Starting phenix.real_space_refine on Sat Jul 4 17:01:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d0i_30535/07_2026/7d0i_30535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d0i_30535/07_2026/7d0i_30535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d0i_30535/07_2026/7d0i_30535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d0i_30535/07_2026/7d0i_30535.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7d0i_30535/07_2026/7d0i_30535.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d0i_30535/07_2026/7d0i_30535.cif" model { file = "/net/cci-nas-00/data/ceres_data/7d0i_30535/07_2026/7d0i_30535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d0i_30535/07_2026/7d0i_30535.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 72 5.16 5 C 14742 2.51 5 N 3516 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22164 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3556 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 408} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.94, per 1000 atoms: 0.18 Number of scatterers: 22164 At special positions: 0 Unit cell: (122.01, 125.745, 153.135, 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 72 16.00 O 3834 8.00 N 3516 7.00 C 14742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 788.9 milliseconds 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 12 sheets defined 78.3% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 197 through 224 removed outlier: 3.966A pdb=" N CYS B 201 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 288 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 335 through 344 Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.908A pdb=" N TYR B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.557A pdb=" N GLU B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.531A pdb=" N PHE B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.678A pdb=" N SER B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 426 removed outlier: 4.134A pdb=" N VAL B 417 " --> pdb=" O ARG B 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 448 removed outlier: 4.100A pdb=" N TYR B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.978A pdb=" N SER B 453 " --> pdb=" O GLY B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 482 through 490 Processing helix chain 'B' and resid 495 through 521 removed outlier: 3.740A pdb=" N LEU B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 556 removed outlier: 3.702A pdb=" N SER B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 577 removed outlier: 4.085A pdb=" N PHE B 575 " --> pdb=" O ARG B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 Processing helix chain 'B' and resid 590 through 599 Processing helix chain 'B' and resid 603 through 624 removed outlier: 3.959A pdb=" N ILE B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 615 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Proline residue: B 618 - end of helix Processing helix chain 'B' and resid 625 through 627 No H-bonds generated for 'chain 'B' and resid 625 through 627' Processing helix chain 'B' and resid 628 through 639 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 197 through 224 removed outlier: 3.967A pdb=" N CYS D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 288 Proline residue: D 277 - end of helix Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 344 through 356 removed outlier: 3.908A pdb=" N TYR D 349 " --> pdb=" O ARG D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.558A pdb=" N GLU D 376 " --> pdb=" O THR D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 388 removed outlier: 3.532A pdb=" N PHE D 388 " --> pdb=" O PHE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 399 Processing helix chain 'D' and resid 400 through 402 No H-bonds generated for 'chain 'D' and resid 400 through 402' Processing helix chain 'D' and resid 403 through 411 removed outlier: 3.678A pdb=" N SER D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 409 " --> pdb=" O LYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 426 removed outlier: 4.134A pdb=" N VAL D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 448 removed outlier: 4.099A pdb=" N TYR D 432 " --> pdb=" O ILE D 428 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASN D 443 " --> pdb=" O PHE D 439 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 removed outlier: 3.977A pdb=" N SER D 453 " --> pdb=" O GLY D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 465 Processing helix chain 'D' and resid 471 through 481 Processing helix chain 'D' and resid 482 through 490 Processing helix chain 'D' and resid 495 through 521 removed outlier: 3.739A pdb=" N LEU D 501 " --> pdb=" O ASN D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 556 removed outlier: 3.702A pdb=" N SER D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE D 555 " --> pdb=" O VAL D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 577 removed outlier: 4.085A pdb=" N PHE D 575 " --> pdb=" O ARG D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 584 Processing helix chain 'D' and resid 590 through 599 Processing helix chain 'D' and resid 603 through 624 removed outlier: 3.960A pdb=" N ILE D 614 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 615 " --> pdb=" O ILE D 611 " (cutoff:3.500A) Proline residue: D 618 - end of helix Processing helix chain 'D' and resid 625 through 627 No H-bonds generated for 'chain 'D' and resid 625 through 627' Processing helix chain 'D' and resid 628 through 639 Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 197 through 224 removed outlier: 3.967A pdb=" N CYS F 201 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 288 Proline residue: F 277 - end of helix Processing helix chain 'F' and resid 301 through 313 Processing helix chain 'F' and resid 335 through 344 Processing helix chain 'F' and resid 344 through 356 removed outlier: 3.909A pdb=" N TYR F 349 " --> pdb=" O ARG F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 removed outlier: 3.556A pdb=" N GLU F 376 " --> pdb=" O THR F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 388 removed outlier: 3.531A pdb=" N PHE F 388 " --> pdb=" O PHE F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 399 Processing helix chain 'F' and resid 400 through 402 No H-bonds generated for 'chain 'F' and resid 400 through 402' Processing helix chain 'F' and resid 403 through 411 removed outlier: 3.678A pdb=" N SER F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU F 409 " --> pdb=" O LYS F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 426 removed outlier: 4.134A pdb=" N VAL F 417 " --> pdb=" O ARG F 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 424 " --> pdb=" O PHE F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 448 removed outlier: 4.101A pdb=" N TYR F 432 " --> pdb=" O ILE F 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN F 443 " --> pdb=" O PHE F 439 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU F 444 " --> pdb=" O ARG F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 453 removed outlier: 3.978A pdb=" N SER F 453 " --> pdb=" O GLY F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 465 Processing helix chain 'F' and resid 471 through 481 Processing helix chain 'F' and resid 482 through 490 Processing helix chain 'F' and resid 495 through 521 removed outlier: 3.739A pdb=" N LEU F 501 " --> pdb=" O ASN F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 556 removed outlier: 3.702A pdb=" N SER F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE F 555 " --> pdb=" O VAL F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 564 through 577 removed outlier: 4.084A pdb=" N PHE F 575 " --> pdb=" O ARG F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 584 Processing helix chain 'F' and resid 590 through 599 Processing helix chain 'F' and resid 603 through 624 removed outlier: 3.958A pdb=" N ILE F 614 " --> pdb=" O GLU F 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 615 " --> pdb=" O ILE F 611 " (cutoff:3.500A) Proline residue: F 618 - end of helix Processing helix chain 'F' and resid 625 through 627 No H-bonds generated for 'chain 'F' and resid 625 through 627' Processing helix chain 'F' and resid 628 through 639 Processing helix chain 'H' and resid 182 through 196 Processing helix chain 'H' and resid 197 through 224 removed outlier: 3.967A pdb=" N CYS H 201 " --> pdb=" O LYS H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 288 Proline residue: H 277 - end of helix Processing helix chain 'H' and resid 301 through 313 Processing helix chain 'H' and resid 335 through 344 Processing helix chain 'H' and resid 344 through 356 removed outlier: 3.909A pdb=" N TYR H 349 " --> pdb=" O ARG H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 383 removed outlier: 3.558A pdb=" N GLU H 376 " --> pdb=" O THR H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 388 removed outlier: 3.532A pdb=" N PHE H 388 " --> pdb=" O PHE H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 399 Processing helix chain 'H' and resid 400 through 402 No H-bonds generated for 'chain 'H' and resid 400 through 402' Processing helix chain 'H' and resid 403 through 411 removed outlier: 3.677A pdb=" N SER H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU H 409 " --> pdb=" O LYS H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 426 removed outlier: 4.133A pdb=" N VAL H 417 " --> pdb=" O ARG H 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 424 " --> pdb=" O PHE H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 426 through 448 removed outlier: 4.102A pdb=" N TYR H 432 " --> pdb=" O ILE H 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN H 443 " --> pdb=" O PHE H 439 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU H 444 " --> pdb=" O ARG H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 453 removed outlier: 3.979A pdb=" N SER H 453 " --> pdb=" O GLY H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 465 Processing helix chain 'H' and resid 471 through 481 Processing helix chain 'H' and resid 482 through 490 Processing helix chain 'H' and resid 495 through 521 removed outlier: 3.741A pdb=" N LEU H 501 " --> pdb=" O ASN H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 556 removed outlier: 3.702A pdb=" N SER H 554 " --> pdb=" O ALA H 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE H 555 " --> pdb=" O VAL H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 564 through 577 removed outlier: 4.084A pdb=" N PHE H 575 " --> pdb=" O ARG H 571 " (cutoff:3.500A) Processing helix chain 'H' and resid 580 through 584 Processing helix chain 'H' and resid 590 through 599 Processing helix chain 'H' and resid 603 through 624 removed outlier: 3.961A pdb=" N ILE H 614 " --> pdb=" O GLU H 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU H 615 " --> pdb=" O ILE H 611 " (cutoff:3.500A) Proline residue: H 618 - end of helix Processing helix chain 'H' and resid 625 through 627 No H-bonds generated for 'chain 'H' and resid 625 through 627' Processing helix chain 'H' and resid 628 through 639 Processing helix chain 'J' and resid 182 through 196 Processing helix chain 'J' and resid 197 through 224 removed outlier: 3.966A pdb=" N CYS J 201 " --> pdb=" O LYS J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 288 Proline residue: J 277 - end of helix Processing helix chain 'J' and resid 301 through 313 Processing helix chain 'J' and resid 335 through 344 Processing helix chain 