain 'A' and resid 157 through 175 removed outlier: 6.399A pdb=" N TRP A 174 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE A 182 " --> pdb=" O TRP A 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 180 through 191 current: chain 'A' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 246 through 248 current: chain 'A' and resid 287 through 288 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 294 through 295 current: chain 'A' and resid 340 through 346 Processing sheet with id=AA5, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 Processing sheet with id=AA8, first strand: chain 'A' and resid 559 through 560 Processing sheet with id=AA9, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 643 removed outlier: 6.857A pdb=" N TYR A 647 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A 658 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR A 649 " --> pdb=" O SER A 656 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 665 through 667 removed outlier: 6.347A pdb=" N THR A 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 574 through 576 removed outlier: 6.547A pdb=" N TYR B 114 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 568 through 569 removed outlier: 6.906A pdb=" N VAL B 124 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL C 667 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLN B 126 " --> pdb=" O VAL C 667 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.992A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 366 through 372 current: chain 'B' and resid 448 through 457 Processing sheet with id=AB6, first strand: chain 'B' and resid 157 through 175 removed outlier: 6.399A pdb=" N TRP B 174 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE B 182 " --> pdb=" O TRP B 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 180 through 191 current: chain 'B' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 246 through 248 current: chain 'B' and resid 287 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 294 through 295 current: chain 'B' and resid 340 through 346 Processing sheet with id=AB7, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AB8, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AB9, first strand: chain 'B' and resid 375 through 379 Processing sheet with id=AC1, first strand: chain 'B' and resid 559 through 560 Processing sheet with id=AC2, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC3, first strand: chain 'B' and resid 638 through 643 removed outlier: 6.856A pdb=" N TYR B 647 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN B 658 " --> pdb=" O TYR B 647 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR B 649 " --> pdb=" O SER B 656 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 574 through 576 removed outlier: 6.547A pdb=" N TYR C 114 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 145 through 152 removed outlier: 6.992A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 366 through 372 current: chain 'C' and resid 448 through 457 Processing sheet with id=AC6, first strand: chain 'C' and resid 157 through 175 removed outlier: 6.399A pdb=" N TRP C 174 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N PHE C 182 " --> pdb=" O TRP C 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 180 through 191 current: chain 'C' and resid 246 through 248 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 246 through 248 current: chain 'C' and resid 287 through 288 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 294 through 295 current: chain 'C' and resid 340 through 346 Processing sheet with id=AC7, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AC8, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AC9, first strand: chain 'C' and resid 375 through 379 Processing sheet with id=AD1, first strand: chain 'C' and resid 559 through 560 Processing sheet with id=AD2, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD3, first strand: chain 'C' and resid 638 through 643 removed outlier: 6.857A pdb=" N TYR C 647 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN C 658 " --> pdb=" O TYR C 647 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR C 649 " --> pdb=" O SER C 656 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100G through 103 Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 10 through 12 current: chain 'I' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100G through 103 Processing sheet with id=AD8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100G through 103 Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 10 through 13 current: chain 'L' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 53 through 54 current: chain 'L' and resid 97 through 98 Processing sheet with id=AE3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE4, first strand: chain 'M' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 10 through 13 current: chain 'M' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 53 through 54 current: chain 'M' and resid 97 through 98 Processing sheet with id=AE5, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 10 through 13 current: chain 'N' and resid 45 through 49 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 53 through 54 current: chain 'N' and resid 97 through 98 548 hydrogen bonds defined for protein. 1410 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: 3.46 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6084 1.34 - 1.46: 4109 1.46 - 1.58: 9844 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 20187 Sorted by residual: bond pdb=" N VAL B 363 " pdb=" CA VAL B 363 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.22e-02 6.72e+03 1.04e+01 bond pdb=" N VAL C 363 " pdb=" CA VAL C 363 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.22e-02 6.72e+03 9.94e+00 bond pdb=" N VAL C 259 " pdb=" CA VAL C 259 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 9.94e+00 bond pdb=" N VAL A 363 " pdb=" CA VAL A 363 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.22e-02 6.72e+03 9.90e+00 bond pdb=" N VAL B 259 " pdb=" CA VAL B 259 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.63e+00 ... (remaining 20182 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 26706 2.51 - 5.03: 656 5.03 - 7.54: 58 7.54 - 10.06: 6 10.06 - 12.57: 3 Bond angle restraints: 27429 Sorted by residual: angle pdb=" N PHE J 100G" pdb=" CA PHE J 100G" pdb=" CB PHE J 100G" ideal model delta sigma weight residual 110.57 98.00 12.57 1.57e+00 4.06e-01 6.41e+01 angle pdb=" N PHE H 100G" pdb=" CA PHE H 100G" pdb=" CB PHE H 100G" ideal model delta sigma weight residual 110.57 98.01 12.56 1.57e+00 4.06e-01 6.40e+01 angle pdb=" N PHE I 100G" pdb=" CA PHE I 100G" pdb=" CB PHE I 100G" ideal model delta sigma weight residual 110.57 98.07 12.50 1.57e+00 4.06e-01 6.33e+01 angle pdb=" CA ILE B 671 " pdb=" C ILE B 671 " pdb=" O ILE B 671 " ideal model delta sigma weight residual 122.63 118.01 4.62 8.70e-01 1.32e+00 2.82e+01 angle pdb=" CA ILE C 671 " pdb=" C ILE C 671 " pdb=" O ILE C 671 " ideal model delta sigma weight residual 