Starting phenix.real_space_refine on Thu Mar 5 12:13:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d0i_30535/03_2026/7d0i_30535.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d0i_30535/03_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_30535/03_2026/7d0i_30535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d0i_30535/03_2026/7d0i_30535.map" model { file = "/net/cci-nas-00/data/ceres_data/7d0i_30535/03_2026/7d0i_30535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d0i_30535/03_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-5986/lib/python3.9/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: 4.72, per 1000 atoms: 0.21 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: 1.74 Conformation dependent library (CDL) restraints added in 987.5 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: 0.68 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: 3.70 Time building geometry restraints manager: 2.42 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: 13332 29.53 - 59.05: 456 59.05 - 88.58: 180 88.58 - 118.10: 114 118.10 - 147.63: 66 Dihedral angle restraints: 14148 sinusoidal: 6564 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 14145 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: 0.06 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.390 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 22.603 147.628 9228 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 covalent geometry : bond 0.01127 (22842) covalent geometry : angle 0.94951 (31068) hydrogen bonds : bond 0.13169 ( 1314) hydrogen bonds : angle 5.55900 ( 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 : 0.795 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: 0.6524 time to fit residues: 386.6886 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 : 0.738 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN D 179 ASN D 443 ASN F 209 GLN H 179 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 ASN J 209 GLN J 443 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.163566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128999 restraints weight = 25848.861| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.61 r_work: 0.3140 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2169 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= 0.129 Angle : 0.663 8.264 31068 Z= 0.297 Chirality : 0.047 0.332 3558 Planarity : 0.004 0.037 3678 Dihedral : 19.947 119.318 4372 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.81 % Allowed : 13.59 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.16), residues: 2496 helix: 0.53 (0.12), residues: 1812 sheet: None (None), residues: 0 loop : -0.99 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 J 473 Details of bonding type rmsd covalent geometry : bond 0.00281 (22842) covalent geometry : angle 0.66261 (31068) hydrogen bonds : bond 0.03698 ( 1314) hydrogen bonds : angle 4.26449 ( 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: 88 poor density : 367 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 TYR cc_start: 0.9099 (t80) cc_final: 0.8800 (t80) REVERT: B 210 ILE cc_start: 0.8356 (pp) cc_final: 0.8135 (mt) REVERT: B 282 MET cc_start: 0.8968 (tpp) cc_final: 0.8506 (tpp) REVERT: B 310 LEU cc_start: 0.8142 (tp) cc_final: 0.7787 (mp) REVERT: B 366 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7695 (tt) REVERT: B 368 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7612 (ptm160) REVERT: B 380 ASN cc_start: 0.8580 (m-40) cc_final: 0.8299 (m110) REVERT: B 391 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 440 ARG cc_start: 0.7856 (ttt180) cc_final: 0.7571 (tmt170) REVERT: B 548 LEU cc_start: 0.7174 (mt) cc_final: 0.6844 (mt) REVERT: B 559 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7774 (mt-10) REVERT: D 210 ILE cc_start: 0.8241 (pp) cc_final: 0.8037 (mt) REVERT: D 260 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6138 (pp) REVERT: D 284 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6461 (mt-10) REVERT: D 296 ASP cc_start: 0.7416 (t0) cc_final: 0.6870 (m-30) REVERT: D 304 ARG cc_start: 0.8349 (tpp-160) cc_final: 0.7976 (tpp-160) REVERT: D 310 LEU cc_start: 0.8070 (tp) cc_final: 0.7632 (mm) REVERT: D 366 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7587 (tt) REVERT: D 367 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7722 (m-70) REVERT: D 380 ASN cc_start: 0.8722 (m-40) cc_final: 0.8444 (m110) REVERT: D 391 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7347 (tm-30) REVERT: D 440 ARG cc_start: 0.7751 (ttt180) cc_final: 0.7302 (tmt170) REVERT: D 559 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7733 (mm-30) REVERT: F 260 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6115 (pp) REVERT: F 280 TRP cc_start: 0.8050 (t-100) cc_final: 0.7245 (t60) REVERT: F 310 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7172 (mm) REVERT: F 366 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7804 (tt) REVERT: F 367 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.8003 (m90) REVERT: F 391 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7141 (tm130) REVERT: F 548 LEU cc_start: 0.6677 (mt) cc_final: 0.6229 (mp) REVERT: H 191 TYR cc_start: 0.9103 (t80) cc_final: 0.8818 (t80) REVERT: H 210 ILE cc_start: 0.8306 (pp) cc_final: 0.8057 (mt) REVERT: H 282 MET cc_start: 0.8971 (tpp) cc_final: 0.8504 (tpp) REVERT: H 310 LEU cc_start: 0.8136 (tp) cc_final: 0.7771 (mp) REVERT: H 366 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7673 (tt) REVERT: H 368 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7637 (ptm160) REVERT: H 380 ASN cc_start: 0.8551 (m-40) cc_final: 0.8251 (m110) REVERT: H 391 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7730 (tm-30) REVERT: H 440 ARG cc_start: 0.7856 (ttt180) cc_final: 0.7563 (tmt170) REVERT: H 519 ILE cc_start: 0.6270 (OUTLIER) cc_final: 0.5690 (mt) REVERT: H 548 LEU cc_start: 0.7201 (mt) cc_final: 0.6889 (mt) REVERT: H 559 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7719 (mm-30) REVERT: J 210 ILE cc_start: 0.8406 (pp) cc_final: 0.8158 (mt) REVERT: J 260 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5807 (pp) REVERT: J 280 TRP cc_start: 0.8015 (t-100) cc_final: 0.7240 (t60) REVERT: J 282 MET cc_start: 0.8983 (tpp) cc_final: 0.8448 (tpp) REVERT: J 284 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6612 (mt-10) REVERT: J 304 ARG cc_start: 0.8408 (tpp-160) cc_final: 0.8060 (tpp-160) REVERT: J 367 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7496 (m-70) REVERT: J 380 ASN cc_start: 0.8756 (m-40) cc_final: 0.8490 (m110) REVERT: J 391 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7449 (tm-30) REVERT: J 440 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7164 (tmt170) REVERT: J 559 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7719 (mm-30) REVERT: J 648 TYR cc_start: 0.8291 (m-80) cc_final: 0.7937 (m-80) REVERT: L 260 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5893 (pp) REVERT: L 280 TRP cc_start: 0.8026 (t-100) cc_final: 0.7199 (t60) REVERT: L 281 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7735 (mm-40) REVERT: L 368 ARG cc_start: 0.7508 (ttt90) cc_final: 0.7110 (ttm-80) REVERT: L 391 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7159 (tm130) REVERT: L 431 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7690 (tp) REVERT: L 440 ARG cc_start: 0.7460 (ttt180) cc_final: 0.7137 (tpt170) REVERT: L 548 LEU cc_start: 0.6610 (mt) cc_final: 0.6202 (mt) REVERT: L 559 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7448 (mm-30) REVERT: L 570 ARG cc_start: 0.8726 (mtt-85) cc_final: 0.8479 (mtt90) REVERT: L 571 ARG cc_start: 