'J' and resid 344 through 356 removed outlier: 3.909A pdb=" N TYR J 349 " --> pdb=" O ARG J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 383 removed outlier: 3.556A pdb=" N GLU J 376 " --> pdb=" O THR J 372 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 388 removed outlier: 3.532A pdb=" N PHE J 388 " --> pdb=" O PHE J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 399 Processing helix chain 'J' and resid 400 through 402 No H-bonds generated for 'chain 'J' and resid 400 through 402' Processing helix chain 'J' and resid 403 through 411 removed outlier: 3.679A pdb=" N SER J 408 " --> pdb=" O ARG J 404 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU J 409 " --> pdb=" O LYS J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 411 through 426 removed outlier: 4.135A pdb=" N VAL J 417 " --> pdb=" O ARG J 413 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU J 424 " --> pdb=" O PHE J 420 " (cutoff:3.500A) Processing helix chain 'J' and resid 426 through 448 removed outlier: 4.101A pdb=" N TYR J 432 " --> pdb=" O ILE J 428 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASN J 443 " --> pdb=" O PHE J 439 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU J 444 " --> pdb=" O ARG J 440 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 453 removed outlier: 3.978A pdb=" N SER J 453 " --> pdb=" O GLY J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 460 through 465 Processing helix chain 'J' and resid 471 through 481 Processing helix chain 'J' and resid 482 through 490 Processing helix chain 'J' and resid 495 through 521 removed outlier: 3.741A pdb=" N LEU J 501 " --> pdb=" O ASN J 497 " (cutoff:3.500A) Processing helix chain 'J' and resid 538 through 556 removed outlier: 3.701A pdb=" N SER J 554 " --> pdb=" O ALA J 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE J 555 " --> pdb=" O VAL J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 564 through 577 removed outlier: 4.083A pdb=" N PHE J 575 " --> pdb=" O ARG J 571 " (cutoff:3.500A) Processing helix chain 'J' and resid 580 through 584 Processing helix chain 'J' and resid 590 through 599 Processing helix chain 'J' and resid 603 through 624 removed outlier: 3.958A pdb=" N ILE J 614 " --> pdb=" O GLU J 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU J 615 " --> pdb=" O ILE J 611 " (cutoff:3.500A) Proline residue: J 618 - end of helix Processing helix chain 'J' and resid 625 through 627 No H-bonds generated for 'chain 'J' and resid 625 through 627' Processing helix chain 'J' and resid 628 through 639 Processing helix chain 'L' and resid 182 through 196 Processing helix chain 'L' and resid 197 through 224 removed outlier: 3.967A pdb=" N CYS L 201 " --> pdb=" O LYS L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 253 through 288 Proline residue: L 277 - end of helix Processing helix chain 'L' and resid 301 through 313 Processing helix chain 'L' and resid 335 through 344 Processing helix chain 'L' and resid 344 through 356 removed outlier: 3.907A pdb=" N TYR L 349 " --> pdb=" O ARG L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 383 removed outlier: 3.557A pdb=" N GLU L 376 " --> pdb=" O THR L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 388 removed outlier: 3.531A pdb=" N PHE L 388 " --> pdb=" O PHE L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 399 Processing helix chain 'L' and resid 400 through 402 No H-bonds generated for 'chain 'L' and resid 400 through 402' Processing helix chain 'L' and resid 403 through 411 removed outlier: 3.679A pdb=" N SER L 408 " --> pdb=" O ARG L 404 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU L 409 " --> pdb=" O LYS L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 426 removed outlier: 4.133A pdb=" N VAL L 417 " --> pdb=" O ARG L 413 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU L 424 " --> pdb=" O PHE L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 448 removed outlier: 4.101A pdb=" N TYR L 432 " --> pdb=" O ILE L 428 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASN L 443 " --> pdb=" O PHE L 439 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU L 444 " --> pdb=" O ARG L 440 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 453 removed outlier: 3.979A pdb=" N SER L 453 " --> pdb=" O GLY L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 460 through 465 Processing helix chain 'L' and resid 471 through 481 Processing helix chain 'L' and resid 482 through 490 Processing helix chain 'L' and resid 495 through 521 removed outlier: 3.740A pdb=" N LEU L 501 " --> pdb=" O ASN L 497 " (cutoff:3.500A) Processing helix chain 'L' and resid 538 through 556 removed outlier: 3.701A pdb=" N SER L 554 " --> pdb=" O ALA L 550 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE L 555 " --> pdb=" O VAL L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 577 removed outlier: 4.086A pdb=" N PHE L 575 " --> pdb=" O ARG L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 580 through 584 Processing helix chain 'L' and resid 590 through 599 Processing helix chain 'L' and resid 603 through 624 removed outlier: 3.960A pdb=" N ILE L 614 " --> pdb=" O GLU L 610 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU L 615 " --> pdb=" O ILE L 611 " (cutoff:3.500A) Proline residue: L 618 - end of helix Processing helix chain 'L' and resid 625 through 627 No H-bonds generated for 'chain 'L' and resid 625 through 627' Processing helix chain 'L' and resid 628 through 639 Processing sheet with id=AA1, first strand: chain 'B' and resid 455 through 457 Processing sheet with id=AA2, first strand: chain 'B' and resid 640 through 643 Processing sheet with id=AA3, first strand: chain 'D' and resid 455 through 457 Processing sheet with id=AA4, first strand: chain 'D' and resid 640 through 643 Processing sheet with id=AA5, first strand: chain 'F' and resid 455 through 457 Processing sheet with id=AA6, first strand: chain 'F' and resid 640 through 643 Processing sheet with id=AA7, first strand: chain 'H' and resid 455 through 457 Processing sheet with id=AA8, first strand: chain 'H' and resid 640 through 643 Processing sheet with id=AA9, first strand: chain 'J' and resid 455 through 457 Processing sheet with id=AB1, first strand: chain 'J' and resid 640 through 643 Processing sheet with id=AB2, first strand: chain 'L' and resid 455 through 457 Processing sheet with id=AB3, first strand: chain 'L' and resid 640 through 643 1314 hydrogen bonds defined for protein. 3834 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: 3.34 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 6129 1.33 - 1.45: 4312 1.45 - 1.57: 12209 1.57 - 1.69: 84 1.69 - 1.80: 108 Bond restraints: 22842 Sorted by residual: bond pdb=" C1 LMN B 801 " pdb=" O5 LMN B 801 " ideal model delta sigma weight residual 1.403 1.548 -0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" C1 LMN L 801 " pdb=" O5 LMN L 801 " ideal model delta sigma weight residual 1.403 1.547 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C1 LMN J 801 " pdb=" O5 LMN J 801 " ideal model delta sigma weight residual 1.403 1.547 -0.144 2.00e-02 2.50e+03 5.18e+01 bond pdb=" C1 LMN H 801 " pdb=" O5 LMN H 801 " ideal model delta sigma weight residual 1.403 1.547 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C1 LMN F 801 " pdb=" O5 LMN F 801 " ideal model delta sigma weight residual 1.403 1.546 -0.143 2.00e-02 2.50e+03 5.13e+01 ... (remaining 22837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 30793 4.24 - 8.48: 245 8.48 - 12.72: 18 12.72 - 16.96: 0 16.96 - 21.20: 12 Bond angle restraints: 31068 Sorted by residual: angle pdb=" CBJ LMN B 802 " pdb=" CBL LMN B 802 " pdb=" CBR LMN B 802 " ideal model delta sigma weight residual 112.20 133.40 -21.20 3.00e+00 1.11e-01 4.99e+01 angle pdb=" CBJ LMN F 802 " pdb=" CBL LMN F 802 " pdb=" CBR LMN F 802 " ideal model delta sigma weight residual 112.20 133.34 -21.14 3.00e+00 1.11e-01 4.97e+01 angle pdb=" CBJ LMN J 802 " pdb=" CBL LMN J 802 " pdb=" CBR LMN J 802 " ideal model delta sigma weight residual 112.20 133.30 -21.10 3.00e+00 1.11e-01 4.95e+01 angle pdb=" CBJ LMN D 802 " pdb=" CBL LMN D 802 " pdb=" CBR LMN D 802 " ideal model delta sigma weight residual 112.20 133.26 -21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" CBJ LMN H 802 " pdb=" CBL LMN H 802 " pdb=" CBR LMN H 802 " ideal model delta sigma weight residual 112.20 133.24 -21.04 3.00e+00 1.11e-01 4.92e+01 ... (remaining 31063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.53: 12552 29.53 - 59.05: 258 59.05 - 88.58: 54 88.58 - 118.10: 6 118.10 - 147.63: 6 Dihedral angle restraints: 12876 sinusoidal: 5292 harmonic: 7584 Sorted by residual: dihedral pdb=" CBH LMN H 801 " pdb=" CBJ LMN H 801 " pdb=" CBL LMN H 801 " pdb=" CBR LMN H 801 " ideal model delta sinusoidal sigma weight residual 181.02 33.39 147.63 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CBH LMN B 801 " pdb=" CBJ LMN B 801 " pdb=" CBL LMN B 801 " pdb=" CBR LMN B 801 " ideal model delta sinusoidal sigma weight residual 181.02 33.45 147.57 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" CBH LMN D 801 " pdb=" CBJ LMN D 801 " pdb=" CBL LMN D 801 " pdb=" CBR LMN D 801 " ideal model delta sinusoidal sigma weight residual 181.02 33.47 147.55 1 3.00e+01 1.11e-03 1.97e+01 ... (remaining 12873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2384 0.045 - 0.090: 926 0.090 - 0.136: 211 0.136 - 0.181: 24 0.181 - 0.226: 13 Chirality restraints: 3558 Sorted by residual: chirality pdb=" CCQ LMN D 801 " pdb=" CCF LMN D 801 " pdb=" CCH LMN D 801 " pdb=" OCB LMN D 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CCQ LMN F 801 " pdb=" CCF LMN F 801 " pdb=" CCH LMN F 801 " pdb=" OCB LMN F 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CCQ LMN L 801 " pdb=" CCF LMN L 801 " pdb=" CCH LMN L 801 " pdb=" OCB LMN L 801 " both_signs ideal model delta sigma weight residual False -2.61 -2.38 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3555 not shown) Planarity restraints: 3678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 617 " 0.031 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO L 618 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO L 618 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 618 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR J 617 " -0.031 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO J 618 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 618 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 618 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 617 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO F 618 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 618 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 618 " -0.026 5.00e-02 4.00e+02 ... (remaining 3675 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4920 2.77 - 3.30: 21272 3.30 - 3.83: 36959 3.83 - 4.37: 44786 4.37 - 4.90: 76623 Nonbonded interactions: 184560 Sorted by model distance: nonbonded pdb=" OAN LMN B 802 " pdb=" OBZ LMN B 802 " model vdw 2.237 3.040 nonbonded pdb=" OAN LMN D 802 " pdb=" OBZ LMN D 802 " model vdw 2.237 3.040 nonbonded pdb=" OAN LMN F 802 " pdb=" OBZ LMN F 802 " model vdw 2.238 3.040 nonbonded pdb=" OAN LMN J 802 " pdb=" OBZ LMN J 802 " model vdw 2.238 3.040 nonbonded pdb=" OAN LMN L 802 " pdb=" OBZ LMN L 802 " model vdw 2.238 3.040 ... (remaining 184555 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: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.820 