122.63 118.04 4.59 8.70e-01 1.32e+00 2.78e+01 ... (remaining 27424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 11258 17.36 - 34.73: 863 34.73 - 52.09: 195 52.09 - 69.45: 50 69.45 - 86.82: 33 Dihedral angle restraints: 12399 sinusoidal: 5346 harmonic: 7053 Sorted by residual: dihedral pdb=" N PHE J 100G" pdb=" C PHE J 100G" pdb=" CA PHE J 100G" pdb=" CB PHE J 100G" ideal model delta harmonic sigma weight residual 122.80 109.23 13.57 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" N PHE H 100G" pdb=" C PHE H 100G" pdb=" CA PHE H 100G" pdb=" CB PHE H 100G" ideal model delta harmonic sigma weight residual 122.80 109.25 13.55 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" N PHE I 100G" pdb=" C PHE I 100G" pdb=" CA PHE I 100G" pdb=" CB PHE I 100G" ideal model delta harmonic sigma weight residual 122.80 109.26 13.54 0 2.50e+00 1.60e-01 2.94e+01 ... (remaining 12396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2730 0.085 - 0.170: 321 0.170 - 0.256: 27 0.256 - 0.341: 0 0.341 - 0.426: 3 Chirality restraints: 3081 Sorted by residual: chirality pdb=" C1 MAN F 6 " pdb=" O6 MAN F 4 " pdb=" C2 MAN F 6 " pdb=" O5 MAN F 6 " both_signs ideal model delta sigma weight residual False 2.40 2.33 0.07 2.00e-02 2.50e+03 1.06e+01 chirality pdb=" C1 MAN K 6 " pdb=" O6 MAN K 4 " pdb=" C2 MAN K 6 " pdb=" O5 MAN K 6 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 9.96e+00 chirality pdb=" C1 MAN D 6 " pdb=" O6 MAN D 4 " pdb=" C2 MAN D 6 " pdb=" O5 MAN D 6 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 9.92e+00 ... (remaining 3078 not shown) Planarity restraints: 3519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 674 " 0.032 2.00e-02 2.50e+03 7.53e-02 7.10e+01 pdb=" CG ASN C 674 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN C 674 " -0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN C 674 " 0.132 2.00e-02 2.50e+03 pdb=" C1 NAG C 902 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 674 " 0.032 2.00e-02 2.50e+03 7.53e-02 7.09e+01 pdb=" CG ASN B 674 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B 674 " -0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN B 674 " 0.132 2.00e-02 2.50e+03 pdb=" C1 NAG B 902 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 674 " -0.032 2.00e-02 2.50e+03 7.52e-02 7.08e+01 pdb=" CG ASN A 674 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN A 674 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN A 674 " -0.131 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " 0.079 2.00e-02 2.50e+03 ... (remaining 3516 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 189 2.60 - 3.18: 16744 3.18 - 3.75: 29717 3.75 - 4.33: 43500 4.33 - 4.90: 72807 Nonbonded interactions: 162957 Sorted by model distance: nonbonded pdb=" SG CYS J 22 " pdb=" SG CYS J 92 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 92 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " model vdw 2.032 3.760 nonbonded pdb=" SG CYS N 23 " pdb=" SG CYS N 88 " model vdw 2.033 3.760 nonbonded pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " model vdw 2.033 3.760 ... (remaining 162952 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.980 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.005 0.146 20235 Z= 0.310 Angle : 0.928 12.571 27558 Z= 0.547 Chirality : 0.054 0.426 3081 Planarity : 0.006 0.079 3507 Dihedral : 13.729 86.817 7836 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.16), residues: 2388 helix: -0.89 (0.29), residues: 294 sheet: -1.01 (0.18), residues: 783 loop : -0.50 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 178 TYR 0.018 0.001 TYR H 91 PHE 0.025 0.002 PHE J 100G TRP 0.009 0.001 TRP N 3 HIS 0.006 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00485 (20187) covalent geometry : angle 0.89187 (27429) SS BOND : bond 0.01331 ( 15) SS BOND : angle 1.94177 ( 30) hydrogen bonds : bond 0.22152 ( 548) hydrogen bonds : angle 10.17860 ( 1410) link_ALPHA1-3 : bond 0.01453 ( 6) link_ALPHA1-3 : angle 2.04757 ( 18) link_ALPHA1-6 : bond 0.02453 ( 6) link_ALPHA1-6 : angle 5.17160 ( 18) link_BETA1-4 : bond 0.00711 ( 9) link_BETA1-4 : angle 4.49589 ( 27) link_NAG-ASN : bond 0.07284 ( 12) link_NAG-ASN : angle 4.36899 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.607 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: B 366 MET cc_start: 0.8733 (mmm) cc_final: 0.8383 (mmm) REVERT: H 53 ASP cc_start: 0.8817 (p0) cc_final: 0.8533 (p0) REVERT: I 43 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8457 (mttt) REVERT: I 53 ASP cc_start: 0.8772 (p0) cc_final: 0.8532 (p0) REVERT: J 43 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8444 (mttp) REVERT: J 53 ASP cc_start: 0.8784 (p0) cc_final: 0.8521 (p0) REVERT: L 77 ASN cc_start: 0.8362 (t0) cc_final: 0.8107 (t0) REVERT: M 77 ASN cc_start: 0.8453 (t0) cc_final: 0.8200 (t0) REVERT: M 93 ASP cc_start: 0.8506 (t0) cc_final: 0.8265 (t0) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1920 time to fit residues: 96.9463 Evaluate side-chains 167 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 40.0000 chunk 235 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 HIS A 534 HIS B 433 HIS ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 HIS C 438 GLN C 534 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.058182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.041226 restraints weight = 94728.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.042981 restraints weight = 42329.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.044193 restraints weight = 25673.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.044997 restraints weight = 18455.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045525 restraints weight = 14717.820| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20235 Z= 0.200 Angle : 0.704 11.666 27558 Z= 0.345 Chirality : 0.045 0.271 3081 Planarity : 0.005 0.041 3507 Dihedral : 5.156 51.848 3375 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.82 % Allowed : 13.38 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2388 helix: -0.10 (0.28), residues: 339 sheet: -0.74 (0.17), residues: 822 loop : -0.32 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 39 TYR 0.021 0.002 TYR B 142 PHE 0.016 0.002 PHE L 83 TRP 0.011 0.001 TRP I 47 HIS 0.015 0.002 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00439 (20187) covalent geometry : angle 0.67369 (27429) SS BOND : bond 0.00428 ( 15) SS BOND : angle 0.83022 ( 30) hydrogen bonds : bond 0.04358 ( 548) hydrogen bonds : angle 7.02682 ( 1410) link_ALPHA1-3 : bond 0.00633 ( 6) link_ALPHA1-3 : angle 1.89505 ( 18) link_ALPHA1-6 : bond 0.00994 ( 6) link_ALPHA1-6 : angle 2.25501 ( 18) link_BETA1-4 : bond 0.00288 ( 9) link_BETA1-4 : angle 3.56575 ( 27) link_NAG-ASN : bond 0.00842 ( 12) link_NAG-ASN : angle 4.43128 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.722 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 366 MET cc_start: 0.9485 (mmm) cc_final: 0.9134 (mmm) REVERT: A 530 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8812 (mp0) REVERT: A 534 