0.8235 (tpt170) cc_final: 0.7949 (mmm-85) outliers start: 88 outliers final: 11 residues processed: 425 average time/residue: 0.6485 time to fit residues: 313.1980 Evaluate side-chains 334 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 306 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 627 SER 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 517 VAL Chi-restraints excluded: chain D residue 624 THR 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 F residue 367 HIS 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 H residue 627 SER 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 517 VAL Chi-restraints excluded: chain J residue 627 SER Chi-restraints excluded: chain L residue 260 LEU Chi-restraints excluded: chain L residue 281 GLN 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: 0.5980 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 99 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN B 209 GLN B 437 ASN D 179 ASN D 209 GLN D 443 ASN F 380 ASN H 179 ASN H 209 GLN H 437 ASN J 179 ASN J 209 GLN J 443 ASN ** L 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 380 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.163617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.129113 restraints weight = 25848.882| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.59 r_work: 0.3239 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2706 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= 0.141 Angle : 0.629 9.809 31068 Z= 0.284 Chirality : 0.049 0.462 3558 Planarity : 0.004 0.044 3678 Dihedral : 14.706 129.052 4356 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 4.85 % Allowed : 13.55 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2496 helix: 1.04 (0.12), residues: 1812 sheet: None (None), residues: 0 loop : -0.53 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 570 TYR 0.017 0.001 TYR D 600 PHE 0.021 0.001 PHE H 442 TRP 0.035 0.001 TRP F 269 HIS 0.005 0.001 HIS D 473 Details of bonding type rmsd covalent geometry : bond 0.00323 (22842) covalent geometry : angle 0.62942 (31068) hydrogen bonds : bond 0.03579 ( 1314) hydrogen bonds : angle 4.18451 ( 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 444 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 332 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ILE cc_start: 0.8455 (pp) cc_final: 0.8213 (mt) REVERT: B 282 MET cc_start: 0.8962 (tpp) cc_final: 0.8505 (tpp) REVERT: B 308 ARG cc_start: 0.7841 (mmm-85) cc_final: 0.7591 (mmt180) REVERT: B 310 LEU cc_start: 0.8212 (tp) cc_final: 0.7852 (mp) REVERT: B 366 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7669 (tt) REVERT: B 368 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7725 (ptm160) REVERT: B 380 ASN cc_start: 0.8583 (m-40) cc_final: 0.8325 (m110) REVERT: B 440 ARG cc_start: 0.7966 (ttt180) cc_final: 0.7631 (tmt170) REVERT: B 548 LEU cc_start: 0.7284 (mt) cc_final: 0.6980 (mt) REVERT: B 559 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7771 (mt-10) REVERT: D 284 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6721 (mt-10) REVERT: D 296 ASP cc_start: 0.7283 (t0) cc_final: 0.6859 (m-30) REVERT: D 304 ARG cc_start: 0.8502 (tpp-160) cc_final: 0.8106 (tpp-160) REVERT: D 310 LEU cc_start: 0.7989 (tp) cc_final: 0.7520 (mm) REVERT: D 366 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7474 (tt) REVERT: D 367 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7733 (m-70) REVERT: D 380 ASN cc_start: 0.8815 (m-40) cc_final: 0.8467 (m-40) REVERT: D 440 ARG cc_start: 0.7566 (ttt180) cc_final: 0.7356 (tmt170) REVERT: D 559 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7731 (mm-30) REVERT: F 269 TRP cc_start: 0.6956 (t60) cc_final: 0.6556 (t60) REVERT: F 280 TRP cc_start: 0.8138 (t-100) cc_final: 0.7254 (t60) REVERT: F 310 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7336 (mm) REVERT: F 366 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7786 (tt) REVERT: F 391 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7005 (tm130) REVERT: F 421 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7938 (mp) REVERT: F 548 LEU cc_start: 0.6444 (mt) cc_final: 0.6138 (mp) REVERT: F 559 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7634 (mt-10) REVERT: H 210 ILE cc_start: 0.8455 (pp) cc_final: 0.8211 (mt) REVERT: H 281 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7699 (mm110) REVERT: H 282 MET cc_start: 0.8978 (tpp) cc_final: 0.8532 (tpp) REVERT: H 310 LEU cc_start: 0.8163 (tp) cc_final: 0.7791 (mp) REVERT: H 366 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7641 (tt) REVERT: H 368 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7786 (ptm160) REVERT: H 380 ASN cc_start: 0.8614 (m-40) cc_final: 0.8324 (m110) REVERT: H 413 ARG cc_start: 0.8251 (mtp180) cc_final: 0.8036 (mtp180) REVERT: H 440 ARG cc_start: 0.7890 (ttt180) cc_final: 0.7601 (tmt170) REVERT: H 452 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7973 (mt) REVERT: H 548 LEU cc_start: 0.7203 (mt) cc_final: 0.6918 (mt) REVERT: H 559 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7799 (mt-10) REVERT: H 570 ARG cc_start: 0.8651 (mtt90) cc_final: 0.8438 (mtt-85) REVERT: H 623 PHE cc_start: 0.8000 (m-10) cc_final: 0.7791 (m-80) REVERT: J 210 ILE cc_start: 0.8422 (pp) cc_final: 0.8217 (mt) REVERT: J 260 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6151 (pp) REVERT: J 280 TRP cc_start: 0.8042 (t-100) cc_final: 0.7183 (t60) REVERT: J 284 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6714 (mt-10) REVERT: J 304 ARG cc_start: 0.8528 (tpp-160) cc_final: 0.8122 (tpp-160) REVERT: J 367 HIS cc_start: 0.8101 (OUTLIER) cc_final: 0.7721 (m-70) REVERT: J 380 ASN cc_start: 0.8793 (m-40) cc_final: 0.8466 (m110) REVERT: J 391 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7550 (tm-30) REVERT: J 559 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7714 (mm-30) REVERT: L 280 TRP cc_start: 0.8056 (t-100) cc_final: 0.7200 (t60) REVERT: L 281 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7935 (mm-40) REVERT: L 366 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7754 (tt) REVERT: L 368 ARG cc_start: 0.7512 (ttt90) cc_final: 0.7111 (ttm-80) REVERT: L 391 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7051 (tm130) REVERT: L 440 ARG cc_start: 0.7438 (ttt180) cc_final: 0.7153 (tpt170) REVERT: L 519 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.7096 (tt) REVERT: L 548 LEU cc_start: 0.6471 (mt) cc_final: 0.6205 (mt) REVERT: L 559 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7595 (mm-30) REVERT: L 571 ARG cc_start: 0.8236 (tpt170) cc_final: 0.7894 (tpt170) REVERT: L 587 MET cc_start: 0.8967 (mtm) cc_final: 0.8640 (mtm) REVERT: L 610 GLU cc_start: 0.7189 (tp30) cc_final: 0.6921 (tt0) outliers start: 112 outliers final: 36 residues processed: 416 average time/residue: 0.6089 time to fit residues: 289.1069 Evaluate side-chains 349 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 296 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 B residue 612 LEU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 624 THR 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 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 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 612 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 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 366 LEU Chi-restraints excluded: chain L residue 452 LEU Chi-restraints excluded: chain L residue 519 ILE 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: 4.9990 chunk 198 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 161 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 0.0020 