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.011 0.145 22842 Z= 0.532 Angle : 0.950 21.201 31068 Z= 0.413 Chirality : 0.049 0.226 3558 Planarity : 0.004 0.046 3678 Dihedral : 14.321 147.628 7956 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.60 % Allowed : 6.23 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.14 (0.15), residues: 2496 helix: -1.08 (0.11), residues: 1818 sheet: None (None), residues: 0 loop : -1.94 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 369 TYR 0.027 0.002 TYR D 600 PHE 0.013 0.002 PHE J 386 TRP 0.011 0.001 TRP H 280 HIS 0.004 0.001 HIS J 473 Details of bonding type rmsd/Z covalent geometry : bond 0.01127 / 0.53 (22842) covalent geometry : angle 0.94951 / 0.41 (31068) hydrogen bonds : bond 0.13169 / 8.64 ( 1314) hydrogen bonds : angle 5.55900 / 4.04 ( 3834) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 470 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 282 MET cc_start: 0.8800 (tpp) cc_final: 0.8456 (tpp) REVERT: B 310 LEU cc_start: 0.7990 (tp) cc_final: 0.7735 (mp) REVERT: B 366 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7890 (tt) REVERT: B 391 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7364 (tm-30) REVERT: B 440 ARG cc_start: 0.7523 (ttt180) cc_final: 0.7321 (tmt170) REVERT: B 548 LEU cc_start: 0.7143 (mt) cc_final: 0.6862 (mt) REVERT: B 559 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7253 (mm-30) REVERT: B 586 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8281 (p0) REVERT: D 282 MET cc_start: 0.8586 (tpp) cc_final: 0.8275 (tpp) REVERT: D 284 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6542 (mt-10) REVERT: D 310 LEU cc_start: 0.7930 (tp) cc_final: 0.7676 (mm) REVERT: D 366 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7724 (tt) REVERT: D 367 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7469 (m-70) REVERT: D 380 ASN cc_start: 0.8331 (m-40) cc_final: 0.8060 (m110) REVERT: D 391 GLN cc_start: 0.7475 (tm-30) cc_final: 0.6923 (tm130) REVERT: D 440 ARG cc_start: 0.7409 (ttt180) cc_final: 0.7060 (tmt170) REVERT: D 548 LEU cc_start: 0.6569 (mt) cc_final: 0.6342 (mp) REVERT: D 559 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7402 (mm-30) REVERT: F 280 TRP cc_start: 0.7706 (t-100) cc_final: 0.7246 (t60) REVERT: F 367 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7644 (m-70) REVERT: F 391 GLN cc_start: 0.7616 (tm-30) cc_final: 0.6925 (tm130) REVERT: F 548 LEU cc_start: 0.6607 (mt) cc_final: 0.6178 (mp) REVERT: F 641 ILE cc_start: 0.8322 (tt) cc_final: 0.7947 (tp) REVERT: F 651 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8501 (p) REVERT: H 282 MET cc_start: 0.8805 (tpp) cc_final: 0.8442 (tpp) REVERT: H 310 LEU cc_start: 0.7985 (tp) cc_final: 0.7715 (mp) REVERT: H 366 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7941 (tt) REVERT: H 391 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7400 (tm-30) REVERT: H 440 ARG cc_start: 0.7454 (ttt180) cc_final: 0.7245 (tmt170) REVERT: H 548 LEU cc_start: 0.7238 (mt) cc_final: 0.6988 (mt) REVERT: H 559 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7326 (mm-30) REVERT: H 586 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8218 (p0) REVERT: H 587 MET cc_start: 0.8348 (mtp) cc_final: 0.8119 (mtm) REVERT: J 280 TRP cc_start: 0.7420 (t-100) cc_final: 0.7201 (t60) REVERT: J 282 MET cc_start: 0.8787 (tpp) cc_final: 0.8481 (tpp) REVERT: J 284 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6713 (mt-10) REVERT: J 367 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.7391 (m-70) REVERT: J 391 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7280 (tm-30) REVERT: J 440 ARG cc_start: 0.7304 (ttt180) cc_final: 0.7017 (tmt170) REVERT: J 559 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7472 (mm-30) REVERT: J 586 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8381 (p0) REVERT: L 280 TRP cc_start: 0.7725 (t-100) cc_final: 0.7207 (t60) REVERT: L 391 GLN cc_start: 0.7585 (tm-30) cc_final: 0.6968 (tm130) REVERT: L 440 ARG cc_start: 0.7324 (ttt180) cc_final: 0.6950 (tmt170) REVERT: L 548 LEU cc_start: 0.6743 (mt) cc_final: 0.6396 (mp) REVERT: L 559 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7226 (mm-30) REVERT: L 571 ARG cc_start: 0.7762 (tpt170) cc_final: 0.7422 (tpt170) REVERT: L 651 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8547 (p) outliers start: 60 outliers final: 7 residues processed: 524 average time/residue: 0.5556 time to fit residues: 332.1514 Evaluate side-chains 321 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 303 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 482 SER Chi-restraints excluded: chain B residue 586 ASN Chi-restraints excluded: chain B residue 651 SER Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 482 SER Chi-restraints excluded: chain D residue 586 ASN Chi-restraints excluded: chain F residue 367 HIS Chi-restraints excluded: chain F residue 651 SER Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 482 SER Chi-restraints excluded: chain H residue 586 ASN Chi-restraints excluded: chain H residue 651 SER Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 586 ASN Chi-restraints excluded: chain L residue 651 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN B 437 ASN B 443 ASN D 179 ASN D 443 ASN H 179 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 437 ASN J 179 ASN J 443 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.163153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.128745 restraints weight = 25957.253| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.61 r_work: 0.3253 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22842 Z= 0.122 Angle : 0.556 7.745 31068 Z= 0.272 Chirality : 0.041 0.171 3558 Planarity : 0.004 0.037 3678 Dihedral : 11.210 115.240 3100 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.68 % Allowed : 13.77 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2496 helix: 0.51 (0.12), residues: 1812 sheet: None (None), residues: 0 loop : -1.00 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 399 TYR 0.018 0.001 TYR D 600 PHE 0.019 0.001 PHE F 442 TRP 0.022 0.001 TRP J 269 HIS 0.004 0.001 HIS B 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (22842) covalent geometry : angle 0.55578 / 0.27 (31068) hydrogen bonds : bond 0.03713 / 2.44 ( 1314) hydrogen bonds : angle 4.26931 / 3.10 ( 3834) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 370 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.9103 (t80) cc_final: 0.8808 (t80) REVERT: B 210 ILE cc_start: 0.8481 (pp) cc_final: 0.8261 (mt) REVERT: B 282 MET cc_start: 0.8971 (tpp) cc_final: 0.8530 (tpp) REVERT: B 310 LEU cc_start: 0.8141 (tp) cc_final: 0.7815 (mp) REVERT: B 366 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7728 (tt) REVERT: B 368 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7677 (ptm160) REVERT: B 380 ASN cc_start: 0.8551 (m-40) cc_final: 0.8247 (m110) REVERT: B 391 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7741 (tm-30) REVERT: B 440 ARG cc_start: 0.7856 (ttt180) cc_final: 0.7617 (tmt170) REVERT: B 548 LEU cc_start: 0.7302 (mt) cc_final: 0.6973 (mt) REVERT: D 210 ILE cc_start: 0.8376 (pp) cc_final: 0.8169 (mt) REVERT: D 260 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6175 (pp) REVERT: D 284 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6592 (mt-10) REVERT: D 296 ASP cc_start: 0.7413 (t0) cc_final: 0.6908 (m-30) REVERT: D 304 ARG cc_start: 0.8378 (tpp-160) cc_final: 0.8019 (tpp-160) REVERT: D 310 LEU cc_start: 0.8059 (tp) cc_final: 0.7660 (mm) REVERT: D 366 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7616 (tt) REVERT: D 367 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7750 (m-70) REVERT: D 380 ASN cc_start: 0.8732 (m-40) cc_final: 0.8423 (m110) REVERT: D 391 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7368 (tm-30) REVERT: D 440 ARG cc_start: 0.7745 (ttt180) cc_final: 0.7356 (tmt170) REVERT: D 559 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7772 (mm-30) REVERT: F 260 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6161 (pp) REVERT: F 280 TRP cc_start: 0.8080 (t-100) cc_final: 0.7314 (t60) REVERT: F 308 ARG cc_start: 0.7572 (mmt-90) cc_final: 0.7250 (mtp85) REVERT: F 310 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7156 (mm) REVERT: F 366 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7827 (tt) REVERT: F 391 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7157 (tm130) REVERT: F 548 LEU cc_start: 0.6711 (mt) cc_final: 0.6262 (mp) REVERT: H 191 TYR cc_start: 0.9099 (t80) cc_final: 0.8816 (t80) REVERT: H 210 ILE cc_start: 0.8437 (pp) cc_final: 0.8189 (mt) REVERT: H 282 MET cc_start: 0.8978 (tpp) cc_final: 0.8526 (tpp) REVERT: H 310 LEU cc_start: 0.8178 (tp) cc_final: 0.7840 (mp) REVERT: H 366 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7701 (tt) REVERT: H 368 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7687 (ptm160) REVERT: H 380 ASN cc_start: 0.8539 (m-40) cc_final: 0.8198 (m110) REVERT: H 391 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7734 (tm-30) REVERT: H 440 ARG cc_start: 0.7865 (ttt180) cc_final: 0.7620 (tmt170) REVERT: H 519 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.5716 (mt) REVERT: H 548 LEU cc_start: 0.7236 (mt) cc_final: 0.6928 (mt) REVERT: H 559 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7732 (mm-30) REVERT: J 210 ILE cc_start: 0.8542 (pp) cc_final: 0.8285 (mt) REVERT: J 260 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5838 (pp) REVERT: J 280 TRP cc_start: 0.8021 (t-100) cc_final: 0.7292 (t60) REVERT: J 282 MET cc_start: 0.8995 (tpp) cc_final: 0.8464 (tpp) REVERT: J 284 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6744 (mt-10) REVERT: J 304 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.8113 (tpp-160) REVERT: J 367 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7525 (m-70) REVERT: J 380 ASN cc_start: 0.8732 (m-40) cc_final: 0.8435 (m110) REVERT: J 391 GLN cc_start: 0.7940 (tm-30) cc_final: 0.7450 (tm-30) REVERT: J 440 ARG cc_start: 0.7461 (ttt180) cc_final: 0.7176 (tmt170) REVERT: J 559 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7746 (mm-30) REVERT: J 648 TYR cc_start: 0.8330 (m-80) cc_final: 0.8009 (m-80) REVERT: L 260 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5936 (pp) REVERT: L 280 TRP cc_start: 0.8050 (t-100) cc_final: 0.7262 (t60) REVERT: L 281 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7846 (mm-40) REVERT: L 310 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7317 (mm) REVERT: L 368 ARG cc_start: 0.7549 (ttt90) cc_final: 0.7144 (ttm-80) REVERT: L 391 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7173 (tm130) REVERT: L 431 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7773 (tp) REVERT: L 440 ARG cc_start: 0.7422 (ttt180) cc_final: 0.7210 (tpt170) REVERT: L 548 LEU cc_start: 0.6641 (mt) cc_final: 0.6233 (mt) REVERT: L 559 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7479 (mm-30) REVERT: L 570 ARG cc_start: 0.8710 (mtt-85) cc_final: 0.8481 (mtt90) REVERT: L 571 ARG cc_start: 0.8225 (tpt170) cc_final: 0.7972 (mmm-85) outliers start: 85 outliers final: 9 residues processed: 427 average time/residue: 0.5563 time to fit residues: 271.6458 Evaluate side-chains 328 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 302 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain D residue 627 SER Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 519 ILE Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 627 