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7265 (t-90) REVERT: A 563 MET cc_start: 0.8765 (mmt) cc_final: 0.8126 (tpp) REVERT: A 601 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8783 (mm) REVERT: B 297 MET cc_start: 0.8487 (ttm) cc_final: 0.8213 (ttp) REVERT: B 530 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8750 (mp0) REVERT: B 534 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7180 (t70) REVERT: B 563 MET cc_start: 0.8805 (mmt) cc_final: 0.8109 (tpp) REVERT: B 601 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8706 (mm) REVERT: B 671 ILE cc_start: 0.8487 (mm) cc_final: 0.7991 (mt) REVERT: C 366 MET cc_start: 0.9453 (mmm) cc_final: 0.8813 (mmm) REVERT: C 530 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8791 (mp0) REVERT: C 534 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7211 (t-90) REVERT: C 563 MET cc_start: 0.8757 (mmt) cc_final: 0.7987 (tpp) REVERT: C 568 MET cc_start: 0.8963 (mtm) cc_final: 0.8335 (mpp) REVERT: C 601 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8710 (mm) REVERT: H 34 MET cc_start: 0.8464 (mmm) cc_final: 0.8084 (mmm) REVERT: H 46 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8008 (tm-30) REVERT: H 89 MET cc_start: 0.8307 (tpp) cc_final: 0.7974 (tpp) REVERT: H 108 MET cc_start: 0.8722 (tpt) cc_final: 0.8509 (tpp) REVERT: I 34 MET cc_start: 0.8300 (mmm) cc_final: 0.7787 (mmm) REVERT: J 34 MET cc_start: 0.8407 (mmm) cc_final: 0.7956 (mmm) REVERT: L 45 GLU cc_start: 0.7676 (mp0) cc_final: 0.7417 (mp0) REVERT: L 89 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8579 (tm-30) REVERT: L 106 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.7948 (pp) REVERT: M 45 GLU cc_start: 0.7322 (mp0) cc_final: 0.7112 (mp0) REVERT: M 77 ASN cc_start: 0.9294 (t0) cc_final: 0.9085 (t0) REVERT: M 78 MET cc_start: 0.9317 (tpp) cc_final: 0.8855 (tpp) REVERT: M 93 ASP cc_start: 0.8740 (t0) cc_final: 0.8420 (t0) REVERT: N 45 GLU cc_start: 0.7348 (mp0) cc_final: 0.6779 (mp0) REVERT: N 78 MET cc_start: 0.9301 (tpp) cc_final: 0.8971 (tpp) REVERT: N 89 GLN cc_start: 0.8995 (tm-30) cc_final: 0.8404 (tm-30) REVERT: N 106 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7964 (pp) outliers start: 38 outliers final: 12 residues processed: 208 average time/residue: 0.1661 time to fit residues: 51.2525 Evaluate side-chains 169 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 223 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 534 HIS ** B 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.056227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.039229 restraints weight = 98318.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.040927 restraints weight = 43925.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.042057 restraints weight = 26973.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.042826 restraints weight = 19606.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043314 restraints weight = 15799.842| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20235 Z= 0.246 Angle : 0.665 12.617 27558 Z= 0.325 Chirality : 0.044 0.312 3081 Planarity : 0.005 0.137 3507 Dihedral : 5.191 47.869 3375 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.40 % Allowed : 11.89 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.17), residues: 2388 helix: 0.75 (0.31), residues: 324 sheet: -0.58 (0.17), residues: 822 loop : -0.14 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 588 TYR 0.018 0.002 TYR L 91 PHE 0.013 0.002 PHE C 384 TRP 0.030 0.001 TRP B 539 HIS 0.009 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00542 (20187) covalent geometry : angle 0.62818 (27429) SS BOND : bond 0.00236 ( 15) SS BOND : angle 1.03272 ( 30) hydrogen bonds : bond 0.03997 ( 548) hydrogen bonds : angle 6.48386 ( 1410) link_ALPHA1-3 : bond 0.00783 ( 6) link_ALPHA1-3 : angle 1.57030 ( 18) link_ALPHA1-6 : bond 0.00421 ( 6) link_ALPHA1-6 : angle 2.23814 ( 18) link_BETA1-4 : bond 0.00402 ( 9) link_BETA1-4 : angle 3.42537 ( 27) link_NAG-ASN : bond 0.00900 ( 12) link_NAG-ASN : angle 4.90557 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 0.640 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 183 MET cc_start: 0.8152 (mtt) cc_final: 0.7818 (ttm) REVERT: A 366 MET cc_start: 0.9387 (mmm) cc_final: 0.8997 (mmm) REVERT: A 530 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8869 (pt0) REVERT: A 534 HIS cc_start: 0.8154 (OUTLIER) cc_final: 0.7764 (t-170) REVERT: A 563 MET cc_start: 0.8795 (mmt) cc_final: 0.8220 (tpp) REVERT: A 601 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8865 (mm) REVERT: B 232 MET cc_start: 0.8010 (mtm) cc_final: 0.7323 (mtm) REVERT: B 297 MET cc_start: 0.8835 (ttm) cc_final: 0.8619 (ttp) REVERT: B 534 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7057 (t-90) REVERT: B 563 MET cc_start: 0.8828 (mmt) cc_final: 0.8102 (tpp) REVERT: B 587 MET cc_start: 0.5050 (tmm) cc_final: 0.4697 (ppp) REVERT: B 671 ILE cc_start: 0.8476 (mm) cc_final: 0.7953 (mp) REVERT: C 183 MET cc_start: 0.8106 (mtt) cc_final: 0.7843 (ttm) REVERT: C 232 MET cc_start: 0.7858 (mtm) cc_final: 0.7240 (mtm) REVERT: C 366 MET cc_start: 0.9279 (mmm) cc_final: 0.8542 (mmm) REVERT: C 534 HIS cc_start: 0.8268 (OUTLIER) cc_final: 0.7900 (t-170) REVERT: C 563 MET cc_start: 0.8741 (mmt) cc_final: 0.8200 (tpp) REVERT: C 587 MET cc_start: 0.5051 (tmm) cc_final: 0.4654 (ppp) REVERT: C 671 ILE cc_start: 0.8596 (mm) cc_final: 0.7766 (mt) REVERT: H 34 MET cc_start: 0.8479 (mmm) cc_final: 0.7827 (mmt) REVERT: H 46 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7980 (tm-30) REVERT: H 89 MET cc_start: 0.8509 (tpp) cc_final: 0.8270 (tpp) REVERT: I 34 MET cc_start: 0.8274 (mmm) cc_final: 0.7532 (mmm) REVERT: J 34 MET cc_start: 0.8462 (mmm) cc_final: 0.7948 (mmm) REVERT: J 46 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7789 (tm-30) REVERT: J 89 MET cc_start: 0.8360 (tpp) cc_final: 0.8003 (tpp) REVERT: L 45 GLU cc_start: 0.7740 (mp0) cc_final: 0.7531 (mp0) REVERT: L 78 MET cc_start: 0.9268 (tpp) cc_final: 0.8885 (tpp) REVERT: L 89 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8869 (tm-30) REVERT: M 33 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9146 (tp) REVERT: M 78 MET cc_start: 0.9381 (tpp) cc_final: 0.8974 (tpp) REVERT: M 93 ASP cc_start: 0.8928 (t0) cc_final: 0.8520 (t0) REVERT: N 33 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9145 (tp) REVERT: N 45 GLU cc_start: 0.7514 (mp0) cc_final: 0.6863 (mp0) REVERT: N 78 MET cc_start: 0.9399 (tpp) cc_final: 0.8979 (tpp) outliers start: 50 outliers final: 17 residues processed: 187 average time/residue: 0.1460 time to fit residues: 41.1085 Evaluate side-chains 158 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 60 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 23 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS A 534 HIS B 311 HIS ** B 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 HIS C 534 HIS ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 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 = 0.3277 r_free = 0.3277 target = 0.055964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.039437 restraints weight = 100147.