chunk 223 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN D 179 ASN D 443 ASN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN J 179 ASN J 443 ASN ** L 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 360 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.126089 restraints weight = 25747.876| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.72 r_work: 0.3184 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22842 Z= 0.112 Angle : 0.570 8.745 31068 Z= 0.260 Chirality : 0.045 0.374 3558 Planarity : 0.004 0.052 3678 Dihedral : 12.998 138.946 4354 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.33 % Allowed : 16.32 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 D 570 TYR 0.014 0.001 TYR H 600 PHE 0.022 0.001 PHE J 222 TRP 0.029 0.001 TRP L 269 HIS 0.003 0.001 HIS D 473 Details of bonding type rmsd covalent geometry : bond 0.00247 (22842) covalent geometry : angle 0.56962 (31068) hydrogen bonds : bond 0.03219 ( 1314) hydrogen bonds : angle 3.99560 ( 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 408 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 331 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 282 MET cc_start: 0.8916 (tpp) cc_final: 0.8435 (tpp) REVERT: B 308 ARG cc_start: 0.7819 (mmm-85) cc_final: 0.7537 (mmt180) REVERT: B 310 LEU cc_start: 0.8173 (tp) cc_final: 0.7822 (mp) REVERT: B 366 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7643 (tt) REVERT: B 368 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7714 (ptm160) REVERT: B 410 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7858 (tp30) REVERT: B 440 ARG cc_start: 0.7842 (ttt180) cc_final: 0.7550 (tmt170) REVERT: B 548 LEU cc_start: 0.7269 (mt) cc_final: 0.6979 (mt) REVERT: B 559 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7766 (mt-10) REVERT: D 191 TYR cc_start: 0.9247 (t80) cc_final: 0.8870 (t80) REVERT: D 296 ASP cc_start: 0.7150 (t0) cc_final: 0.6887 (m-30) REVERT: D 304 ARG cc_start: 0.8480 (tpp-160) cc_final: 0.8081 (tpp-160) REVERT: D 310 LEU cc_start: 0.7948 (tp) cc_final: 0.7480 (mm) REVERT: D 366 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7535 (tt) REVERT: D 367 HIS cc_start: 0.8108 (OUTLIER) cc_final: 0.7809 (m-70) REVERT: D 380 ASN cc_start: 0.8667 (m-40) cc_final: 0.8399 (m-40) REVERT: D 410 GLU cc_start: 0.8122 (tp30) cc_final: 0.7891 (tp30) REVERT: D 421 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7828 (tp) REVERT: D 440 ARG cc_start: 0.7505 (ttt180) cc_final: 0.7237 (tmt170) REVERT: D 559 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7618 (mm-30) REVERT: F 269 TRP cc_start: 0.6800 (t60) cc_final: 0.6475 (t60) REVERT: F 280 TRP cc_start: 0.8154 (t-100) cc_final: 0.7236 (t60) REVERT: F 308 ARG cc_start: 0.7524 (mmt-90) cc_final: 0.7292 (mmm-85) REVERT: F 366 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7655 (tt) REVERT: F 368 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7310 (ptm160) REVERT: F 395 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6512 (mtt-85) REVERT: F 421 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7921 (mp) REVERT: F 431 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7544 (pp) REVERT: F 548 LEU cc_start: 0.6502 (mt) cc_final: 0.6194 (mt) REVERT: H 282 MET cc_start: 0.8927 (tpp) cc_final: 0.8458 (tpp) REVERT: H 310 LEU cc_start: 0.8089 (tp) cc_final: 0.7697 (mp) REVERT: H 366 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7613 (tt) REVERT: H 368 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7718 (ptm160) REVERT: H 380 ASN cc_start: 0.8560 (m-40) cc_final: 0.8256 (m110) REVERT: H 399 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7741 (mtp180) REVERT: H 431 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7816 (pp) REVERT: H 440 ARG cc_start: 0.7873 (ttt180) cc_final: 0.7546 (tmt170) REVERT: H 452 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7936 (mt) REVERT: H 548 LEU cc_start: 0.7234 (mt) cc_final: 0.6947 (mt) REVERT: H 559 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7815 (mt-10) REVERT: H 623 PHE cc_start: 0.8023 (m-10) cc_final: 0.7796 (m-80) REVERT: J 210 ILE cc_start: 0.8238 (pp) cc_final: 0.8023 (mt) REVERT: J 269 TRP cc_start: 0.6356 (t60) cc_final: 0.5919 (t-100) REVERT: J 280 TRP cc_start: 0.8144 (t-100) cc_final: 0.7266 (t60) REVERT: J 282 MET cc_start: 0.8975 (tpp) cc_final: 0.8454 (tpp) REVERT: J 304 ARG cc_start: 0.8515 (tpp-160) cc_final: 0.8088 (tpp-160) REVERT: J 380 ASN cc_start: 0.8678 (m-40) cc_final: 0.8376 (m110) REVERT: J 444 GLU cc_start: 0.7275 (mp0) cc_final: 0.7012 (mp0) REVERT: J 559 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7604 (mm-30) REVERT: L 269 TRP cc_start: 0.7071 (t60) cc_final: 0.6569 (t60) REVERT: L 280 TRP cc_start: 0.8037 (t-100) cc_final: 0.7109 (t60) REVERT: L 281 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7825 (mm-40) REVERT: L 366 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7761 (tt) REVERT: L 368 ARG cc_start: 0.7483 (ttt90) cc_final: 0.7120 (ttm-80) REVERT: L 391 GLN cc_start: 0.7612 (tm-30) cc_final: 0.6907 (tm130) REVERT: L 422 ASN cc_start: 0.8502 (m-40) cc_final: 0.8198 (m110) REVERT: L 431 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7508 (pp) REVERT: L 440 ARG cc_start: 0.7446 (ttt180) cc_final: 0.7140 (tpt170) REVERT: L 548 LEU cc_start: 0.6501 (mt) cc_final: 0.6245 (mt) REVERT: L 571 ARG cc_start: 0.8210 (tpt170) cc_final: 0.7860 (tpt170) REVERT: L 587 MET cc_start: 0.8822 (mtm) cc_final: 0.8488 (mtm) REVERT: L 610 GLU cc_start: 0.7148 (tp30) cc_final: 0.6921 (tt0) outliers start: 77 outliers final: 26 residues processed: 384 average time/residue: 0.6566 time to fit residues: 285.5802 Evaluate side-chains 346 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 304 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 180 VAL 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 372 THR Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 395 ARG 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 624 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 431 ILE 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 452 LEU Chi-restraints excluded: chain J residue 479 ILE Chi-restraints excluded: chain J residue 617 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 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 624 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 140 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 235 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 227 optimal weight: 0.0770 chunk 229 optimal weight: 3.