SER Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 431 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 246 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 ASN B 209 GLN D 179 ASN D 209 GLN D 443 ASN F 209 GLN F 380 ASN H 179 ASN H 209 GLN J 179 ASN J 209 GLN J 443 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129326 restraints weight = 25971.999| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.61 r_work: 0.3254 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22842 Z= 0.118 Angle : 0.530 7.558 31068 Z= 0.256 Chirality : 0.040 0.171 3558 Planarity : 0.004 0.040 3678 Dihedral : 10.472 106.916 3082 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.46 % Allowed : 13.90 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2496 helix: 1.10 (0.12), residues: 1836 sheet: None (None), residues: 0 loop : -0.54 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 570 TYR 0.016 0.001 TYR D 600 PHE 0.022 0.001 PHE H 442 TRP 0.031 0.001 TRP F 269 HIS 0.004 0.001 HIS J 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22842) covalent geometry : angle 0.53000 / 0.26 (31068) hydrogen bonds : bond 0.03462 / 2.26 ( 1314) hydrogen bonds : angle 4.09727 / 2.97 ( 3834) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 349 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ILE cc_start: 0.8434 (pp) cc_final: 0.8210 (mt) REVERT: B 282 MET cc_start: 0.8896 (tpp) cc_final: 0.8472 (tpp) REVERT: B 308 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7613 (mmt180) REVERT: B 310 LEU cc_start: 0.8191 (tp) cc_final: 0.7849 (mp) REVERT: B 366 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7666 (tt) REVERT: B 368 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7702 (ptm160) REVERT: B 380 ASN cc_start: 0.8586 (m-40) cc_final: 0.8285 (m110) REVERT: B 440 ARG cc_start: 0.7936 (ttt180) cc_final: 0.7633 (tmt170) REVERT: B 548 LEU cc_start: 0.7281 (mt) cc_final: 0.6977 (mt) REVERT: D 210 ILE cc_start: 0.8292 (pp) cc_final: 0.8033 (mt) REVERT: D 284 GLU cc_start: 0.7416 (mm-30) cc_final: 0.6742 (mt-10) REVERT: D 296 ASP cc_start: 0.7208 (t0) cc_final: 0.6821 (m-30) REVERT: D 304 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.8101 (tpp-160) REVERT: D 310 LEU cc_start: 0.7969 (tp) cc_final: 0.7509 (mm) REVERT: D 366 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7562 (tt) REVERT: D 367 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7766 (m-70) REVERT: D 380 ASN cc_start: 0.8794 (m-40) cc_final: 0.8457 (m110) REVERT: D 559 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7747 (mm-30) REVERT: F 269 TRP cc_start: 0.6859 (t60) cc_final: 0.6599 (t60) REVERT: F 280 TRP cc_start: 0.8114 (t-100) cc_final: 0.7236 (t60) REVERT: F 310 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7299 (mm) REVERT: F 366 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7799 (tt) REVERT: F 391 GLN cc_start: 0.7735 (tm-30) cc_final: 0.6998 (tm130) REVERT: F 410 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7807 (tp30) REVERT: F 421 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7930 (mp) REVERT: F 422 ASN cc_start: 0.8505 (m-40) cc_final: 0.8297 (m110) REVERT: F 431 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7698 (pp) REVERT: F 548 LEU cc_start: 0.6425 (mt) cc_final: 0.6124 (mp) REVERT: F 559 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: H 210 ILE cc_start: 0.8441 (pp) cc_final: 0.8220 (mt) REVERT: H 281 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7660 (mm110) REVERT: H 282 MET cc_start: 0.8917 (tpp) cc_final: 0.8499 (tpp) REVERT: H 310 LEU cc_start: 0.8095 (tp) cc_final: 0.7732 (mp) REVERT: H 366 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7635 (tt) REVERT: H 368 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7789 (ptm160) REVERT: H 380 ASN cc_start: 0.8535 (m-40) cc_final: 0.8205 (m110) REVERT: H 440 ARG cc_start: 0.7860 (ttt180) cc_final: 0.7628 (tmt170) REVERT: H 452 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7980 (mt) REVERT: H 548 LEU cc_start: 0.7200 (mt) cc_final: 0.6915 (mt) REVERT: H 559 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7791 (mt-10) REVERT: J 210 ILE cc_start: 0.8351 (pp) cc_final: 0.8114 (mt) REVERT: J 260 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6213 (pp) REVERT: J 280 TRP cc_start: 0.7992 (t-100) cc_final: 0.7171 (t60) REVERT: J 282 MET cc_start: 0.8975 (tpp) cc_final: 0.8510 (tpp) REVERT: J 284 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6701 (mt-10) REVERT: J 304 ARG cc_start: 0.8502 (tpp-160) cc_final: 0.8105 (tpp-160) REVERT: J 367 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7723 (m-70) REVERT: J 380 ASN cc_start: 0.8759 (m-40) cc_final: 0.8419 (m110) REVERT: J 391 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7540 (tm-30) REVERT: J 559 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7678 (mm-30) REVERT: L 280 TRP cc_start: 0.8086 (t-100) cc_final: 0.7224 (t60) REVERT: L 281 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7932 (mm-40) REVERT: L 310 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7399 (mm) REVERT: L 366 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7760 (tt) REVERT: L 368 ARG cc_start: 0.7576 (ttt90) cc_final: 0.7186 (ttm-80) REVERT: L 391 GLN cc_start: 0.7804 (tm-30) cc_final: 0.7059 (tm130) REVERT: L 422 ASN cc_start: 0.8519 (m-40) cc_final: 0.8237 (m110) REVERT: L 440 ARG cc_start: 0.7412 (ttt180) cc_final: 0.7151 (tpt170) REVERT: L 548 LEU cc_start: 0.6428 (mt) cc_final: 0.6153 (mt) REVERT: L 559 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7579 (mm-30) REVERT: L 571 ARG cc_start: 0.8251 (tpt170) cc_final: 0.7858 (tpt170) REVERT: L 587 MET cc_start: 0.8929 (mtm) cc_final: 0.8625 (mtm) outliers start: 103 outliers final: 29 residues processed: 422 average time/residue: 0.5133 time to fit residues: 249.3986 Evaluate side-chains 351 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 304 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 310 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 559 GLU Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 617 THR Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 617 THR Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 218 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 225 optimal weight: 0.0070 overall best weight: 0.8402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN D 179 ASN D 209 GLN D 443 ASN F 209 GLN H 209 GLN J 179 ASN J 209 GLN J 443 ASN L 360 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.161374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125101 restraints weight = 25960.529| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.72 r_work: 0.3195 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22842 Z= 0.115 Angle : 0.525 9.276 31068 Z= 0.251 Chirality : 0.040 0.342 3558 Planarity : 0.004 0.046 3678 Dihedral : 10.070 98.554 3082 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 3.94 % Allowed : 15.84 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.17), residues: 2496 helix: 1.48 (0.12), residues: 1764 sheet: None (None), residues: 0 loop : -0.44 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 399 TYR 0.014 0.001 TYR D 600 PHE 0.024 0.001 PHE B 442 TRP 0.027 0.001 TRP L 269 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (22842) covalent geometry : angle 0.52496 / 0.25 (31068) hydrogen bonds : bond 0.03275 / 2.14 ( 1314) hydrogen bonds : angle 4.00866 / 2.91 ( 3834) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 333 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ILE cc_start: 0.8336 (pp) cc_final: 0.8115 (mt) REVERT: B 282 MET cc_start: 0.8918 (tpp) cc_final: 0.8458 (tpp) REVERT: B 308 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7541 (mmt180) REVERT: B 310 LEU cc_start: 0.8162 (tp) cc_final: 0.7812 (mp) REVERT: B 366 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7606 (tt) REVERT: B 368 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7718 (ptm160) REVERT: B 380 ASN cc_start: 0.8704 (m-40) cc_final: 0.8406 (m110) REVERT: B 409 GLU cc_start: 0.8097 (tp30) cc_final: 0.7616 (tp30) REVERT: B 410 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7852 (tp30) REVERT: B 440 ARG cc_start: 0.7882 (ttt180) cc_final: 0.7594 (tmt170) REVERT: B 548 LEU cc_start: 0.7269 (mt) cc_final: 0.6987 (mt) REVERT: D 296 ASP cc_start: 0.7124 (t0) cc_final: 0.6779 (m-30) REVERT: D 304 ARG cc_start: 0.8484 (tpp-160) cc_final: 0.8082 (tpp-160) REVERT: D 310 LEU cc_start: 0.7931 (tp) cc_final: 0.7463 (mm) REVERT: D 366 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7547 (tt) REVERT: D 380 ASN cc_start: 0.8703 (m-40) cc_final: 0.8407 (m110) REVERT: D 409 GLU cc_start: 0.8264 (tp30) cc_final: 0.8056 (mm-30) REVERT: D 421 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7820 (tp) REVERT: D 559 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7645 (mm-30) REVERT: F 269 TRP cc_start: 0.6824 (t60) cc_final: 0.6617 (t60) REVERT: F 280 TRP cc_start: 0.8158 (t-100) cc_final: 0.7256 (t60) REVERT: F 366 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7686 (tt) REVERT: F 368 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7339 (ptm160) REVERT: F 410 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7773 (tp30) REVERT: F 421 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7917 (mp) REVERT: F 422 ASN cc_start: 0.8465 (m-40) cc_final: 0.8200 (m110) REVERT: F 431 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7631 (pp) REVERT: F 548 LEU cc_start: 0.6500 (mt) cc_final: 0.6208 (mt) REVERT: F 559 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: H 281 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7669 (mm110) REVERT: H 282 MET cc_start: 0.8925 (tpp) cc_final: 0.8461 (tpp) REVERT: H 310 LEU cc_start: 0.8071 (tp) cc_final: 0.7683 (mp) REVERT: H 366 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7612 (tt) REVERT: H 368 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7773 (ptm160) REVERT: H 380 ASN cc_start: 0.8689 (m-40) cc_final: 0.8380 (m110) REVERT: H 440 ARG cc_start: 0.7942 (ttt180) cc_final: 0.7597 (tmt170) REVERT: H 452 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7965 (mt) REVERT: H 548 LEU cc_start: 0.7203 (mt) cc_final: 0.6928 (mt) REVERT: H 559 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7861 (mt-10) REVERT: H 566 GLU cc_start: 0.8118 (tt0) cc_final: 0.7775 (tm-30) REVERT: J 210 ILE cc_start: 0.8282 (pp) cc_final: 0.8016 (mt) REVERT: J 275 ASP cc_start: 0.8743 (t0) cc_final: 0.8488 (t0) REVERT: J 280 TRP cc_start: 0.8060 (t-100) cc_final: 0.7166 (t60) REVERT: J 281 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7426 (tp-100) REVERT: J 282 MET cc_start: 0.8954 (tpp) cc_final: 0.8428 (tpp) REVERT: J 304 ARG cc_start: 0.8499 (tpp-160) cc_final: 0.8071 (tpp-160) REVERT: J 380 ASN cc_start: 0.8685 (m-40) cc_final: 0.8372 (m110) REVERT: J 444 GLU cc_start: 0.7296 (mp0) cc_final: 0.7036 (mp0) REVERT: J 559 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7638 (mm-30) REVERT: L 269 TRP cc_start: 0.7009 (t60) cc_final: 0.6511 (t60) REVERT: L 280 TRP cc_start: 0.8052 (t-100) cc_final: 0.7131 (t60) REVERT: L 281 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7848 (mm-40) REVERT: L 310 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7389 (mm) REVERT: L 366 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7763 (tt) REVERT: L 368 ARG cc_start: 0.7515 (ttt90) cc_final: 0.7149 (ttm-80) REVERT: L 391 GLN cc_start: 0.7548 (tm-30) cc_final: 