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.041163 restraints weight = 43898.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.042331 restraints weight = 26643.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.043113 restraints weight = 19126.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.043665 restraints weight = 15277.741| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20235 Z= 0.180 Angle : 0.602 12.294 27558 Z= 0.291 Chirality : 0.043 0.287 3081 Planarity : 0.004 0.053 3507 Dihedral : 5.089 47.114 3375 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.73 % Allowed : 13.14 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2388 helix: 0.79 (0.31), residues: 324 sheet: -0.37 (0.17), residues: 867 loop : -0.10 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 588 TYR 0.015 0.001 TYR J 90 PHE 0.011 0.001 PHE B 508 TRP 0.026 0.001 TRP C 539 HIS 0.011 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00397 (20187) covalent geometry : angle 0.56368 (27429) SS BOND : bond 0.00504 ( 15) SS BOND : angle 1.05687 ( 30) hydrogen bonds : bond 0.03538 ( 548) hydrogen bonds : angle 6.28285 ( 1410) link_ALPHA1-3 : bond 0.00715 ( 6) link_ALPHA1-3 : angle 1.47116 ( 18) link_ALPHA1-6 : bond 0.00411 ( 6) link_ALPHA1-6 : angle 2.10827 ( 18) link_BETA1-4 : bond 0.00314 ( 9) link_BETA1-4 : angle 3.32598 ( 27) link_NAG-ASN : bond 0.00817 ( 12) link_NAG-ASN : angle 4.75320 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8212 (mtt) cc_final: 0.7823 (ttm) REVERT: A 366 MET cc_start: 0.9330 (mmm) cc_final: 0.8669 (mmm) REVERT: A 534 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7484 (t-90) REVERT: A 563 MET cc_start: 0.8869 (mmt) cc_final: 0.7651 (tpp) REVERT: A 601 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8976 (mm) REVERT: A 718 ASP cc_start: 0.8703 (t0) cc_final: 0.8335 (t0) REVERT: B 183 MET cc_start: 0.8047 (mtt) cc_final: 0.7526 (ttm) REVERT: B 297 MET cc_start: 0.8933 (ttm) cc_final: 0.8676 (ttm) REVERT: B 366 MET cc_start: 0.9139 (mmm) cc_final: 0.8351 (mmm) REVERT: B 563 MET cc_start: 0.8884 (mmt) cc_final: 0.8147 (tpp) REVERT: B 601 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8829 (mm) REVERT: B 671 ILE cc_start: 0.8754 (mm) cc_final: 0.8331 (mp) REVERT: C 183 MET cc_start: 0.8075 (mtt) cc_final: 0.7633 (ttm) REVERT: C 232 MET cc_start: 0.7922 (mtm) cc_final: 0.7302 (mtm) REVERT: C 366 MET cc_start: 0.9301 (mmm) cc_final: 0.8501 (mmm) REVERT: C 428 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8257 (ttt90) REVERT: C 523 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8715 (mmm-85) REVERT: C 534 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7447 (t-90) REVERT: C 563 MET cc_start: 0.8838 (mmt) cc_final: 0.8301 (tpp) REVERT: C 601 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8816 (mm) REVERT: C 671 ILE cc_start: 0.8762 (mm) cc_final: 0.8219 (mp) REVERT: C 718 ASP cc_start: 0.8673 (t0) cc_final: 0.8321 (t0) REVERT: H 34 MET cc_start: 0.8542 (mmm) cc_final: 0.8025 (mmm) REVERT: H 46 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8012 (tm-30) REVERT: I 34 MET cc_start: 0.8410 (mmm) cc_final: 0.7696 (mmm) REVERT: I 108 MET cc_start: 0.8877 (tpt) cc_final: 0.8470 (tpp) REVERT: J 34 MET cc_start: 0.8398 (mmm) cc_final: 0.7791 (mmt) REVERT: J 108 MET cc_start: 0.8926 (tpt) cc_final: 0.8665 (tpp) REVERT: L 45 GLU cc_start: 0.7801 (mp0) cc_final: 0.7576 (mp0) REVERT: L 89 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8819 (tm-30) REVERT: M 33 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9159 (tp) REVERT: M 42 LYS cc_start: 0.8615 (tptp) cc_final: 0.8248 (tptt) REVERT: M 78 MET cc_start: 0.9360 (tpp) cc_final: 0.9012 (tpp) REVERT: M 93 ASP cc_start: 0.8983 (t0) cc_final: 0.8706 (t0) REVERT: N 45 GLU cc_start: 0.7714 (mp0) cc_final: 0.7419 (mp0) REVERT: N 54 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9380 (mm) REVERT: N 78 MET cc_start: 0.9346 (tpp) cc_final: 0.8946 (tpp) outliers start: 36 outliers final: 15 residues processed: 175 average time/residue: 0.1525 time to fit residues: 40.3456 Evaluate side-chains 149 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 68 optimal weight: 9.9990 chunk 168 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 185 optimal weight: 0.8980 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 370 GLN A 534 HIS B 534 HIS ** B 637 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 534 HIS ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN N 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.056953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.040404 restraints weight = 98950.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.042193 restraints weight = 43145.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043394 restraints weight = 26082.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.044210 restraints weight = 18686.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044771 restraints weight = 14879.338| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 20235 Z= 0.106 Angle : 0.592 12.441 27558 Z= 0.283 Chirality : 0.043 0.287 3081 Planarity : 0.003 0.048 3507 Dihedral : 4.919 48.191 3375 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.01 % Allowed : 13.72 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.17), residues: 2388 helix: 0.78 (0.31), residues: 321 sheet: -0.19 (0.17), residues: 870 loop : -0.11 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 16 TYR 0.012 0.001 TYR B 380 PHE 0.009 0.001 PHE B 508 TRP 0.014 0.001 TRP B 539 HIS 0.012 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00243 (20187) covalent geometry : angle 0.55104 (27429) SS BOND : bond 0.00165 ( 15) SS BOND : angle 2.27402 ( 30) hydrogen bonds : bond 0.03375 ( 548) hydrogen bonds : angle 6.08375 ( 1410) link_ALPHA1-3 : bond 0.00817 ( 6) link_ALPHA1-3 : angle 1.38904 ( 18) link_ALPHA1-6 : bond 0.00456 ( 6) link_ALPHA1-6 : angle 2.02239 ( 18) link_BETA1-4 : bond 0.00298 ( 9) link_BETA1-4 : angle 3.16508 ( 27) link_NAG-ASN : bond 0.00860 ( 12) link_NAG-ASN : angle 4.67114 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.8879 (mtp) cc_final: 0.8419 (mtp) REVERT: A 183 MET cc_start: 0.8169 (mtt) cc_final: 0.7873 (ttm) REVERT: A 366 MET cc_start: 0.9339 (mmm) cc_final: 0.8719 (mmm) REVERT: A 530 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8921 (mp0) REVERT: A 534 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.7717 (t-90) REVERT: A 563 MET cc_start: 0.8744 (mmt) cc_final: 0.8513 (tpp) REVERT: A 587 MET cc_start: 0.4387 (ppp) cc_final: 0.3698 (ppp) REVERT: A 599 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8486 (tpp-160) REVERT: A 718 ASP cc_start: 0.8758 (t0) cc_final: 0.8334 (t0) REVERT: B 183 MET cc_start: 0.8060 (mtt) cc_final: 0.7546 (ttm) REVERT: B 297 MET cc_start: 0.8924 (ttm) cc_final: 0.8694 (ttm) REVERT: B 366 MET cc_start: 0.9159 (mmm) cc_final: 0.8330 (mmm) REVERT: B 534 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7193 (t-90) REVERT: B 563 MET cc_start: 0.8880 (mmt) cc_final: 0.8190 (tpp) REVERT: B 601 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8835 (mm) REVERT: B 671 ILE cc_start: 0.8615 (mm) cc_final: 0.7993 (mp) REVERT: B 718 ASP cc_start: 0.8666 (t0) cc_final: 0.8292 (t0) REVERT: C 183 MET cc_start: 0.8107 (mtt) cc_final: 0.7685 (ttm) REVERT: C 232 MET cc_start: 0.7880 (mtm) cc_final: 0.7299 (mtm) REVERT: C 366 MET cc_start: 0.9293 (mmm) cc_final: 0.8449 (mmm) REVERT: C 428 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8342 (ttt90) REVERT: C 534 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7541 (t-90) REVERT: C 563 MET cc_start: 0.8842 (mmt) cc_final: 0.8397 (tpp) REVERT: C 599 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8588 (tpp-160) REVERT: C 601 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 671 ILE cc_start: 0.8686 (mm) cc_final: 0.8206 (mp) REVERT: C 718 ASP cc_start: 0.8697 (t0) cc_final: 0.8303 (t0) REVERT: H 34 MET cc_start: 0.8608 (mmm) cc_final: 0.7998 (mmt) REVERT: H 46 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7901 (tm-30) REVERT: H 89 MET cc_start: 0.8345 (tpp) cc_final: 0.8027 (tpp) REVERT: I 34 MET cc_start: 0.8476 (mmm) cc_final: 0.7880 (mmm) REVERT: I 108 MET cc_start: 0.8935 (tpt) cc_final: 0.8453 (tpp) REVERT: J 34 MET cc_start: 0.8437 (mmm) cc_final: 0.7884 (mmt) REVERT: J 89 MET cc_start: 0.8362 (tpp) cc_final: 0.7933 (tpp) REVERT: J 108 MET cc_start: 0.8907 (tpt) cc_final: 0.8608 (tpt) REVERT: L 33 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9133 (tp) REVERT: L 45 GLU cc_start: 0.7788 (mp0) cc_final: 0.7553 (mp0) REVERT: L 89 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8871 (tm-30) REVERT: M 33 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9189 (tp) REVERT: M 42 LYS cc_start: 0.8612 (tptp) cc_final: 0.8270 (tptp) REVERT: M 78 MET cc_start: 0.9331 (tpp) cc_final: 0.8991 (tpp) REVERT: M 93 ASP cc_start: 0.8958 (t0) cc_final: 0.8705 (t0) REVERT: N 33 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9125 (tp) REVERT: N 45 GLU cc_start: 0.7786 (mp0) cc_final: 0.7141 (mp0) REVERT: N 54 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9359 (mm) REVERT: N 78 MET cc_start: 0.9289 (tpp) cc_final: 0.8913 (tpp) outliers start: 42 outliers final: 13 residues processed: 177 average time/residue: 0.1471 time to fit residues: 39.1414 Evaluate side-chains 159 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 529 CYS Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 ASN B 620 ASN B 637 HIS C 534 HIS C 616 GLN C 620 ASN M 27 GLN N 55 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.038497 restraints weight = 100789.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.040162 restraints weight = 44566.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.041281 restraints weight = 27231.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.042053 restraints weight = 19712.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.042567 restraints weight = 15798.108| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 20235 Z= 0.237 Angle : 0.641 12.126 27558 Z= 0.305 Chirality : 0.044 0.300 3081 Planarity : 0.004 0.066 3507 Dihedral : 5.104 47.081 3375 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.16 % Allowed : 14.53 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.17), residues: 2388 helix: 0.77 (0.31), residues: 321 sheet: -0.18 (0.17), residues: 870 loop : -0.18 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 16 TYR 0.012 0.001 TYR M 71 PHE 0.010 0.001 PHE A 319 TRP 0.020 0.001 TRP A 539 HIS 0.017 0.002 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00526 (20187) covalent geometry : angle 0.60303 (27429) SS BOND : bond 0.00226 ( 15) SS BOND : angle 2.01652 ( 30) hydrogen bonds : bond 0.03452 ( 548) hydrogen bonds : angle 6.00232 ( 1410) link_ALPHA1-3 : bond 0.00590 ( 6) link_ALPHA1-3 : angle 1.46253 ( 18) link_ALPHA1-6 : bond 0.00448 ( 6) link_ALPHA1-6 : angle 2.04739 ( 18) link_BETA1-4 : bond 0.00412 ( 9) link_BETA1-4 : angle 3.36060 ( 27) link_NAG-ASN : bond 0.00880 ( 12) link_NAG-ASN : angle 4.72559 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 0.830 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: A 183 MET cc_start: 0.8116 (mtt) cc_final: 0.7824 (ttm) REVERT: A 366 MET cc_start: 0.9334 (mmm) cc_final: 0.8691 (mmm) REVERT: A 534 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7629 (t70) REVERT: A 563 MET cc_start: 0.8959 (mmt) cc_final: 0.8396 (tpp) REVERT: A 587 MET cc_start: 0.4833 (ppp) cc_final: 0.3820 (ppp) REVERT: A 599 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8487 (tpp-160) REVERT: A 620 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8817 (t0) REVERT: A 718 ASP cc_start: 0.8752 (t0) cc_final: 0.8377 (t0) REVERT: B 183 MET cc_start: 0.7964 (mtt) cc_final: 0.7568 (ttm) REVERT: B 297 MET cc_start: 0.9003 (ttm) cc_final: 0.8794 (ttm) REVERT: B 366 MET cc_start: 0.9149 (mmm) cc_final: 0.8332 (mmm) REVERT: B 534 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7743 (t70) REVERT: B 567 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7523 (p) REVERT: B 620 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8681 (t0) REVERT: B 671 ILE cc_start: 0.8634 (mm) cc_final: 0.8170 (mt) REVERT: B 718 ASP cc_start: 0.8656 (t0) cc_final: 0.8292 (t0) REVERT: C 183 MET cc_start: 0.8057 (mtt) cc_final: 0.7681 (ttm) REVERT: C 232 MET cc_start: 0.8140 (mtm) cc_final: 0.7750 (mtm) REVERT: C 366 MET cc_start: 0.9316 (mmm) cc_final: 0.8520 (mmm) REVERT: C 534 HIS cc_start: 0.7757 (OUTLIER) cc_final: 0.7433 (t-90) REVERT: C 563 MET cc_start: 0.8933 (mmt) cc_final: 0.8408 (tpp) REVERT: C 567 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7301 (p) REVERT: C 620 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8685 (t0) REVERT: C 671 ILE cc_start: 0.8753 (mm) cc_final: 0.8171 (mt) REVERT: C 718 ASP cc_start: 0.8701 (t0) cc_final: 0.8348 (t0) REVERT: H 34 MET cc_start: 0.8603 (mmm) cc_final: 0.8029 (mmm) REVERT: H 46 GLU cc_start: 0.8472 (tm-30) cc_final: 0.7888 (tm-30) REVERT: I 34 MET cc_start: 0.8495 (mmm) cc_final: 0.7791 (mmm) REVERT: I 108 MET cc_start: 0.8908 (tpt) cc_final: 0.8406 (tpp) REVERT: J 34 MET cc_start: 0.8474 (mmm) cc_final: 0.7827 (mmt) REVERT: L 45 GLU cc_start: 0.7797 (mp0) cc_final: 0.7502 (mp0) REVERT: L 89 GLN cc_start: 0.9170 (tm-30) cc_final: 0.8840 (tm-30) REVERT: M 78 MET cc_start: 0.9365 (tpp) cc_final: 0.9053 (tpp) REVERT: M 93 ASP cc_start: 0.9037 (t0) cc_final: 0.8605 (t0) REVERT: N 45 GLU cc_start: 0.8035 (mp0) cc_final: 0.7626 (mp0) REVERT: N 54 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9348 (mm) REVERT: N 78 MET cc_start: 0.9280 (tpp) cc_final: 0.8940 (tpp) outliers start: 45 outliers final: 24 residues processed: 166 average time/residue: 0.1562 time to fit residues: 39.2166 Evaluate side-chains 156 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 122 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 529 CYS Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 232 optimal weight: 7.9990 chunk 137 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 168 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS A 534 HIS A 620 ASN B 172 GLN B 263 HIS B 534 HIS B 620 ASN ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 GLN C 620 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.053878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.037829 restraints weight = 100801.