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 373 HIS D 179 ASN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN H 209 GLN H 373 HIS J 179 ASN L 380 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.163097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127911 restraints weight = 25824.030| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.68 r_work: 0.3150 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3283 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= 0.124 Angle : 0.570 10.273 31068 Z= 0.262 Chirality : 0.045 0.358 3558 Planarity : 0.004 0.042 3678 Dihedral : 12.506 141.767 4352 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.90 % Allowed : 16.32 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.58 (0.17), residues: 2496 helix: 1.65 (0.12), residues: 1758 sheet: None (None), residues: 0 loop : -0.35 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 570 TYR 0.014 0.001 TYR H 600 PHE 0.026 0.001 PHE H 442 TRP 0.028 0.001 TRP L 269 HIS 0.004 0.001 HIS F 588 Details of bonding type rmsd covalent geometry : bond 0.00282 (22842) covalent geometry : angle 0.56952 (31068) hydrogen bonds : bond 0.03305 ( 1314) hydrogen bonds : angle 3.99403 ( 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 424 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 334 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7625 (mm110) REVERT: B 282 MET cc_start: 0.8916 (tpp) cc_final: 0.8452 (tpp) REVERT: B 308 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7572 (mmt180) REVERT: B 310 LEU cc_start: 0.8159 (tp) cc_final: 0.7787 (mp) REVERT: B 366 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7572 (tt) REVERT: B 368 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7705 (ptm160) REVERT: B 409 GLU cc_start: 0.8139 (tp30) cc_final: 0.7612 (tp30) REVERT: B 410 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7938 (tp30) REVERT: B 440 ARG cc_start: 0.7882 (ttt180) cc_final: 0.7569 (tmt170) REVERT: B 548 LEU cc_start: 0.7259 (mt) cc_final: 0.6970 (mt) REVERT: B 559 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7727 (mt-10) REVERT: D 304 ARG cc_start: 0.8493 (tpp-160) cc_final: 0.8109 (tpp-160) REVERT: D 310 LEU cc_start: 0.7941 (tp) cc_final: 0.7468 (mm) REVERT: D 366 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7459 (tt) REVERT: D 368 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7788 (ptm160) REVERT: D 380 ASN cc_start: 0.8711 (m-40) cc_final: 0.8400 (m-40) REVERT: D 420 PHE cc_start: 0.7961 (m-10) cc_final: 0.7760 (m-10) REVERT: D 421 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8030 (tp) REVERT: D 431 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.6852 (mp) REVERT: D 559 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7628 (mm-30) REVERT: F 197 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8818 (mtmm) REVERT: F 269 TRP cc_start: 0.6817 (OUTLIER) cc_final: 0.6481 (t60) REVERT: F 280 TRP cc_start: 0.8154 (t-100) cc_final: 0.7281 (t60) REVERT: F 366 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7635 (tt) REVERT: F 368 ARG cc_start: 0.7953 (ttm110) cc_final: 0.7347 (ptm160) REVERT: F 395 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7062 (mtm180) REVERT: F 421 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7908 (mp) REVERT: F 431 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7531 (pp) REVERT: F 548 LEU cc_start: 0.6842 (mt) cc_final: 0.6477 (mt) REVERT: H 281 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7663 (mm110) REVERT: H 282 MET cc_start: 0.8918 (tpp) cc_final: 0.8462 (tpp) REVERT: H 310 LEU cc_start: 0.8108 (tp) cc_final: 0.7627 (mp) REVERT: H 366 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7559 (tt) REVERT: H 368 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7731 (ptm160) REVERT: H 380 ASN cc_start: 0.8637 (m-40) cc_final: 0.8337 (m110) REVERT: H 440 ARG cc_start: 0.7913 (ttt180) cc_final: 0.7541 (tmt170) REVERT: H 452 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7897 (mt) REVERT: H 548 LEU cc_start: 0.7224 (mt) cc_final: 0.6964 (mt) REVERT: H 559 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7770 (mt-10) REVERT: J 210 ILE cc_start: 0.8147 (pp) cc_final: 0.7941 (mt) REVERT: J 269 TRP cc_start: 0.6439 (t60) cc_final: 0.6006 (t-100) REVERT: J 280 TRP cc_start: 0.8188 (t-100) cc_final: 0.7318 (t60) REVERT: J 281 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7348 (tp-100) REVERT: J 304 ARG cc_start: 0.8509 (tpp-160) cc_final: 0.8076 (tpp-160) REVERT: J 367 HIS cc_start: 0.8049 (OUTLIER) cc_final: 0.7682 (m-70) REVERT: J 368 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7861 (ptm160) REVERT: J 380 ASN cc_start: 0.8735 (m-40) cc_final: 0.8431 (m110) REVERT: J 422 ASN cc_start: 0.8508 (m-40) cc_final: 0.8290 (m110) REVERT: J 431 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.6831 (mp) REVERT: J 559 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7581 (mm-30) REVERT: L 269 TRP cc_start: 0.6886 (t60) cc_final: 0.6628 (t60) REVERT: L 280 TRP cc_start: 0.8093 (t-100) cc_final: 0.7157 (t60) REVERT: L 281 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7759 (mm-40) REVERT: L 308 ARG cc_start: 0.7557 (mmt-90) cc_final: 0.7163 (mtp85) REVERT: L 366 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7658 (tt) REVERT: L 368 ARG cc_start: 0.7425 (ttt90) cc_final: 0.7044 (ttm-80) REVERT: L 391 GLN cc_start: 0.7527 (tm-30) cc_final: 0.6805 (tm130) REVERT: L 422 ASN cc_start: 0.8478 (m-40) cc_final: 0.8175 (m110) REVERT: L 431 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7505 (pp) REVERT: L 440 ARG cc_start: 0.7432 (ttt180) cc_final: 0.7086 (tpt170) REVERT: L 478 ARG cc_start: 0.9328 (OUTLIER) cc_final: 0.9088 (ptt90) REVERT: L 548 LEU cc_start: 0.6650 (mt) cc_final: 0.6425 (mt) REVERT: L 571 ARG cc_start: 0.8166 (tpt170) cc_final: 0.7770 (tpt170) REVERT: L 587 MET cc_start: 0.8768 (mtm) cc_final: 0.8486 (mtm) outliers start: 90 outliers final: 38 residues processed: 391 average time/residue: 0.7005 time to fit residues: 308.2714 Evaluate side-chains 372 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 309 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 368 ARG Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 431 ILE 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 197 LYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 395 ARG 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 624 THR Chi-restraints excluded: chain H residue 220 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 213 optimal weight: 0.9980 chunk 195 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 156 optimal weight: 0.2980 chunk 183 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS F 209 GLN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 ASN L 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 = 0.3836 r_free = 0.3836 target = 0.165103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130132 restraints weight = 25843.014| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.86 r_work: 0.3228 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22842 Z= 0.112 Angle : 0.549 10.459 31068 Z= 0.254 Chirality : 0.043 0.360 3558 Planarity : 0.004 0.060 3678 Dihedral : 12.186 142.921 4350 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.16 % Allowed : 16.54 % Favored : 79.31 % 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: 1.77 (0.17), residues: 2496 helix: 1.79 (0.12), residues: 1758 sheet: None (None), residues: 0 loop : -0.27 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 570 TYR 0.012 0.001 TYR B 600 PHE 0.019 0.001 PHE D 222 TRP 0.022 0.001 TRP L 269 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd covalent geometry : bond 0.00250 (22842) covalent geometry : angle 0.54935 (31068) hydrogen bonds : bond 0.03138 ( 1314) hydrogen bonds : angle 3.90345 ( 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 424 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 328 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 281 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7731 (mm110) REVERT: B 282 MET cc_start: 0.8934 (tpp) cc_final: 0.8487 (tpp) REVERT: B 308 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7586 (mmt180) REVERT: B 310 LEU cc_start: 0.8146 (tp) cc_final: 0.7787 (mp) REVERT: B 366 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7503 (tt) REVERT: B 368 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7841 (ptm160) REVERT: B 409 GLU cc_start: 0.8155 (tp30) cc_final: 0.7648 (tp30) REVERT: B 410 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7863 (tp30) REVERT: B 413 ARG cc_start: 0.7783 (mtp180) cc_final: 0.7567 (mtm110) REVERT: B 440 ARG cc_start: 0.7940 (ttt180) cc_final: 0.7736 (tmt170) REVERT: B 548 LEU cc_start: 0.7283 (mt) cc_final: 0.7011 (mt) REVERT: B 559 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7768 (mt-10) REVERT: D 191 TYR cc_start: 0.9231 (t80) cc_final: 0.8783 (t80) REVERT: D 304 ARG cc_start: 0.8547 (tpp-160) cc_final: 0.8165 (tpp-160) REVERT: D 310 LEU cc_start: 0.7923 (tp) cc_final: 0.7465 (mm) REVERT: D 366 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7458 (tt) REVERT: D 368 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7864 (ptm160) REVERT: D 380 ASN cc_start: 0.8720 (m-40) cc_final: 0.8442 (m110) REVERT: D 413 ARG cc_start: 0.7891 (mtm110) cc_final: 0.7612 (mtp180) REVERT: D 431 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.6939 (mp) REVERT: D 478 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.9014 (ptt90) REVERT: D 559 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7606 (mm-30) REVERT: F 197 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8831 (mtmm) REVERT: F 269 TRP cc_start: 0.6847 (OUTLIER) cc_final: 0.6504 (t60) REVERT: F 280 TRP cc_start: 0.8166 (t-100) cc_final: 0.7249 (t60) REVERT: F 366 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7573 (tt) REVERT: F 368 ARG cc_start: 0.8003 (ttm110) cc_final: 0.7445 (ptm160) REVERT: F 395 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7137 (mtm180) REVERT: F 431 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7690 (pp) REVERT: F 478 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8956 (ptt90) REVERT: F 548 LEU cc_start: 0.7040 (mt) cc_final: 0.6686 (mt) REVERT: H 281 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7741 (mm110) REVERT: H 282 MET cc_start: 0.8938 (tpp) cc_final: 0.8493 (tpp) REVERT: H 310 LEU cc_start: 0.8093 (tp) cc_final: 0.7610 (mp) REVERT: H 366 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7486 (tt) REVERT: H 368 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7858 (ptm160) REVERT: H 399 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7919 (mtp180) REVERT: H 440 ARG cc_start: 0.7952 (ttt180) cc_final: 0.7675 (tmt170) REVERT: H 452 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8033 (mt) REVERT: H 548 LEU cc_start: 0.7258 (mt) cc_final: 0.6999 (mt) REVERT: J 191 TYR cc_start: 0.9239 (t80) cc_final: 0.8889 (t80) REVERT: J 210 ILE cc_start: 0.8220 (pp) cc_final: 0.7976 (mt) REVERT: J 269 TRP cc_start: 0.6430 (t60) cc_final: 0.5981 (t-100) REVERT: J 280 TRP cc_start: 0.8195 (t-100) cc_final: 0.7344 (t60) REVERT: J 281 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7450 (tp-100) REVERT: J 304 ARG cc_start: 0.8551 (tpp-160) cc_final: 0.8337 (tpp-160) REVERT: J 367 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7757 (m-70) REVERT: J 368 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7864 (ptm160) REVERT: J 380 ASN cc_start: 0.8698 (m-40) cc_final: 0.8406 (m110) REVERT: J 409 GLU cc_start: 0.8217 (tp30) cc_final: 0.7861 (tt0) REVERT: J 422 ASN cc_start: 0.8568 (m-40) cc_final: 0.8191 (m110) REVERT: J 431 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.6965 (mp) REVERT: J 478 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.9004 (ptt90) REVERT: J 559 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7529 (mm-30) REVERT: J 648 TYR cc_start: 0.8178 (m-80) cc_final: 0.7967 (m-80) REVERT: L 197 LYS cc_start: 0.9111 (mttm) cc_final: 0.8852 (mtmm) REVERT: L 269 TRP cc_start: 0.7029 (t60) cc_final: 0.6756 (t60) REVERT: L 280 TRP cc_start: 0.8105 (t-100) cc_final: 0.7179 (t60) REVERT: L 281 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7848 (mm-40) REVERT: L 366 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7660 (tt) REVERT: L 368 ARG cc_start: 0.7471 (ttt90) cc_final: 0.7093 (ttm-80) REVERT: L 422 ASN cc_start: 0.8504 (m-40) cc_final: 0.8184 (m110) REVERT: L 431 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7653 (pp) REVERT: L 440 ARG cc_start: 0.7438 (ttt180) cc_final: 0.7171 (tpt170) REVERT: L 478 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8952 (ptt90) REVERT: L 548 LEU cc_start: 0.6715 (mt) cc_final: 0.6504 (mt) REVERT: L 571 ARG cc_start: 0.8188 (tpt170) cc_final: 0.7791 (tpt170) REVERT: L 587 MET cc_start: 0.8742 (mtm) cc_final: 0.8496 (mtm) outliers start: 96 outliers final: 38 residues processed: 393 average time/residue: 0.7022 time to fit residues: 311.6190 Evaluate side-chains 379 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 316 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 221 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 372 THR Chi-restraints excluded: chain D residue 431 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 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 269 TRP Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 395 ARG 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 H residue 220 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 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 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 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: 4.9990 chunk 85 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 127 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 149 optimal weight: 0.2980 chunk 125 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 GLN L 380 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.162393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127479 restraints weight = 25824.352| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.88 r_work: 0.3138 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22842 Z= 0.155 Angle : 0.583 11.093 31068 Z= 0.273 Chirality : 0.045 0.371 3558 Planarity : 0.004 0.055 3678 Dihedral : 12.413 146.953 4350 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 4.37 % Allowed : 16.71 % Favored : 78.92 % 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: 1.64 (0.17), residues: 2496 helix: 1.66 (0.12), residues: 1764 sheet: None (None), residues: 0 loop : -0.23 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 570 TYR 0.014 0.001 TYR B 600 PHE 0.028 0.001 PHE B 442 TRP 0.022 0.001 TRP B 269 HIS 0.006 0.001 HIS B 588 Details of bonding type rmsd covalent geometry : bond 0.00365 (22842) covalent geometry : angle 0.58324 (31068) hydrogen bonds : bond 0.03497 ( 1314) hydrogen bonds : angle 4.09321 ( 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 431 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 330 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ILE cc_start: 0.5384 (OUTLIER) cc_final: 0.5089 (tt) REVERT: B 281 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7688 (mm110) REVERT: B 282 MET cc_start: 0.8970 (tpp) cc_final: 0.8517 (tpp) REVERT: B 310 LEU cc_start: 0.8235 (tp) cc_final: 0.7868 (mp) REVERT: B 366 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7531 (tt) REVERT: B 368 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7821 (ptm160) REVERT: B 409 GLU cc_start: 0.8187 (tp30) cc_final: 0.7709 (tp30) REVERT: B 410 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7976 (tp30) REVERT: B 440 ARG cc_start: 0.7986 (ttt180) cc_final: 0.7693 (tmt170) REVERT: B 548 LEU cc_start: 0.7285 (mt) cc_final: 0.7025 (mt) REVERT: B 559 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7769 (mt-10) REVERT: D 304 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.8171 (tpp-160) REVERT: D 310 LEU cc_start: 0.8045 (tp) cc_final: 0.7574 (mm) REVERT: D 366 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7317 (tt) REVERT: D 367 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7896 (m-70) REVERT: D 368 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7814 (ptm160) REVERT: D 380 ASN cc_start: 0.8750 (m-40) cc_final: 0.8431 (m-40) REVERT: D 431 