0.6888 (tm130) REVERT: L 422 ASN cc_start: 0.8502 (m-40) cc_final: 0.8253 (m110) REVERT: L 431 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7539 (pp) REVERT: L 440 ARG cc_start: 0.7464 (ttt180) cc_final: 0.7176 (tpt170) REVERT: L 548 LEU cc_start: 0.6493 (mt) cc_final: 0.6238 (mt) REVERT: L 571 ARG cc_start: 0.8230 (tpt170) cc_final: 0.7869 (tpt170) REVERT: L 587 MET cc_start: 0.8838 (mtm) cc_final: 0.8532 (mtm) outliers start: 91 outliers final: 35 residues processed: 400 average time/residue: 0.5538 time to fit residues: 252.7030 Evaluate side-chains 356 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 304 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 559 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 140 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 235 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN B 373 HIS D 179 ASN D 373 HIS ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN H 209 GLN H 373 HIS J 179 ASN J 209 GLN L 380 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.163376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127517 restraints weight = 25771.465| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.70 r_work: 0.3163 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22842 Z= 0.123 Angle : 0.534 10.108 31068 Z= 0.255 Chirality : 0.041 0.344 3558 Planarity : 0.004 0.058 3678 Dihedral : 9.855 90.718 3078 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.33 % Allowed : 16.06 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.56 (0.17), residues: 2496 helix: 1.55 (0.12), residues: 1794 sheet: None (None), residues: 0 loop : -0.18 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 570 TYR 0.014 0.001 TYR B 600 PHE 0.026 0.001 PHE H 442 TRP 0.026 0.001 TRP L 269 HIS 0.004 0.001 HIS J 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (22842) covalent geometry : angle 0.53443 / 0.25 (31068) hydrogen bonds : bond 0.03312 / 2.17 ( 1314) hydrogen bonds : angle 3.99886 / 2.90 ( 3834) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 335 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ILE cc_start: 0.8277 (pp) cc_final: 0.8023 (mt) REVERT: B 281 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7614 (mm110) REVERT: B 282 MET cc_start: 0.8980 (tpp) cc_final: 0.8504 (tpp) REVERT: B 308 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7535 (mmt180) REVERT: B 310 LEU cc_start: 0.8179 (tp) cc_final: 0.7813 (mp) REVERT: B 366 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7574 (tt) REVERT: B 368 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7735 (ptm160) REVERT: B 380 ASN cc_start: 0.8637 (m-40) cc_final: 0.8335 (m110) REVERT: B 409 GLU cc_start: 0.8034 (tp30) cc_final: 0.7566 (tp30) REVERT: B 410 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7937 (tp30) REVERT: B 440 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7638 (tmt170) REVERT: B 548 LEU cc_start: 0.7263 (mt) cc_final: 0.6974 (mt) REVERT: D 296 ASP cc_start: 0.7139 (t0) cc_final: 0.6653 (m-30) REVERT: D 304 ARG cc_start: 0.8461 (tpp-160) cc_final: 0.8074 (tpp-160) REVERT: D 310 LEU cc_start: 0.7959 (tp) cc_final: 0.7477 (mm) REVERT: D 366 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7468 (tt) REVERT: D 367 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7777 (m-70) REVERT: D 368 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7807 (ptm160) REVERT: D 380 ASN cc_start: 0.8703 (m-40) cc_final: 0.8397 (m110) REVERT: D 409 GLU cc_start: 0.8313 (tp30) cc_final: 0.8103 (mm-30) REVERT: D 559 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7615 (mm-30) REVERT: F 269 TRP cc_start: 0.6960 (OUTLIER) cc_final: 0.6653 (t60) REVERT: F 280 TRP cc_start: 0.8171 (t-100) cc_final: 0.7318 (t60) REVERT: F 366 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7644 (tt) REVERT: F 368 ARG cc_start: 0.7964 (ttm110) cc_final: 0.7345 (ptm160) REVERT: F 410 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7731 (tp30) REVERT: F 421 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7926 (mp) REVERT: F 422 ASN cc_start: 0.8447 (m-40) cc_final: 0.8126 (m110) REVERT: F 431 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7566 (pp) REVERT: F 548 LEU cc_start: 0.6618 (mt) cc_final: 0.6376 (mt) REVERT: F 559 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: H 281 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7639 (mm110) REVERT: H 282 MET cc_start: 0.8988 (tpp) cc_final: 0.8510 (tpp) REVERT: H 310 LEU cc_start: 0.8111 (tp) cc_final: 0.7629 (mp) REVERT: H 366 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7536 (tt) REVERT: H 368 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7778 (ptm160) REVERT: H 380 ASN cc_start: 0.8623 (m-40) cc_final: 0.8305 (m110) REVERT: H 399 ARG cc_start: 0.8012 (mtm110) cc_final: 0.7544 (mtp180) REVERT: H 440 ARG cc_start: 0.7942 (ttt180) cc_final: 0.7578 (tmt170) REVERT: H 452 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7952 (mt) REVERT: H 548 LEU cc_start: 0.7214 (mt) cc_final: 0.6950 (mt) REVERT: H 559 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7768 (mt-10) REVERT: H 587 MET cc_start: 0.8813 (ttm) cc_final: 0.8573 (ttm) REVERT: J 210 ILE cc_start: 0.8213 (pp) cc_final: 0.7914 (mt) REVERT: J 269 TRP cc_start: 0.6344 (t60) cc_final: 0.5997 (t-100) REVERT: J 280 TRP cc_start: 0.8220 (t-100) cc_final: 0.7332 (t60) REVERT: J 281 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7436 (tp-100) REVERT: J 304 ARG cc_start: 0.8475 (tpp-160) cc_final: 0.8038 (tpp-160) REVERT: J 367 HIS cc_start: 0.8044 (OUTLIER) cc_final: 0.7701 (m-70) REVERT: J 380 ASN cc_start: 0.8688 (m-40) cc_final: 0.8372 (m110) REVERT: J 409 GLU cc_start: 0.8248 (tp30) cc_final: 0.7839 (tt0) REVERT: J 422 ASN cc_start: 0.8469 (m-40) cc_final: 0.8071 (m110) REVERT: J 431 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.6803 (mp) REVERT: J 559 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7575 (mm-30) REVERT: L 269 TRP cc_start: 0.7047 (t60) cc_final: 0.6653 (t60) REVERT: L 280 TRP cc_start: 0.8123 (t-100) cc_final: 0.7194 (t60) REVERT: L 281 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7816 (mm-40) REVERT: L 308 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.7273 (mmm-85) REVERT: L 310 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7396 (mm) REVERT: L 366 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7709 (tt) REVERT: L 368 ARG cc_start: 0.7459 (ttt90) cc_final: 0.7078 (ttm-80) REVERT: L 391 GLN cc_start: 0.7571 (tm-30) cc_final: 0.6852 (tm130) REVERT: L 422 ASN cc_start: 0.8481 (m-40) cc_final: 0.8219 (m110) REVERT: L 440 ARG cc_start: 0.7442 (ttt180) cc_final: 0.7058 (tpt170) REVERT: L 478 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.9086 (ptt90) REVERT: L 548 LEU cc_start: 0.6610 (mt) cc_final: 0.6391 (mt) REVERT: L 571 ARG cc_start: 0.8187 (tpt170) cc_final: 0.7775 (tpt170) REVERT: L 587 MET cc_start: 0.8834 (mtm) cc_final: 0.8558 (mtm) REVERT: L 610 GLU cc_start: 0.7508 (tp30) cc_final: 0.6980 (tt0) outliers start: 100 outliers final: 44 residues processed: 407 average time/residue: 0.5404 time to fit residues: 251.1389 Evaluate side-chains 381 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 315 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 559 GLU Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 368 ARG Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 254 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 213 optimal weight: 0.9980 chunk 195 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 156 optimal weight: 0.0970 chunk 183 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN D 179 ASN D 209 GLN H 209 GLN L 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.164791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129407 restraints weight = 25971.244| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.70 r_work: 0.3182 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22842 Z= 0.107 Angle : 0.519 10.568 31068 Z= 0.246 Chirality : 0.040 0.351 3558 Planarity : 0.004 0.051 3678 Dihedral : 9.735 85.037 3078 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.98 % Allowed : 16.80 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.17), residues: 2496 helix: 1.76 (0.12), residues: 1764 sheet: None (None), residues: 0 loop : -0.23 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 570 TYR 0.012 0.001 TYR F 600 PHE 0.030 0.001 PHE B 442 TRP 0.023 0.001 TRP H 269 HIS 0.004 0.001 HIS J 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (22842) covalent geometry : angle 0.51882 / 0.25 (31068) hydrogen bonds : bond 0.03131 / 2.05 ( 1314) hydrogen bonds : angle 3.87603 / 2.80 ( 3834) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 340 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ILE cc_start: 0.8316 (pp) cc_final: 0.8019 (mt) REVERT: B 253 ILE cc_start: 0.5452 (OUTLIER) cc_final: 0.5243 (tt) REVERT: B 281 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7697 (mm110) REVERT: B 282 MET cc_start: 0.8922 (tpp) cc_final: 0.8478 (tpp) REVERT: B 308 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7579 (mmt180) REVERT: B 310 LEU cc_start: 0.8167 (tp) cc_final: 0.7811 (mp) REVERT: B 366 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7495 (tt) REVERT: B 368 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7782 (ptm160) REVERT: B 380 ASN cc_start: 0.8643 (m-40) cc_final: 0.8351 (m110) REVERT: B 409 GLU cc_start: 0.8135 (tp30) cc_final: 0.7656 (tp30) REVERT: B 410 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7815 (tp30) REVERT: B 413 ARG cc_start: 0.7744 (mtp180) cc_final: 0.7530 (mtm110) REVERT: B 431 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7780 (pp) REVERT: B 440 ARG cc_start: 0.7948 (ttt180) cc_final: 0.7723 (tmt170) REVERT: B 548 LEU cc_start: 0.7256 (mt) cc_final: 0.6984 (mt) REVERT: D 191 TYR cc_start: 0.9224 (t80) cc_final: 0.8829 (t80) REVERT: D 281 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7598 (mm-40) REVERT: D 296 ASP cc_start: 0.7243 (t0) cc_final: 0.6967 (m-30) REVERT: D 304 ARG cc_start: 0.8505 (tpp-160) cc_final: 0.8123 (tpp-160) REVERT: D 310 LEU cc_start: 0.7846 (tp) cc_final: 0.7397 (mm) REVERT: D 366 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7461 (tt) REVERT: D 367 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7959 (m-70) REVERT: D 368 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7839 (ptm160) REVERT: D 380 ASN cc_start: 0.8707 (m-40) cc_final: 0.8405 (m110) REVERT: D 409 GLU cc_start: 0.8304 (tp30) cc_final: 0.8095 (mm-30) REVERT: D 478 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.9022 (ptt90) REVERT: D 548 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6576 (mp) REVERT: D 559 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7570 (mm-30) REVERT: F 197 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8793 (mtmm) REVERT: F 269 TRP cc_start: 0.6955 (OUTLIER) cc_final: 0.6664 (t60) REVERT: F 280 TRP cc_start: 0.8144 (t-100) cc_final: 0.7208 (t60) REVERT: F 366 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7566 (tt) REVERT: F 368 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7369 (ptm160) REVERT: F 421 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7950 (mp) REVERT: F 431 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7620 (pp) REVERT: F 478 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8973 (ptt90) REVERT: F 548 LEU cc_start: 0.6821 (mt) cc_final: 0.6454 (mt) REVERT: F 559 