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.039363 restraints weight = 45526.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.040421 restraints weight = 28119.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.041111 restraints weight = 20497.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.041600 restraints weight = 16651.640| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20235 Z= 0.277 Angle : 0.682 12.175 27558 Z= 0.327 Chirality : 0.044 0.310 3081 Planarity : 0.004 0.046 3507 Dihedral : 5.335 45.845 3375 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.40 % Allowed : 14.53 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2388 helix: 0.61 (0.30), residues: 324 sheet: -0.38 (0.17), residues: 840 loop : -0.18 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 16 TYR 0.013 0.002 TYR L 71 PHE 0.012 0.002 PHE A 319 TRP 0.025 0.001 TRP A 539 HIS 0.010 0.002 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00609 (20187) covalent geometry : angle 0.64621 (27429) SS BOND : bond 0.00231 ( 15) SS BOND : angle 1.84586 ( 30) hydrogen bonds : bond 0.03589 ( 548) hydrogen bonds : angle 6.04630 ( 1410) link_ALPHA1-3 : bond 0.00537 ( 6) link_ALPHA1-3 : angle 1.41808 ( 18) link_ALPHA1-6 : bond 0.00521 ( 6) link_ALPHA1-6 : angle 2.02229 ( 18) link_BETA1-4 : bond 0.00456 ( 9) link_BETA1-4 : angle 3.45324 ( 27) link_NAG-ASN : bond 0.00907 ( 12) link_NAG-ASN : angle 4.84382 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 132 time to evaluate : 0.554 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: A 183 MET cc_start: 0.7983 (mtt) cc_final: 0.7704 (ttm) REVERT: A 366 MET cc_start: 0.9378 (mmm) cc_final: 0.8719 (mmm) REVERT: A 534 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7684 (t-90) REVERT: A 563 MET cc_start: 0.8742 (mmt) cc_final: 0.8407 (tpp) REVERT: A 587 MET cc_start: 0.5085 (ppp) cc_final: 0.4083 (ppp) REVERT: A 599 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8508 (tpp-160) REVERT: A 620 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8699 (t0) REVERT: A 718 ASP cc_start: 0.8744 (t0) cc_final: 0.8406 (t0) REVERT: B 183 MET cc_start: 0.8014 (mtt) cc_final: 0.7659 (ttm) REVERT: B 297 MET cc_start: 0.9083 (ttm) cc_final: 0.8881 (ttm) REVERT: B 534 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7530 (t-90) REVERT: B 567 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7620 (p) REVERT: B 568 MET cc_start: 0.8775 (mmm) cc_final: 0.7725 (tpp) REVERT: B 620 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8565 (t0) REVERT: B 718 ASP cc_start: 0.8626 (t0) cc_final: 0.8300 (t0) REVERT: C 183 MET cc_start: 0.8041 (mtt) cc_final: 0.7718 (ttm) REVERT: C 366 MET cc_start: 0.9374 (mmm) cc_final: 0.8580 (mmm) REVERT: C 428 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8206 (ttt90) REVERT: C 523 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8703 (mmm-85) REVERT: C 563 MET cc_start: 0.8908 (mmt) cc_final: 0.8674 (tpp) REVERT: C 567 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7712 (p) REVERT: C 601 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8923 (mm) REVERT: C 620 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8633 (t0) REVERT: C 718 ASP cc_start: 0.8666 (t0) cc_final: 0.8329 (t0) REVERT: H 34 MET cc_start: 0.8670 (mmm) cc_final: 0.7953 (mmt) REVERT: I 34 MET cc_start: 0.8586 (mmm) cc_final: 0.7871 (mmm) REVERT: J 34 MET cc_start: 0.8548 (mmm) cc_final: 0.7914 (mmt) REVERT: J 108 MET cc_start: 0.8908 (tpt) cc_final: 0.8433 (tpp) REVERT: L 45 GLU cc_start: 0.7893 (mp0) cc_final: 0.7582 (mp0) REVERT: L 89 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8905 (tm-30) REVERT: M 78 MET cc_start: 0.9359 (tpp) cc_final: 0.9065 (tpp) REVERT: M 93 ASP cc_start: 0.9093 (t0) cc_final: 0.8679 (t0) REVERT: N 78 MET cc_start: 0.9274 (tpp) cc_final: 0.8943 (tpp) outliers start: 50 outliers final: 26 residues processed: 173 average time/residue: 0.1662 time to fit residues: 42.5750 Evaluate side-chains 161 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 428 ARG Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 620 ASN Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 529 CYS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 100 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 191 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 221 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS B 172 GLN ** B 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.054795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.038613 restraints weight = 100295.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.040255 restraints weight = 44549.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.041363 restraints weight = 27272.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.042130 restraints weight = 19795.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.042625 restraints weight = 15870.643| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20235 Z= 0.141 Angle : 0.629 12.475 27558 Z= 0.295 Chirality : 0.043 0.306 3081 Planarity : 0.003 0.044 3507 Dihedral : 5.145 47.021 3375 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.77 % Allowed : 15.25 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.17), residues: 2388 helix: 0.62 (0.30), residues: 324 sheet: -0.21 (0.17), residues: 837 loop : -0.14 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 16 TYR 0.009 0.001 TYR I 100E PHE 0.011 0.001 PHE B 508 TRP 0.023 0.001 TRP B 539 HIS 0.011 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00320 (20187) covalent geometry : angle 0.59242 (27429) SS BOND : bond 0.00200 ( 15) SS BOND : angle 1.60086 ( 30) hydrogen bonds : bond 0.03344 ( 548) hydrogen bonds : angle 5.97137 ( 1410) link_ALPHA1-3 : bond 0.00777 ( 6) link_ALPHA1-3 : angle 1.35371 ( 18) link_ALPHA1-6 : bond 0.00370 ( 6) link_ALPHA1-6 : angle 1.92611 ( 18) link_BETA1-4 : bond 0.00252 ( 9) link_BETA1-4 : angle 3.25350 ( 27) link_NAG-ASN : bond 0.00863 ( 12) link_NAG-ASN : angle 4.74226 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.519 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: A 183 MET cc_start: 0.7783 (mtt) cc_final: 0.7506 (ttm) REVERT: A 366 MET cc_start: 0.9374 (mmm) cc_final: 0.8693 (mmm) REVERT: A 534 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7921 (t-170) REVERT: A 563 MET cc_start: 0.8775 (mmt) cc_final: 0.8399 (tpp) REVERT: A 567 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8152 (p) REVERT: A 587 MET cc_start: 0.5214 (ppp) cc_final: 0.3980 (ppp) REVERT: A 599 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8510 (tpp-160) REVERT: A 718 ASP cc_start: 0.8724 (t0) cc_final: 0.8310 (t0) REVERT: B 183 MET cc_start: 0.7862 (mtt) cc_final: 0.7516 (ttm) REVERT: B 232 MET cc_start: 0.8029 (mtp) cc_final: 0.7195 (ptp) REVERT: B 534 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7366 (t70) REVERT: B 567 VAL cc_start: 0.7813 (OUTLIER) cc_final: 0.7365 (p) REVERT: B 568 MET cc_start: 0.8800 (mmm) cc_final: 0.8117 (mmm) REVERT: B 587 MET cc_start: 0.4434 (ppp) cc_final: 0.2897 (ppp) REVERT: B 671 ILE cc_start: 0.8620 (mm) cc_final: 0.8061 (mt) REVERT: B 718 ASP cc_start: 0.8615 (t0) cc_final: 0.8241 (t0) REVERT: C 183 MET cc_start: 0.7957 (mtt) cc_final: 0.7681 (ttm) REVERT: C 366 MET cc_start: 0.9369 (mmm) cc_final: 0.8518 (mmm) REVERT: C 428 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8324 (ttt90) REVERT: C 563 MET cc_start: 0.8936 (mmt) cc_final: 0.7964 (tpp) REVERT: C 567 VAL cc_start: 0.7933 (OUTLIER) cc_final: 0.7408 (p) REVERT: C 601 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8904 (mm) REVERT: C 677 MET cc_start: 0.8640 (tpp) cc_final: 0.8436 (tpp) REVERT: C 718 ASP cc_start: 0.8638 (t0) cc_final: 0.8241 (t0) REVERT: H 46 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7868 (tm-30) REVERT: H 89 MET cc_start: 0.8399 (tpp) cc_final: 0.8040 (tpp) REVERT: I 34 MET cc_start: 0.8606 (mmm) cc_final: 0.7947 (mmm) REVERT: I 108 MET cc_start: 0.8846 (tpt) cc_final: 0.8407 (tpp) REVERT: J 34 MET cc_start: 0.8509 (mmm) cc_final: 0.7910 (mmt) REVERT: J 89 MET cc_start: 0.8291 (tpp) cc_final: 0.7931 (tpp) REVERT: J 107 THR cc_start: 0.9145 (t) cc_final: 0.8884 (p) REVERT: J 108 MET cc_start: 0.8965 (tpt) cc_final: 0.8337 (tpp) REVERT: L 45 GLU cc_start: 0.7928 (mp0) cc_final: 0.7524 (mp0) REVERT: L 78 MET cc_start: 0.9169 (tpp) cc_final: 0.8757 (tpp) REVERT: L 89 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8831 (tm-30) REVERT: M 33 ILE cc_start: 0.9450 (OUTLIER) cc_final: 0.9205 (tp) REVERT: M 45 GLU cc_start: 0.8015 (mp0) cc_final: 0.7806 (mp0) REVERT: M 78 MET cc_start: 0.9323 (tpp) cc_final: 0.9044 (tpp) REVERT: N 45 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8141 (mp0) REVERT: N 78 MET cc_start: 0.9139 (tpp) cc_final: 0.8820 (tpp) outliers start: 37 outliers final: 22 residues processed: 160 average time/residue: 0.1611 time to fit residues: 38.1081 Evaluate side-chains 154 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 529 CYS Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 69 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 166 optimal weight: 0.3980 chunk 176 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS B 248 HIS B 534 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.054573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.038330 restraints weight = 101369.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.039975 restraints weight = 45090.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.041087 restraints weight = 27762.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.041832 restraints weight = 20235.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.042360 restraints weight = 16338.475| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20235 Z= 0.189 Angle : 0.653 12.333 27558 Z= 0.308 Chirality : 0.043 0.307 3081 Planarity : 0.004 0.043 3507 Dihedral : 5.166 47.186 3375 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.87 % Allowed : 14.96 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2388 helix: 0.62 (0.30), residues: 324 sheet: -0.20 (0.17), residues: 822 loop : -0.19 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 16 TYR 0.011 0.001 TYR M 91 PHE 0.009 0.001 PHE B 508 TRP 0.016 0.001 TRP B 539 HIS 0.010 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00422 (20187) covalent geometry : angle 0.61809 (27429) SS BOND : bond 0.00263 ( 15) SS BOND : angle 1.35545 ( 30) hydrogen bonds : bond 0.03449 ( 548) hydrogen bonds : angle 5.93916 ( 1410) link_ALPHA1-3 : bond 0.00660 ( 6) link_ALPHA1-3 : angle 1.37139 ( 18) link_ALPHA1-6 : bond 0.00390 ( 6) link_ALPHA1-6 : angle 1.91396 ( 18) link_BETA1-4 : bond 0.00297 ( 9) link_BETA1-4 : angle 3.30773 ( 27) link_NAG-ASN : bond 0.00836 ( 12) link_NAG-ASN : angle 4.76152 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.651 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: A 183 MET cc_start: 0.7719 (mtt) cc_final: 0.7390 (ttm) REVERT: A 366 MET cc_start: 0.9385 (mmm) cc_final: 0.8664 (mmm) REVERT: A 534 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7622 (t-90) REVERT: A 563 MET cc_start: 0.8743 (mmt) cc_final: 0.8432 (tpp) REVERT: A 567 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8074 (p) REVERT: A 587 MET cc_start: 0.5387 (ppp) cc_final: 0.4200 (ppp) REVERT: A 599 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8517 (tpp-160) REVERT: A 718 ASP cc_start: 0.8674 (t0) cc_final: 0.8242 (t0) REVERT: B 183 MET cc_start: 0.7758 (mtt) cc_final: 0.7367 (ttt) REVERT: B 232 MET cc_start: 0.8084 (mtp) cc_final: 0.7279 (ptp) REVERT: B 534 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7432 (t-90) REVERT: B 567 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7583 (p) REVERT: B 568 MET cc_start: 0.8822 (mmm) cc_final: 0.7807 (tpp) REVERT: B 587 MET cc_start: 0.4618 (ppp) cc_final: 0.3358 (ppp) REVERT: B 601 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8830 (mm) REVERT: B 718 ASP cc_start: 0.8612 (t0) cc_final: 0.8225 (t0) REVERT: C 183 MET cc_start: 0.7965 (mtt) cc_final: 0.7708 (ttm) REVERT: C 232 MET cc_start: 0.8300 (mtm) cc_final: 0.7786 (mtm) REVERT: C 366 MET cc_start: 0.9362 (mmm) cc_final: 0.8499 (mmm) REVERT: C 428 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8223 (ttt90) REVERT: C 563 MET cc_start: 0.8655 (mmt) cc_final: 0.8424 (tpp) REVERT: C 567 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7331 (p) REVERT: C 568 MET cc_start: 0.8671 (mmt) cc_final: 0.7458 (tpp) REVERT: C 601 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8901 (mm) REVERT: C 718 ASP cc_start: 0.8623 (t0) cc_final: 0.8199 (t0) REVERT: H 34 MET cc_start: 0.8689 (mmm) cc_final: 0.8008 (mmt) REVERT: H 46 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7617 (tm-30) REVERT: I 34 MET cc_start: 0.8386 (mmm) cc_final: 0.7644 (mmm) REVERT: I 108 MET cc_start: 0.8871 (tpt) cc_final: 0.8391 (tpp) REVERT: J 34 MET cc_start: 0.8465 (mmm) cc_final: 0.7847 (mmt) REVERT: J 82 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9151 (mp) REVERT: J 108 MET cc_start: 0.8947 (tpt) cc_final: 0.8373 (tpp) REVERT: L 45 GLU cc_start: 0.7858 (mp0) cc_final: 0.7425 (mp0) REVERT: L 78 MET cc_start: 0.9209 (tpp) cc_final: 0.8803 (tpp) REVERT: L 89 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8871 (tm-30) REVERT: M 78 MET cc_start: 0.9268 (tpp) cc_final: 0.9010 (tpp) REVERT: N 45 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8106 (mp0) REVERT: N 78 MET cc_start: 0.9134 (tpp) cc_final: 0.8818 (tpp) outliers start: 39 outliers final: 27 residues processed: 158 average time/residue: 0.1374 time to fit residues: 32.3648 Evaluate side-chains 163 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 534 HIS Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 529 CYS Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS A 616 GLN A 637 HIS B 172 GLN C 263 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.054000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.037539 restraints weight = 101458.