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: F 587 MET cc_start: 0.8687 (mtm) cc_final: 0.8450 (mtm) REVERT: H 282 MET cc_start: 0.8922 (tpp) cc_final: 0.8476 (tpp) REVERT: H 310 LEU cc_start: 0.8096 (tp) cc_final: 0.7606 (mp) REVERT: H 366 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7481 (tt) REVERT: H 368 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7794 (ptm160) REVERT: H 380 ASN cc_start: 0.8629 (m-40) cc_final: 0.8308 (m110) REVERT: H 409 GLU cc_start: 0.8148 (tp30) cc_final: 0.7652 (tp30) REVERT: H 440 ARG cc_start: 0.7936 (ttt180) cc_final: 0.7647 (tmt170) REVERT: H 452 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8019 (mt) REVERT: H 548 LEU cc_start: 0.7246 (mt) cc_final: 0.6979 (mt) REVERT: H 587 MET cc_start: 0.8758 (ttm) cc_final: 0.8527 (ttm) REVERT: J 191 TYR cc_start: 0.9248 (t80) cc_final: 0.8891 (t80) REVERT: J 210 ILE cc_start: 0.8155 (pp) cc_final: 0.7867 (mt) REVERT: J 269 TRP cc_start: 0.6366 (t60) cc_final: 0.5993 (t-100) REVERT: J 280 TRP cc_start: 0.8163 (t-100) cc_final: 0.7318 (t60) REVERT: J 281 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7406 (tp-100) REVERT: J 282 MET cc_start: 0.8949 (tpp) cc_final: 0.8401 (tpp) REVERT: J 304 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.8307 (tpp-160) REVERT: J 367 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7748 (m-70) REVERT: J 368 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7815 (ptm160) REVERT: J 380 ASN cc_start: 0.8635 (m-40) cc_final: 0.8323 (m110) REVERT: J 409 GLU cc_start: 0.8273 (tp30) cc_final: 0.8058 (mm-30) REVERT: J 422 ASN cc_start: 0.8511 (m-40) cc_final: 0.8107 (m110) REVERT: J 431 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.6899 (mp) REVERT: J 478 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.9016 (ptt90) REVERT: J 559 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7529 (mm-30) REVERT: L 269 TRP cc_start: 0.7044 (OUTLIER) cc_final: 0.6749 (t60) REVERT: L 280 TRP cc_start: 0.8091 (t-100) cc_final: 0.7148 (t60) REVERT: L 281 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7812 (mm-40) REVERT: L 308 ARG cc_start: 0.7556 (mmt-90) cc_final: 0.7294 (mmm-85) REVERT: L 366 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7645 (tt) REVERT: L 368 ARG cc_start: 0.7422 (ttt90) cc_final: 0.7052 (ttm-80) REVERT: L 431 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7610 (pp) REVERT: L 440 ARG cc_start: 0.7409 (ttt180) cc_final: 0.7137 (tpt170) REVERT: L 478 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8974 (ptt90) REVERT: L 548 LEU cc_start: 0.6694 (mt) cc_final: 0.6484 (mt) REVERT: L 566 GLU cc_start: 0.7973 (tt0) cc_final: 0.7524 (tt0) REVERT: L 571 ARG cc_start: 0.8176 (tpt170) cc_final: 0.7763 (tpt170) REVERT: L 587 MET cc_start: 0.8685 (mtm) cc_final: 0.8435 (mtm) REVERT: L 610 GLU cc_start: 0.7496 (tp30) cc_final: 0.7007 (tt0) outliers start: 92 outliers final: 39 residues processed: 405 average time/residue: 0.5302 time to fit residues: 245.8939 Evaluate side-chains 384 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 478 ARG Chi-restraints excluded: chain F residue 559 GLU Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 365 LEU Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 368 ARG Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 269 TRP Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 0.0030 chunk 127 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 209 optimal weight: 3.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN F 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.163798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.128400 restraints weight = 25911.922| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.71 r_work: 0.3164 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22842 Z= 0.118 Angle : 0.526 10.527 31068 Z= 0.251 Chirality : 0.040 0.343 3558 Planarity : 0.004 0.044 3678 Dihedral : 9.770 82.714 3078 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.94 % Allowed : 17.36 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.17), residues: 2496 helix: 1.80 (0.12), residues: 1764 sheet: None (None), residues: 0 loop : -0.15 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 570 TYR 0.012 0.001 TYR H 600 PHE 0.029 0.001 PHE H 442 TRP 0.022 0.001 TRP H 269 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (22842) covalent geometry : angle 0.52645 / 0.25 (31068) hydrogen bonds : bond 0.03200 / 2.09 ( 1314) hydrogen bonds : angle 3.89746 / 2.82 ( 3834) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 332 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ILE cc_start: 0.5447 (OUTLIER) cc_final: 0.5136 (tt) REVERT: B 281 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7685 (mm110) REVERT: B 282 MET cc_start: 0.8917 (tpp) cc_final: 0.8468 (tpp) REVERT: B 310 LEU cc_start: 0.8170 (tp) cc_final: 0.7810 (mp) REVERT: B 366 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7448 (tt) REVERT: B 368 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7771 (ptm160) REVERT: B 409 GLU cc_start: 0.8116 (tp30) cc_final: 0.7639 (tp30) REVERT: B 410 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7795 (tp30) REVERT: B 413 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7553 (mtm110) REVERT: B 440 ARG cc_start: 0.7952 (ttt180) cc_final: 0.7666 (tmt170) REVERT: B 548 LEU cc_start: 0.7247 (mt) cc_final: 0.6973 (mt) REVERT: D 191 TYR cc_start: 0.9228 (t80) cc_final: 0.8792 (t80) REVERT: D 296 ASP cc_start: 0.7309 (t0) cc_final: 0.7071 (m-30) REVERT: D 304 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.8126 (tpp-160) REVERT: D 310 LEU cc_start: 0.7879 (tp) cc_final: 0.7411 (mm) REVERT: D 366 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7438 (tt) REVERT: D 367 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7882 (m-70) REVERT: D 368 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7863 (ptm160) REVERT: D 380 ASN cc_start: 0.8751 (m-40) cc_final: 0.8448 (m110) REVERT: D 409 GLU cc_start: 0.8306 (tp30) cc_final: 0.8091 (mm-30) REVERT: D 478 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.9055 (ptt90) REVERT: D 548 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6641 (mp) REVERT: D 559 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7566 (mm-30) REVERT: F 197 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8838 (mtmm) REVERT: F 269 TRP cc_start: 0.6963 (OUTLIER) cc_final: 0.6691 (t60) REVERT: F 280 TRP cc_start: 0.8159 (t-100) cc_final: 0.7303 (t60) REVERT: F 366 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7549 (tt) REVERT: F 368 ARG cc_start: 0.7931 (ttm110) cc_final: 0.7341 (ptm160) REVERT: F 421 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7944 (mp) REVERT: F 422 ASN cc_start: 0.8412 (m-40) cc_final: 0.8108 (m110) REVERT: F 431 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7547 (pp) REVERT: F 478 ARG cc_start: 0.9323 (OUTLIER) cc_final: 0.9002 (ptt90) REVERT: F 548 LEU cc_start: 0.7035 (mt) cc_final: 0.6725 (mt) REVERT: F 559 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: F 587 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8435 (mtm) REVERT: H 281 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7675 (mm110) REVERT: H 282 MET cc_start: 0.8920 (tpp) cc_final: 0.8472 (tpp) REVERT: H 310 LEU cc_start: 0.8160 (tp) cc_final: 0.7880 (mp) REVERT: H 366 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7454 (tt) REVERT: H 368 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7825 (ptm160) REVERT: H 380 ASN cc_start: 0.8612 (m-40) cc_final: 0.8312 (m110) REVERT: H 409 GLU cc_start: 0.8141 (tp30) cc_final: 0.7644 (tp30) REVERT: H 440 ARG cc_start: 0.7919 (ttt180) cc_final: 0.7639 (tmt170) REVERT: H 452 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8008 (mt) REVERT: H 548 LEU cc_start: 0.7347 (mt) cc_final: 0.7098 (mt) REVERT: H 587 MET cc_start: 0.8714 (ttm) cc_final: 0.8511 (ttm) REVERT: H 623 PHE cc_start: 0.7816 (m-10) cc_final: 0.7564 (m-80) REVERT: J 210 ILE cc_start: 0.8141 (pp) cc_final: 0.7841 (mt) REVERT: J 269 TRP cc_start: 0.6386 (t60) cc_final: 0.6012 (t-100) REVERT: J 280 TRP cc_start: 0.8128 (t-100) cc_final: 0.7306 (t60) REVERT: J 281 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7392 (tp-100) REVERT: J 304 ARG cc_start: 0.8524 (tpp-160) cc_final: 0.8302 (tpp-160) REVERT: J 367 HIS cc_start: 0.8174 (OUTLIER) cc_final: 0.7881 (m-70) REVERT: J 368 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7756 (ptm160) REVERT: J 380 ASN cc_start: 0.8629 (m-40) cc_final: 0.8314 (m110) REVERT: J 409 GLU cc_start: 0.8228 (tp30) cc_final: 0.8019 (mm-30) REVERT: J 422 ASN cc_start: 0.8534 (m-40) cc_final: 0.8164 (m110) REVERT: J 431 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.6882 (mp) REVERT: J 478 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.9043 (ptt90) REVERT: J 559 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7525 (mm-30) REVERT: L 197 LYS cc_start: 0.9086 (mttm) cc_final: 0.8842 (mtmm) REVERT: L 269 TRP cc_start: 0.7029 (OUTLIER) cc_final: 0.6734 (t60) REVERT: L 280 TRP cc_start: 0.8111 (t-100) cc_final: 0.7159 (t60) REVERT: L 281 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7814 (mm-40) REVERT: L 366 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7673 (tt) REVERT: L 368 ARG cc_start: 0.7423 (ttt90) cc_final: 0.7050 (ttm-80) REVERT: L 422 ASN cc_start: 0.8465 (m-40) cc_final: 0.8155 (m110) REVERT: L 431 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7530 (pp) REVERT: L 440 ARG cc_start: 0.7436 (ttt180) cc_final: 0.7046 (tpt170) REVERT: L 478 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.9009 (ptt90) REVERT: L 566 GLU cc_start: 0.8000 (tt0) cc_final: 0.7549 (tt0) REVERT: L 571 ARG cc_start: 0.8136 (tpt170) cc_final: 0.7679 (tpt170) REVERT: L 587 MET cc_start: 0.8675 (mtm) cc_final: 0.8430 (mtm) REVERT: L 610 GLU cc_start: 0.7506 (tp30) cc_final: 0.7045 (tt0) outliers start: 91 outliers final: 43 residues processed: 395 average time/residue: 0.5420 time to fit residues: 244.2043 Evaluate side-chains 397 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 323 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 478 ARG Chi-restraints excluded: chain F residue 559 GLU Chi-restraints excluded: chain F residue 587 MET Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 624 THR Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 368 ARG Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 452 LEU Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 269 TRP Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 611 ILE Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 245 optimal weight: 0.3980 chunk 167 optimal weight: 0.7980 chunk 243 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN B 380 ASN J 209 GLN L 360 ASN L 380 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.164707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129651 restraints weight = 25892.540| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.68 r_work: 0.3197 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22842 Z= 0.107 Angle : 0.516 10.482 31068 Z= 0.246 Chirality : 0.040 0.338 3558 Planarity : 0.004 0.039 3678 Dihedral : 9.697 79.680 3078 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.81 % Allowed : 17.58 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.93 (0.17), residues: 2496 helix: 1.85 (0.12), residues: 1770 sheet: None (None), residues: 0 loop : -0.07 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 570 TYR 0.012 0.001 TYR L 600 PHE 0.034 0.001 PHE B 442 TRP 0.024 0.001 TRP B 269 HIS 0.004 0.001 HIS J 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (22842) covalent geometry : angle 0.51609 / 0.25 (31068) hydrogen bonds : bond 0.03089 / 2.02 ( 1314) hydrogen bonds : angle 3.83418 / 2.77 ( 3834) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 331 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ILE cc_start: 0.8324 (pp) cc_final: 0.8000 (mt) REVERT: B 253 ILE cc_start: 0.5480 (OUTLIER) cc_final: 0.5144 (tt) REVERT: B 281 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7682 (mm110) REVERT: B 282 MET cc_start: 0.8922 (tpp) cc_final: 0.8479 (tpp) REVERT: B 308 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7590 (mmt180) REVERT: B 310 LEU cc_start: 0.8161 (tp) cc_final: 0.7797 (mp) REVERT: B 366 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7491 (tt) REVERT: B 368 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7793 (ptm160) REVERT: B 409 GLU cc_start: 0.8133 (tp30) cc_final: 0.7664 (tp30) REVERT: B 413 ARG cc_start: 0.7709 (mtp180) cc_final: 0.7473 (mtm110) REVERT: B 440 ARG cc_start: 0.7958 (ttt180) cc_final: 0.7694 (tmt170) REVERT: B 548 LEU cc_start: 0.7229 (mt) cc_final: 0.6976 (mt) REVERT: D 191 TYR cc_start: 0.9232 (t80) cc_final: 0.8838 (t80) REVERT: D 281 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7599 (mm-40) REVERT: D 304 ARG cc_start: 0.8528 (tpp-160) cc_final: 0.8142 (tpp-160) REVERT: D 310 LEU cc_start: 0.7848 (tp) cc_final: 0.7396 (mm) REVERT: D 366 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7508 (tt) REVERT: D 367 HIS cc_start: 0.8261 (OUTLIER) cc_final: 0.7921 (m-70) REVERT: D 368 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7904 (ptm160) REVERT: D 380 ASN cc_start: 0.8695 (m-40) cc_final: 0.8392 (m110) REVERT: D 409 GLU cc_start: 0.8346 (tp30) cc_final: 0.8124 (mm-30) REVERT: D 410 GLU cc_start: 0.8036 (tp30) cc_final: 0.7805 (mm-30) REVERT: D 413 ARG cc_start: 0.7964 (mtm110) cc_final: 0.7694 (mtp180) REVERT: D 478 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.9021 (ptt90) REVERT: D 548 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6617 (mp) REVERT: D 559 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7614 (mm-30) REVERT: F 197 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8804 (mttp) REVERT: F 269 TRP cc_start: 0.7045 (OUTLIER) cc_final: 0.6799 (t60) REVERT: F 275 ASP cc_start: 0.8947 (t0) cc_final: 0.8716 (t0) REVERT: F 280 TRP cc_start: 0.8151 (t-100) cc_final: 0.7234 (t60) REVERT: F 366 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7549 (tt) REVERT: F 368 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7420 (ptm160) REVERT: F 413 ARG cc_start: 0.8373 (mtp180) cc_final: 0.7933 (mtm180) REVERT: F 421 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7943 (mp) REVERT: F 431 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7634 (pp) REVERT: F 478 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8971 (ptt90) REVERT: F 548 LEU cc_start: 0.7094 (mt) cc_final: 0.6790 (mt) REVERT: F 559 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: F 587 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8492 (mtm) REVERT: H 280 TRP cc_start: 0.8172 (t-100) cc_final: 0.7175 (t60) REVERT: H 281 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7709 (mm110) REVERT: H 282 MET cc_start: 0.8928 (tpp) cc_final: 0.8488 (tpp) REVERT: H 310 LEU cc_start: 0.8151 (tp) cc_final: 0.7883 (mp) REVERT: H 366 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7453 (tt) REVERT: H 368 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7865 (ptm160) REVERT: H 409 GLU cc_start: 0.8180 (tp30) cc_final: 0.7666 (tp30) REVERT: H 440 ARG cc_start: 0.7952 (ttt180) cc_final: 0.7664 (tmt170) REVERT: H 452 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8034 (mt) REVERT: H 548 LEU cc_start: 0.7331 (mt) cc_final: 0.7082 (mt) REVERT: H 587 MET cc_start: 0.8717 (ttm) cc_final: 0.8427 (ttm) REVERT: H 623 PHE cc_start: 0.7782 (m-10) cc_final: 0.7563 (m-10) REVERT: J 191 TYR cc_start: 0.9238 (t80) cc_final: 0.8872 (t80) REVERT: J 210 ILE cc_start: 0.8141 (pp) cc_final: 0.7832 (mt) REVERT: J 269 TRP cc_start: 0.6359 (t60) cc_final: 0.5983 (t-100) REVERT: J 280 TRP cc_start: 0.8157 (t-100) cc_final: 0.7326 (t60) REVERT: J 281 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7431 (tp-100) REVERT: J 304 ARG cc_start: 0.8520 (tpp-160) cc_final: 0.8298 (tpp-160) REVERT: J 367 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7897 (m-70) REVERT: J 368 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7904 (ptm160) REVERT: J 380 ASN cc_start: 0.8565 (m-40) cc_final: 0.8271 (m110) REVERT: J 409 GLU cc_start: 0.8229 (tp30) cc_final: 0.8018 (mm-30) REVERT: J 422 ASN cc_start: 0.8530 (m-40) cc_final: 0.8162 (m110) REVERT: J 431 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.6895 (mp) REVERT: J 478 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.9008 (ptt90) REVERT: J 559 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7561 (mm-30) REVERT: L 269 TRP cc_start: 0.7033 (OUTLIER) cc_final: 0.6750 (t60) REVERT: L 280 TRP cc_start: 0.8073 (t-100) cc_final: 0.7122 (t60) REVERT: L 281 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7822 (mm-40) REVERT: L 308 ARG cc_start: 0.7580 (mmt-90) cc_final: 0.7177 (mtp85) REVERT: L 366 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7650 (tt) REVERT: L 368 ARG cc_start: 0.7443 (ttt90) cc_final: 0.7090 (ttm-80) REVERT: L 413 ARG cc_start: 0.8369 (mtp180) cc_final: 0.7920 (mtm180) REVERT: L 431 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7597 (pp) REVERT: L 440 ARG cc_start: 0.7372 (ttt180) cc_final: 0.7038 (tpt170) REVERT: L 478 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8972 (ptt90) REVERT: L 566 GLU cc_start: 0.7988 (tt0) cc_final: 0.7538 (tt0) REVERT: L 571 ARG cc_start: 0.8155 (tpt170) cc_final: 0.7686 (tpt170) REVERT: L 587 MET cc_start: 0.8649 (mtm) cc_final: 0.8417 (mtm) outliers start: 88 outliers final: 35 residues processed: 389 average time/residue: 0.5727 time to fit residues: 253.1072 Evaluate side-chains 386 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 319 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 197 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 478 ARG Chi-restraints excluded: chain F residue 555 ILE Chi-restraints excluded: chain F residue 559 GLU Chi-restraints excluded: chain F residue 587 MET Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain J residue 180 VAL Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 368 ARG Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 269 TRP Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 555 ILE Chi-restraints excluded: chain L residue 611 ILE Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 218 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 83 optimal weight: 0.4980 chunk 170 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 153 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 236 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN F 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.164143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128765 restraints weight = 25985.813| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.71 r_work: 0.3197 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22842 Z= 0.104 Angle : 0.513 10.384 31068 Z= 0.245 Chirality : 0.040 0.337 3558 Planarity : 0.004 0.038 3678 Dihedral : 9.641 77.172 3078 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.38 % Allowed : 18.23 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.17), residues: 2496 helix: 1.92 (0.12), residues: 1770 sheet: None (None), residues: 0 loop : -0.03 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 570 TYR 0.011 0.001 TYR F 600 PHE 0.036 0.001 PHE H 442 TRP 0.025 0.001 TRP H 269 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (22842) covalent geometry : angle 0.51258 / 0.25 (31068) hydrogen bonds : bond 0.03047 / 2.00 ( 1314) hydrogen bonds : angle 3.80044 / 2.75 ( 3834) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 328 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ILE cc_start: 0.5617 (OUTLIER) cc_final: 0.5222 (tt) REVERT: B 281 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7662 (mm110) REVERT: B 282 MET cc_start: 0.8931 (tpp) cc_final: 0.8481 (tpp) REVERT: B 308 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7607 (mmt180) REVERT: B 310 LEU cc_start: 0.8147 (tp) cc_final: 0.7793 (mp) REVERT: B 368 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7820 (ptm160) REVERT: B 399 ARG cc_start: 0.8104 (mtp180) cc_final: 0.7898 (mmm-85) REVERT: B 409 GLU cc_start: 0.8101 (tp30) cc_final: 0.7640 (tp30) REVERT: B 413 ARG cc_start: 0.7667 (mtp180) cc_final: 0.7423 (mtm110) REVERT: B 440 ARG cc_start: 0.7998 (ttt180) cc_final: 0.7705 (tmt170) REVERT: B 548 LEU cc_start: 0.7201 (mt) cc_final: 0.6953 (mt) REVERT: B 566 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: D 191 TYR cc_start: 0.9222 (t80) cc_final: 0.8818 (t80) REVERT: D 281 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7295 (tp-100) REVERT: D 304 ARG cc_start: 0.8550 (tpp-160) cc_final: 0.8160 (tpp-160) REVERT: D 310 LEU cc_start: 0.7829 (tp) cc_final: 0.7381 (mm) REVERT: D 366 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7541 (tt) REVERT: D 367 HIS cc_start: 0.8298 (OUTLIER) cc_final: 0.7977 (m-70) REVERT: D 368 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7936 (ptm160) REVERT: D 380 ASN cc_start: 0.8672 (m-40) cc_final: 0.8376 (m110) REVERT: D 409 GLU cc_start: 0.8330 (tp30) cc_final: 0.8110 (mm-30) REVERT: D 439 PHE cc_start: 0.8528 (m-10) cc_final: 0.8289 (m-10) REVERT: D 478 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.9025 (ptt90) REVERT: D 548 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6739 (mp) REVERT: D 559 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7597 (mm-30) REVERT: F 269 TRP cc_start: 0.7006 (OUTLIER) cc_final: 0.6748 (t60) REVERT: F 275 ASP cc_start: 0.8945 (t0) cc_final: 0.8704 (t0) REVERT: F 280 TRP cc_start: 0.8190 (t-100) cc_final: 0.7218 (t60) REVERT: F 366 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7576 (tt) REVERT: F 368 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7752 (ptm160) REVERT: F 413 ARG cc_start: 0.8324 (mtp180) cc_final: 0.7927 (mtm180) REVERT: F 421 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7949 (mp) REVERT: F 431 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7667 (pp) REVERT: F 478 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8972 (ptt90) REVERT: F 548 LEU cc_start: 0.7022 (mt) cc_final: 0.6713 (mt) REVERT: F 559 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: F 566 GLU cc_start: 0.7994 (tt0) cc_final: 0.7552 (tt0) REVERT: F 587 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8350 (mtm) REVERT: H 280 TRP cc_start: 0.8166 (t-100) cc_final: 0.7195 (t60) REVERT: H 281 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7713 (mm110) REVERT: H 282 MET cc_start: 0.8936 (tpp) cc_final: 0.8488 (tpp) REVERT: H 310 LEU cc_start: 0.8115 (tp) cc_final: 0.7837 (mp) REVERT: H 368 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7889 (ptm160) REVERT: H 409 GLU cc_start: 0.8208 (tp30) cc_final: 0.7675 (tp30) REVERT: H 431 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7803 (pp) REVERT: H 440 ARG cc_start: 0.7930 (ttt180) cc_final: 0.7663 (tmt170) REVERT: H 452 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8021 (mt) REVERT: H 548 LEU