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.039125 restraints weight = 45470.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.040193 restraints weight = 28190.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.040868 restraints weight = 20680.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.041363 restraints weight = 16928.204| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20235 Z= 0.251 Angle : 0.688 12.277 27558 Z= 0.326 Chirality : 0.044 0.312 3081 Planarity : 0.004 0.043 3507 Dihedral : 5.308 46.220 3375 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 15.20 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.17), residues: 2388 helix: 0.51 (0.30), residues: 324 sheet: -0.28 (0.18), residues: 807 loop : -0.25 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 16 TYR 0.013 0.002 TYR M 71 PHE 0.011 0.001 PHE A 319 TRP 0.012 0.001 TRP B 539 HIS 0.014 0.001 HIS B 534 Details of bonding type rmsd covalent geometry : bond 0.00556 (20187) covalent geometry : angle 0.65382 (27429) SS BOND : bond 0.00257 ( 15) SS BOND : angle 1.34110 ( 30) hydrogen bonds : bond 0.03567 ( 548) hydrogen bonds : angle 5.98812 ( 1410) link_ALPHA1-3 : bond 0.00600 ( 6) link_ALPHA1-3 : angle 1.35882 ( 18) link_ALPHA1-6 : bond 0.00424 ( 6) link_ALPHA1-6 : angle 1.94669 ( 18) link_BETA1-4 : bond 0.00393 ( 9) link_BETA1-4 : angle 3.43144 ( 27) link_NAG-ASN : bond 0.00856 ( 12) link_NAG-ASN : angle 4.79652 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.614 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: A 183 MET cc_start: 0.7684 (mtt) cc_final: 0.7352 (ttm) REVERT: A 366 MET cc_start: 0.9389 (mmm) cc_final: 0.8591 (mmm) REVERT: A 534 HIS cc_start: 0.7594 (t-90) cc_final: 0.7376 (t70) REVERT: A 567 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7919 (p) REVERT: A 587 MET cc_start: 0.5784 (ppp) cc_final: 0.4568 (ppp) REVERT: A 599 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8472 (tpp-160) REVERT: A 718 ASP cc_start: 0.8656 (t0) cc_final: 0.8208 (t0) REVERT: B 183 MET cc_start: 0.7751 (mtt) cc_final: 0.7470 (ttm) REVERT: B 232 MET cc_start: 0.8146 (mtp) cc_final: 0.7382 (ptp) REVERT: B 534 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7568 (t70) REVERT: B 567 VAL cc_start: 0.7536 (OUTLIER) cc_final: 0.7253 (p) REVERT: B 568 MET cc_start: 0.8743 (mmm) cc_final: 0.7785 (tpp) REVERT: B 587 MET cc_start: 0.5203 (ppp) cc_final: 0.3874 (ppp) REVERT: B 601 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 718 ASP cc_start: 0.8608 (t0) cc_final: 0.8196 (t0) REVERT: C 183 MET cc_start: 0.7890 (mtt) cc_final: 0.7630 (ttm) REVERT: C 232 MET cc_start: 0.8321 (mtm) cc_final: 0.7812 (mtm) REVERT: C 366 MET cc_start: 0.9365 (mmm) cc_final: 0.8506 (mmm) REVERT: C 428 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8222 (ttt90) REVERT: C 553 VAL cc_start: 0.9131 (p) cc_final: 0.8830 (m) REVERT: C 563 MET cc_start: 0.8618 (mmt) cc_final: 0.8202 (tpp) REVERT: C 567 VAL cc_start: 0.7650 (OUTLIER) cc_final: 0.7111 (p) REVERT: C 601 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8838 (mm) REVERT: C 718 ASP cc_start: 0.8639 (t0) cc_final: 0.8194 (t0) REVERT: H 34 MET cc_start: 0.8698 (mmm) cc_final: 0.7517 (mmm) REVERT: H 89 MET cc_start: 0.8355 (tpp) cc_final: 0.8017 (tpp) REVERT: I 34 MET cc_start: 0.8373 (mmm) cc_final: 0.7585 (mmm) REVERT: I 108 MET cc_start: 0.8892 (tpt) cc_final: 0.8419 (tpp) REVERT: J 34 MET cc_start: 0.8509 (mmm) cc_final: 0.7877 (mmt) REVERT: J 82 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9167 (mp) REVERT: J 108 MET cc_start: 0.8844 (tpt) cc_final: 0.8598 (tpp) REVERT: L 45 GLU cc_start: 0.7867 (mp0) cc_final: 0.7444 (mp0) REVERT: L 78 MET cc_start: 0.9243 (tpp) cc_final: 0.8845 (tpp) REVERT: L 89 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8932 (tm-30) REVERT: M 78 MET cc_start: 0.9303 (tpp) cc_final: 0.9051 (tpp) REVERT: N 78 MET cc_start: 0.9136 (tpp) cc_final: 0.8828 (tpp) outliers start: 37 outliers final: 27 residues processed: 154 average time/residue: 0.1445 time to fit residues: 33.3119 Evaluate side-chains 157 residues out of total 2085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 428 ARG Chi-restraints excluded: chain B residue 534 HIS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 428 ARG Chi-restraints excluded: chain C residue 529 CYS Chi-restraints excluded: chain C residue 530 GLU Chi-restraints excluded: chain C residue 534 HIS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 587 MET Chi-restraints excluded: chain C residue 601 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 100 ILE Chi-restraints excluded: chain J residue 45 LEU Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 222 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 137 optimal weight: 0.4980 chunk 145 optimal weight: 0.6980 chunk 196 optimal weight: 0.0670 chunk 220 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 118 optimal weight: 0.0970 chunk 84 optimal weight: 6.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS B 172 GLN B 370 GLN B 438 GLN B 534 HIS C 248 HIS C 507 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.055663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.039633 restraints weight = 99925.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.041321 restraints weight = 43845.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.042452 restraints weight = 26636.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.043220 restraints weight = 19216.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.043727 restraints weight = 15356.943| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20235 Z= 0.106 Angle : 0.654 12.804 27558 Z= 0.306 Chirality : 0.044 0.309 3081 Planarity : 0.003 0.044 3507 Dihedral : 5.029 48.816 3375 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.53 % Allowed : 15.35 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2388 helix: 0.22 (0.29), residues: 342 sheet: -0.12 (0.18), residues: 813 loop : -0.13 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 16 TYR 0.010 0.001 TYR C 296 PHE 0.010 0.001 PHE J 29 TRP 0.009 0.001 TRP A 247 HIS 0.012 0.001 HIS C 534 Details of bonding type rmsd covalent geometry : bond 0.00242 (20187) covalent geometry : angle 0.62148 (27429) SS BOND : bond 0.00274 ( 15) SS BOND : angle 1.03078 ( 30) hydrogen bonds : bond 0.03257 ( 548) hydrogen bonds : angle 5.89267 ( 1410) link_ALPHA1-3 : bond 0.00782 ( 6) link_ALPHA1-3 : angle 1.30717 ( 18) link_ALPHA1-6 : bond 0.00435 ( 6) link_ALPHA1-6 : angle 1.73717 ( 18) link_BETA1-4 : bond 0.00302 ( 9) link_BETA1-4 : angle 3.11454 ( 27) link_NAG-ASN : bond 0.00851 ( 12) link_NAG-ASN : angle 4.70365 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3204.01 seconds wall clock time: 56 minutes 17.62 seconds (3377.62 seconds total)