cc_start: 0.7346 (mt) cc_final: 0.7113 (mt) REVERT: H 587 MET cc_start: 0.8772 (ttm) cc_final: 0.8471 (ttm) REVERT: J 191 TYR cc_start: 0.9232 (t80) cc_final: 0.8854 (t80) REVERT: J 210 ILE cc_start: 0.8124 (pp) cc_final: 0.7825 (mt) REVERT: J 269 TRP cc_start: 0.6460 (t60) cc_final: 0.6112 (t-100) REVERT: J 280 TRP cc_start: 0.8149 (t-100) cc_final: 0.7322 (t60) REVERT: J 281 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7369 (tp-100) REVERT: J 304 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.8290 (tpp-160) REVERT: J 367 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7901 (m-70) REVERT: J 368 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7820 (ptm160) REVERT: J 409 GLU cc_start: 0.8367 (tp30) cc_final: 0.8164 (mm-30) REVERT: J 431 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.6909 (mp) REVERT: J 478 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.9011 (ptt90) REVERT: J 559 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7567 (mm-30) REVERT: L 269 TRP cc_start: 0.7019 (OUTLIER) cc_final: 0.6751 (t60) REVERT: L 280 TRP cc_start: 0.8077 (t-100) cc_final: 0.7121 (t60) REVERT: L 281 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7830 (mm-40) REVERT: L 366 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7652 (tt) REVERT: L 368 ARG cc_start: 0.7466 (ttt90) cc_final: 0.7137 (ttm-80) REVERT: L 413 ARG cc_start: 0.8348 (mtp180) cc_final: 0.7926 (mtm180) REVERT: L 431 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7645 (pp) REVERT: L 440 ARG cc_start: 0.7416 (ttt180) cc_final: 0.7041 (tpt170) REVERT: L 478 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8976 (ptt90) REVERT: L 566 GLU cc_start: 0.7982 (tt0) cc_final: 0.7542 (tt0) REVERT: L 571 ARG cc_start: 0.8178 (tpt170) cc_final: 0.7704 (tpt170) REVERT: L 587 MET cc_start: 0.8678 (mtm) cc_final: 0.8448 (mtm) outliers start: 78 outliers final: 36 residues processed: 376 average time/residue: 0.6167 time to fit residues: 263.6082 Evaluate side-chains 379 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 312 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 478 ARG Chi-restraints excluded: chain F residue 555 ILE Chi-restraints excluded: chain F residue 559 GLU Chi-restraints excluded: chain F residue 587 MET Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain H residue 431 ILE Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 368 ARG Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 269 TRP Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 555 ILE Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 132 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN L 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.164221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128823 restraints weight = 25961.257| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.70 r_work: 0.3175 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22842 Z= 0.117 Angle : 0.522 10.428 31068 Z= 0.251 Chirality : 0.040 0.339 3558 Planarity : 0.004 0.041 3678 Dihedral : 9.681 77.631 3078 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.33 % Allowed : 18.53 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.17), residues: 2496 helix: 1.88 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : -0.00 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 570 TYR 0.012 0.001 TYR L 600 PHE 0.040 0.001 PHE B 442 TRP 0.026 0.001 TRP B 269 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (22842) covalent geometry : angle 0.52225 / 0.25 (31068) hydrogen bonds : bond 0.03178 / 2.08 ( 1314) hydrogen bonds : angle 3.87012 / 2.80 ( 3834) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4992 Ramachandran restraints generated. 2496 Oldfield, 0 Emsley, 2496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 319 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ILE cc_start: 0.5523 (OUTLIER) cc_final: 0.5050 (tt) REVERT: B 281 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7695 (mm110) REVERT: B 282 MET cc_start: 0.8921 (tpp) cc_final: 0.8472 (tpp) REVERT: B 308 ARG cc_start: 0.7857 (mmm-85) cc_final: 0.7595 (mmt180) REVERT: B 310 LEU cc_start: 0.8167 (tp) cc_final: 0.7810 (mp) REVERT: B 368 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7844 (ptm160) REVERT: B 409 GLU cc_start: 0.8085 (tp30) cc_final: 0.7669 (tp30) REVERT: B 413 ARG cc_start: 0.7623 (mtp180) cc_final: 0.7372 (mtm110) REVERT: B 440 ARG cc_start: 0.7996 (ttt180) cc_final: 0.7706 (tmt170) REVERT: B 548 LEU cc_start: 0.7335 (mt) cc_final: 0.7102 (mt) REVERT: D 191 TYR cc_start: 0.9239 (t80) cc_final: 0.8797 (t80) REVERT: D 281 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7579 (mm-40) REVERT: D 304 ARG cc_start: 0.8536 (tpp-160) cc_final: 0.8140 (tpp-160) REVERT: D 310 LEU cc_start: 0.7861 (tp) cc_final: 0.7402 (mm) REVERT: D 366 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7532 (tt) REVERT: D 367 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7949 (m-70) REVERT: D 368 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7911 (ptm160) REVERT: D 380 ASN cc_start: 0.8677 (m-40) cc_final: 0.8384 (m110) REVERT: D 409 GLU cc_start: 0.8297 (tp30) cc_final: 0.8084 (mm-30) REVERT: D 478 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.9044 (ptt90) REVERT: D 548 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6756 (mp) REVERT: D 559 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7603 (mm-30) REVERT: F 269 TRP cc_start: 0.6976 (OUTLIER) cc_final: 0.6738 (t60) REVERT: F 275 ASP cc_start: 0.8785 (t0) cc_final: 0.8486 (t0) REVERT: F 280 TRP cc_start: 0.8171 (t-100) cc_final: 0.7233 (t60) REVERT: F 366 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7569 (tt) REVERT: F 413 ARG cc_start: 0.8348 (mtp180) cc_final: 0.7947 (mtm180) REVERT: F 421 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7934 (mp) REVERT: F 431 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7624 (pp) REVERT: F 478 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.9001 (ptt90) REVERT: F 548 LEU cc_start: 0.7007 (mt) cc_final: 0.6713 (mt) REVERT: F 559 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: F 587 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8446 (mtm) REVERT: H 281 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7682 (mm110) REVERT: H 282 MET cc_start: 0.8930 (tpp) cc_final: 0.8481 (tpp) REVERT: H 310 LEU cc_start: 0.8117 (tp) cc_final: 0.7842 (mp) REVERT: H 368 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7868 (ptm160) REVERT: H 409 GLU cc_start: 0.8218 (tp30) cc_final: 0.7690 (tp30) REVERT: H 440 ARG cc_start: 0.7957 (ttt180) cc_final: 0.7666 (tmt170) REVERT: H 548 LEU cc_start: 0.7338 (mt) cc_final: 0.7112 (mt) REVERT: H 587 MET cc_start: 0.8742 (ttm) cc_final: 0.8441 (ttm) REVERT: J 210 ILE cc_start: 0.8151 (pp) cc_final: 0.7839 (mt) REVERT: J 269 TRP cc_start: 0.6467 (t60) cc_final: 0.6126 (t-100) REVERT: J 280 TRP cc_start: 0.8122 (t-100) cc_final: 0.7317 (t60) REVERT: J 281 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7337 (tp-100) REVERT: J 366 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7556 (tt) REVERT: J 367 HIS cc_start: 0.8232 (OUTLIER) cc_final: 0.7919 (m-70) REVERT: J 368 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7722 (ptm160) REVERT: J 409 GLU cc_start: 0.8354 (tp30) cc_final: 0.8139 (mm-30) REVERT: J 431 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.6896 (mp) REVERT: J 478 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.9017 (ptt90) REVERT: J 559 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7570 (mm-30) REVERT: L 197 LYS cc_start: 0.9078 (mttm) cc_final: 0.8805 (mttp) REVERT: L 269 TRP cc_start: 0.7018 (OUTLIER) cc_final: 0.6741 (t60) REVERT: L 280 TRP cc_start: 0.8084 (t-100) cc_final: 0.7131 (t60) REVERT: L 281 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7816 (mm-40) REVERT: L 366 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7619 (tt) REVERT: L 368 ARG cc_start: 0.7442 (ttt90) cc_final: 0.7093 (ttm-80) REVERT: L 413 ARG cc_start: 0.8321 (mtp180) cc_final: 0.7909 (mtm180) REVERT: L 431 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7624 (pp) REVERT: L 440 ARG cc_start: 0.7418 (ttt180) cc_final: 0.7029 (tpt170) REVERT: L 478 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.9001 (ptt90) REVERT: L 566 GLU cc_start: 0.7991 (tt0) cc_final: 0.7536 (tt0) REVERT: L 587 MET cc_start: 0.8675 (mtm) cc_final: 0.8453 (mtm) outliers start: 77 outliers final: 36 residues processed: 368 average time/residue: 0.5866 time to fit residues: 245.3335 Evaluate side-chains 371 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 306 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 478 ARG Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 548 LEU Chi-restraints excluded: chain D residue 624 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 478 ARG Chi-restraints excluded: chain F residue 555 ILE Chi-restraints excluded: chain F residue 559 GLU Chi-restraints excluded: chain F residue 587 MET Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 281 GLN Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 ARG Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 LEU Chi-restraints excluded: chain J residue 260 LEU Chi-restraints excluded: chain J residue 281 GLN Chi-restraints excluded: chain J residue 366 LEU Chi-restraints excluded: chain J residue 367 HIS Chi-restraints excluded: chain J residue 368 ARG Chi-restraints excluded: chain J residue 431 ILE Chi-restraints excluded: chain J residue 478 ARG Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain J residue 624 THR Chi-restraints excluded: chain L residue 180 VAL Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain L residue 221 THR Chi-restraints excluded: chain L residue 258 LEU Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 269 TRP Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 431 ILE Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 478 ARG Chi-restraints excluded: chain L residue 519 ILE Chi-restraints excluded: chain L residue 555 ILE Chi-restraints excluded: chain L residue 624 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 0.8980 chunk 192 optimal weight: 0.8980 chunk 143 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 221 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 206 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 209 GLN B 380 ASN F 380 ASN H 209 GLN H 380 ASN L 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130838 restraints weight = 25868.512| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.68 r_work: 0.3210 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22842 Z= 0.101 Angle : 0.505 10.354 31068 Z= 0.244 Chirality : 0.039 0.334 3558 Planarity : 0.004 0.043 3678 Dihedral : 9.554 76.135 3078 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.99 % Allowed : 19.22 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.17), residues: 2496 helix: 1.99 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : 0.06 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 570 TYR 0.011 0.001 TYR L 600 PHE 0.040 0.001 PHE H 442 TRP 0.025 0.001 TRP B 269 HIS 0.003 0.001 HIS B 588 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (22842) covalent geometry : angle 0.50507 / 0.24 (31068) hydrogen bonds : bond 0.03003 / 1.97 ( 1314) hydrogen bonds : angle 3.78058 / 2.73 ( 3834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7275.28 seconds wall clock time: 124 minutes 34.60 seconds (7474.60 seconds total)