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.6975 (mp) REVERT: D 559 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7606 (mm-30) REVERT: F 269 TRP cc_start: 0.6896 (OUTLIER) cc_final: 0.6623 (t60) REVERT: F 280 TRP cc_start: 0.8211 (t-100) cc_final: 0.7359 (t60) REVERT: F 366 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7596 (tt) REVERT: F 368 ARG cc_start: 0.8002 (ttm110) cc_final: 0.7760 (ptm160) REVERT: F 421 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7972 (mp) REVERT: F 478 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.9081 (ptt90) REVERT: F 548 LEU cc_start: 0.6984 (mt) cc_final: 0.6662 (mt) REVERT: H 281 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7731 (mm110) REVERT: H 282 MET cc_start: 0.8971 (tpp) cc_final: 0.8522 (tpp) REVERT: H 310 LEU cc_start: 0.8199 (tp) cc_final: 0.7921 (mp) REVERT: H 366 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7522 (tt) REVERT: H 368 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7824 (ptm160) REVERT: H 399 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7927 (mtp180) REVERT: H 440 ARG cc_start: 0.8035 (ttt180) cc_final: 0.7720 (tmt170) REVERT: H 452 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7996 (mt) REVERT: H 548 LEU cc_start: 0.7114 (mt) cc_final: 0.6890 (mt) REVERT: J 210 ILE cc_start: 0.8287 (pp) cc_final: 0.8026 (mt) REVERT: J 269 TRP cc_start: 0.6460 (t60) cc_final: 0.6056 (t-100) REVERT: J 280 TRP cc_start: 0.8090 (t-100) cc_final: 0.7271 (t60) REVERT: J 281 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7355 (tp-100) REVERT: J 304 ARG cc_start: 0.8574 (tpp-160) cc_final: 0.8359 (tpp-160) REVERT: J 367 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7831 (m-70) REVERT: J 368 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7811 (ptm160) REVERT: J 380 ASN cc_start: 0.8747 (m-40) cc_final: 0.8435 (m110) REVERT: J 409 GLU cc_start: 0.8256 (tp30) cc_final: 0.7851 (tt0) REVERT: J 422 ASN cc_start: 0.8591 (m-40) cc_final: 0.8345 (m110) REVERT: J 431 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.6904 (mp) REVERT: J 559 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7564 (mm-30) REVERT: L 269 TRP cc_start: 0.7087 (OUTLIER) cc_final: 0.6744 (t60) REVERT: L 280 TRP cc_start: 0.8173 (t-100) cc_final: 0.7331 (t60) REVERT: L 281 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7853 (mm-40) REVERT: L 366 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7684 (tt) REVERT: L 368 ARG cc_start: 0.7475 (ttt90) cc_final: 0.7099 (ttm-80) REVERT: L 440 ARG cc_start: 0.7420 (ttt180) cc_final: 0.7063 (tpt170) REVERT: L 478 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.9066 (ptt90) REVERT: L 587 MET cc_start: 0.8800 (mtm) cc_final: 0.8581 (mtm) outliers start: 101 outliers final: 47 residues processed: 395 average time/residue: 0.6964 time to fit residues: 311.3043 Evaluate side-chains 381 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 310 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 624 THR 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 372 THR Chi-restraints excluded: chain D residue 431 ILE 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 254 THR Chi-restraints excluded: chain F residue 258 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 624 THR Chi-restraints excluded: chain H residue 220 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 269 TRP Chi-restraints excluded: chain L residue 273 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 245 optimal weight: 7.9990 chunk 167 optimal weight: 0.0770 chunk 243 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 222 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 380 ASN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 380 ASN L 205 HIS L 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.163221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128543 restraints weight = 25832.389| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.87 r_work: 0.3191 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22842 Z= 0.106 Angle : 0.546 11.359 31068 Z= 0.253 Chirality : 0.043 0.358 3558 Planarity : 0.004 0.038 3678 Dihedral : 12.016 145.783 4350 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.77 % Allowed : 17.84 % 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: 1.88 (0.17), residues: 2496 helix: 1.82 (0.12), residues: 1770 sheet: None (None), residues: 0 loop : -0.11 (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 F 600 PHE 0.025 0.001 PHE D 442 TRP 0.030 0.001 TRP D 269 HIS 0.004 0.001 HIS D 473 Details of bonding type rmsd covalent geometry : bond 0.00231 (22842) covalent geometry : angle 0.54607 (31068) hydrogen bonds : bond 0.03095 ( 1314) hydrogen bonds : angle 3.87239 ( 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 404 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 317 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ILE cc_start: 0.5389 (OUTLIER) cc_final: 0.5080 (tt) REVERT: B 281 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7709 (mm110) REVERT: B 282 MET cc_start: 0.8938 (tpp) cc_final: 0.8502 (tpp) REVERT: B 308 ARG cc_start: 0.7874 (mmm-85) cc_final: 0.7628 (mmt180) REVERT: B 310 LEU cc_start: 0.8169 (tp) cc_final: 0.7814 (mp) REVERT: B 366 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7497 (tt) REVERT: B 368 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7822 (ptm160) REVERT: B 409 GLU cc_start: 0.8160 (tp30) cc_final: 0.7682 (tp30) REVERT: B 440 ARG cc_start: 0.7936 (ttt180) cc_final: 0.7687 (tmt170) REVERT: B 548 LEU cc_start: 0.7401 (mt) cc_final: 0.7137 (mt) REVERT: B 559 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7768 (mt-10) REVERT: D 191 TYR cc_start: 0.9255 (t80) cc_final: 0.8881 (t80) REVERT: D 304 ARG cc_start: 0.8556 (tpp-160) cc_final: 0.8185 (tpp-160) REVERT: D 310 LEU cc_start: 0.7946 (tp) cc_final: 0.7493 (mm) REVERT: D 366 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7432 (tt) REVERT: D 368 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7904 (ptm160) REVERT: D 380 ASN cc_start: 0.8681 (m-40) cc_final: 0.8425 (m110) REVERT: D 431 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7658 (mm) REVERT: D 559 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7626 (mm-30) REVERT: F 269 TRP cc_start: 0.6850 (OUTLIER) cc_final: 0.6543 (t60) REVERT: F 275 ASP cc_start: 0.8807 (t0) cc_final: 0.8550 (t0) REVERT: F 280 TRP cc_start: 0.8222 (t-100) cc_final: 0.7338 (t60) REVERT: F 366 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7587 (tt) REVERT: F 368 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7770 (ptm160) REVERT: F 413 ARG cc_start: 0.8371 (mtp180) cc_final: 0.7897 (mtm180) REVERT: F 431 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7659 (pp) REVERT: F 478 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8960 (ptt90) REVERT: F 548 LEU cc_start: 0.7011 (mt) cc_final: 0.6703 (mt) REVERT: F 570 ARG cc_start: 0.8680 (mtt90) cc_final: 0.8439 (mpt180) REVERT: H 281 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7715 (mm110) REVERT: H 282 MET cc_start: 0.8940 (tpp) cc_final: 0.8512 (tpp) REVERT: H 310 LEU cc_start: 0.8133 (tp) cc_final: 0.7877 (mp) REVERT: H 366 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7498 (tt) REVERT: H 368 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7859 (ptm160) REVERT: H 409 GLU cc_start: 0.8213 (tp30) cc_final: 0.7732 (tp30) REVERT: H 440 ARG cc_start: 0.7894 (ttt180) cc_final: 0.7644 (tmt170) REVERT: H 452 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7983 (mt) REVERT: H 548 LEU cc_start: 0.7346 (mt) cc_final: 0.7115 (mt) REVERT: H 623 PHE cc_start: 0.7848 (m-10) cc_final: 0.7573 (m-80) REVERT: J 191 TYR cc_start: 0.9244 (t80) cc_final: 0.8837 (t80) REVERT: J 210 ILE cc_start: 0.8172 (pp) cc_final: 0.7894 (mt) REVERT: J 269 TRP cc_start: 0.6522 (t60) cc_final: 0.6128 (t-100) REVERT: J 280 TRP cc_start: 0.8084 (t-100) cc_final: 0.7273 (t60) REVERT: J 281 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7420 (tp-100) REVERT: J 304 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8361 (tpp-160) REVERT: J 367 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7915 (m-70) REVERT: J 368 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7900 (ptm160) REVERT: J 380 ASN cc_start: 0.8679 (m-40) cc_final: 0.8395 (m110) REVERT: J 431 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.6920 (mp) REVERT: J 559 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7565 (mm-30) REVERT: J 648 TYR cc_start: 0.8185 (m-80) cc_final: 0.7958 (m-80) REVERT: L 269 TRP cc_start: 0.7081 (OUTLIER) cc_final: 0.6765 (t60) REVERT: L 280 TRP cc_start: 0.8145 (t-100) cc_final: 0.7284 (t60) REVERT: L 281 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7863 (mm-40) REVERT: L 366 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7688 (tt) REVERT: L 368 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7143 (ttm-80) REVERT: L 421 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7815 (mp) REVERT: L 431 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7683 (pp) REVERT: L 440 ARG cc_start: 0.7425 (ttt180) cc_final: 0.7062 (tpt170) REVERT: L 478 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8957 (ptt90) REVERT: L 566 GLU cc_start: 0.8049 (tt0) cc_final: 0.7604 (tt0) REVERT: L 587 MET cc_start: 0.8740 (mtm) cc_final: 0.8495 (mtm) outliers start: 87 outliers final: 40 residues processed: 373 average time/residue: 0.7228 time to fit residues: 303.9133 Evaluate side-chains 372 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 307 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 281 GLN Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 555 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 366 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 431 ILE 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 254 THR Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 366 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 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 221 THR Chi-restraints excluded: chain J residue 254 THR Chi-restraints excluded: chain J residue 258 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 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 269 TRP Chi-restraints excluded: chain L residue 273 LEU Chi-restraints excluded: chain L residue 281 GLN Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 421 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 555 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: 0.6980 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 0.0060 chunk 83 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 153 optimal weight: 0.0870 chunk 103 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 236 optimal weight: 0.0170 overall best weight: 0.3012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN F 209 GLN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN L 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.168117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.134438 restraints weight = 25748.365| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.83 r_work: 0.3294 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22842 Z= 0.093 Angle : 0.527 10.642 31068 Z= 0.243 Chirality : 0.041 0.345 3558 Planarity : 0.004 0.036 3678 Dihedral : 11.635 143.338 4350 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.73 % Allowed : 19.22 % Favored : 78.05 % 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: 2.12 (0.17), residues: 2496 helix: 1.95 (0.12), residues: 1812 sheet: None (None), residues: 0 loop : 0.01 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 570 TYR 0.011 0.001 TYR F 600 PHE 0.042 0.001 PHE B 442 TRP 0.035 0.001 TRP D 269 HIS 0.003 0.000 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00191 (22842) covalent geometry : angle 0.52747 (31068) hydrogen bonds : bond 0.02825 ( 1314) hydrogen bonds : angle 3.69457 ( 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 398 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 335 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ILE cc_start: 0.5499 (OUTLIER) cc_final: 0.5051 (tt) REVERT: B 280 TRP cc_start: 0.8188 (t-100) cc_final: 0.7233 (t60) REVERT: B 282 MET cc_start: 0.8933 (tpp) cc_final: 0.8475 (tpp) REVERT: B 308 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7588 (mmt180) REVERT: B 310 LEU cc_start: 0.8103 (tp) cc_final: 0.7790 (mp) REVERT: B 368 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7918 (ptm160) REVERT: B 409 GLU cc_start: 0.7981 (tp30) cc_final: 0.7601 (tp30) REVERT: B 548 LEU cc_start: 0.7367 (mt) cc_final: 0.7115 (mp) REVERT: B 559 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7629 (pt0) REVERT: D 191 TYR cc_start: 0.9182 (t80) cc_final: 0.8694 (t80) REVERT: D 281 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7269 (tp-100) REVERT: D 304 ARG cc_start: 0.8542 (tpp-160) cc_final: 0.8179 (tpp-160) REVERT: D 310 LEU cc_start: 0.7794 (tp) cc_final: 0.7359 (mm) REVERT: D 366 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7562 (tt) REVERT: D 368 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7952 (ptm160) REVERT: D 431 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7590 (tp) REVERT: D 437 ASN cc_start: 0.8312 (m-40) cc_final: 0.7887 (m110) REVERT: D 559 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7647 (mm-30) REVERT: F 269 TRP cc_start: 0.7131 (OUTLIER) cc_final: 0.6753 (t60) REVERT: F 275 ASP cc_start: 0.8733 (t0) cc_final: 0.8477 (t0) REVERT: F 280 TRP cc_start: 0.8192 (t-100) cc_final: 0.7227 (t60) REVERT: F 366 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7582 (tt) REVERT: F 413 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7886 (mtm180) REVERT: F 478 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.9007 (ptt90) REVERT: F 548 LEU cc_start: 0.6954 (mt) cc_final: 0.6686 (mt) REVERT: H 280 TRP cc_start: 0.8160 (t-100) cc_final: 0.7287 (t60) REVERT: H 281 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7679 (mm110) REVERT: H 282 MET cc_start: 0.8932 (tpp) cc_final: 0.8482 (tpp) REVERT: H 310 LEU cc_start: 0.8055 (tp) cc_final: 0.7772 (mp) REVERT: H 368 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7910 (ptm160) REVERT: H 409 GLU cc_start: 0.8162 (tp30) cc_final: 0.7730 (tp30) REVERT: H 548 LEU cc_start: 0.7144 (mt) cc_final: 0.6939 (mt) REVERT: J 191 TYR cc_start: 0.9205 (t80) cc_final: 0.8790 (t80) REVERT: J 210 ILE cc_start: 0.8198 (pp) cc_final: 0.7979 (mt) REVERT: J 269 TRP cc_start: 0.6178 (t60) cc_final: 0.5782 (t-100) REVERT: J 280 TRP cc_start: 0.8129 (t-100) cc_final: 0.7329 (t60) REVERT: J 304 ARG cc_start: 0.8571 (tpp-160) cc_final: 0.8295 (tpp-160) REVERT: J 367 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7945 (m-70) REVERT: J 368 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7848 (ptm160) REVERT: J 431 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7434 (pp) REVERT: J 437 ASN cc_start: 0.8312 (m-40) cc_final: 0.7933 (m110) REVERT: J 559 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7591 (mm-30) REVERT: J 623 PHE cc_start: 0.7776 (m-10) cc_final: 0.7553 (m-80) REVERT: L 269 TRP cc_start: 0.7074 (OUTLIER) cc_final: 0.6872 (t60) REVERT: L 280 TRP cc_start: 0.8065 (t-100) cc_final: 0.7146 (t60) REVERT: L 366 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7670 (tt) REVERT: L 391 GLN cc_start: 0.7431 (tm-30) cc_final: 0.7065 (tm-30) REVERT: L 413 ARG cc_start: 0.8242 (mtp180) cc_final: 0.7815 (mtm180) REVERT: L 440 ARG cc_start: 0.7408 (ttt180) cc_final: 0.7137 (tmt170) REVERT: L 571 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7836 (tpt170) outliers start: 63 outliers final: 27 residues processed: 370 average time/residue: 0.7363 time to fit residues: 306.4122 Evaluate side-chains 349 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 431 ILE Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 624 THR 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 269 TRP Chi-restraints excluded: chain F residue 366 LEU 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 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 254 THR Chi-restraints excluded: chain J residue 258 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 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 269 TRP Chi-restraints excluded: chain L residue 273 LEU Chi-restraints excluded: chain L residue 366 LEU Chi-restraints excluded: chain L residue 452 LEU 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: 8.9990 chunk 142 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 238 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 209 GLN L 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.160595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125725 restraints weight = 26010.073| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.85 r_work: 0.3133 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22842 Z= 0.172 Angle : 0.602 10.831 31068 Z= 0.286 Chirality : 0.046 0.355 3558 Planarity : 0.004 0.060 3678 Dihedral : 12.139 147.577 4350 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.51 % Allowed : 20.22 % Favored : 77.27 % 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: 1.88 (0.17), residues: 2496 helix: 1.75 (0.12), residues: 1800 sheet: None (None), residues: 0 loop : 0.01 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 399 TYR 0.015 0.001 TYR J 648 PHE 0.027 0.001 PHE J 222 TRP 0.034 0.001 TRP D 269 HIS 0.007 0.001 HIS J 473 Details of bonding type rmsd covalent geometry : bond 0.00408 (22842) covalent geometry : angle 0.60174 (31068) hydrogen bonds : bond 0.03501 ( 1314) hydrogen bonds : angle 4.07763 ( 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 378 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 320 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ILE cc_start: 0.5426 (OUTLIER) cc_final: 0.5016 (tt) REVERT: B 282 MET cc_start: 0.8981 (tpp) cc_final: 0.8523 (tpp) REVERT: B 308 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7664 (mmt180) REVERT: B 310 LEU cc_start: 0.8202 (tp) cc_final: 0.7848 (mp) REVERT: B 368 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7833 (ptm160) REVERT: B 409 GLU cc_start: 0.8036 (tp30) cc_final: 0.7587 (tp30) REVERT: B 548 LEU cc_start: 0.7409 (mt) cc_final: 0.7166 (mt) REVERT: B 559 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7757 (mt-10) REVERT: D 310 LEU cc_start: 0.8042 (tp) cc_final: 0.7564 (mm) REVERT: D 366 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7523 (tt) REVERT: D 367 HIS cc_start: 0.8235 (t70) cc_final: 0.7908 (m-70) REVERT: D 368 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7929 (ptm160) REVERT: D 380 ASN cc_start: 0.8642 (m-40) cc_final: 0.8345 (m-40) REVERT: D 431 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7019 (mp) REVERT: D 444 GLU cc_start: 0.7418 (mp0) cc_final: 0.7100 (mp0) REVERT: D 559 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7597 (mm-30) REVERT: F 269 TRP cc_start: 0.6943 (OUTLIER) cc_final: 0.6649 (t60) REVERT: F 280 TRP cc_start: 0.8216 (t-100) cc_final: 0.7357 (t60) REVERT: F 366 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7582 (tt) REVERT: F 413 ARG cc_start: 0.8449 (mtp180) cc_final: 0.8073 (mtm180) REVERT: F 478 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8955 (ptt90) REVERT: F 548 LEU cc_start: 0.7037 (mt) cc_final: 0.6747 (mt) REVERT: H 281 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7640 (mm110) REVERT: H 282 MET cc_start: 0.8989 (tpp) cc_final: 0.8522 (tpp) REVERT: H 283 ARG cc_start: 0.8113 (ttt-90) cc_final: 0.7784 (ttt180) REVERT: H 310 LEU cc_start: 0.8222 (tp) cc_final: 0.7949 (mp) REVERT: H 368 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7851 (ptm160) REVERT: H 409 GLU cc_start: 0.8326 (tp30) cc_final: 0.7839 (tt0) REVERT: H 548 LEU cc_start: 0.7220 (mt) cc_final: 0.7006 (mt) REVERT: H 623 PHE cc_start: 0.7595 (m-10) cc_final: 0.7287 (m-10) REVERT: J 210 ILE cc_start: 0.8244 (pp) cc_final: 0.7939 (mt) REVERT: J 269 TRP cc_start: 0.6485 (t60) cc_final: 0.6078 (t-100) REVERT: J 280 TRP cc_start: 0.8099 (t-100) cc_final: 0.7286 (t60) REVERT: J 367 HIS cc_start: 0.8207 (OUTLIER) cc_final: 0.7912 (m-70) REVERT: J 368 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7912 (ptm160) REVERT: J 380 ASN cc_start: 0.8688 (m-40) cc_final: 0.8384 (m110) REVERT: J 431 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.6963 (mp) REVERT: J 553 ARG cc_start: 0.7233 (mtm180) cc_final: 0.6985 (mtp85) REVERT: J 559 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7498 (mm-30) REVERT: J 623 PHE cc_start: 0.8120 (m-10) cc_final: 0.7883 (m-10) REVERT: L 269 TRP cc_start: 0.7029 (OUTLIER) cc_final: 0.6711 (t60) REVERT: L 280 TRP cc_start: 0.8193 (t-100) cc_final: 0.7301 (t60) REVERT: L 281 GLN cc_start: 0.8037 (mm110) cc_final: 0.7695 (mm-40) REVERT: L 366 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7645 (tt) REVERT: L 413 ARG cc_start: 0.8564 (mtp180) cc_final: 0.8128 (mtm180) REVERT: L 440 ARG cc_start: 0.7458 (ttt180) cc_final: 0.7078 (tpt170) REVERT: L 478 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8998 (ptt90) outliers start: 58 outliers final: 35 residues processed: 353 average time/residue: 0.7415 time to fit residues: 294.0361 Evaluate side-chains 353 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 302 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 368 ARG Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain D residue 281 GLN Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 368 ARG Chi-restraints excluded: chain D residue 372 THR Chi-restraints excluded: chain D residue 431 ILE 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 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 452 LEU Chi-restraints excluded: chain F residue 478 ARG Chi-restraints excluded: chain F residue 555 ILE 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 555 ILE 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 367 HIS Chi-restraints excluded: chain J residue 368 ARG Chi-restraints excluded: chain J residue 431 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 254 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 273 LEU Chi-restraints excluded: chain L residue 366 LEU 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: 4.9990 chunk 192 optimal weight: 0.6980 chunk 143 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 221 optimal weight: 0.7980 chunk 232 optimal weight: 8.9990 chunk 249 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 ASN ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN H 209 GLN H 380 ASN L 209 GLN L 360 ASN L 380 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.164703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130480 restraints weight = 25786.542| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.85 r_work: 0.3200 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22842 Z= 0.105 Angle : 0.550 10.237 31068 Z= 0.258 Chirality : 0.043 0.352 3558 Planarity : 0.004 0.064 3678 Dihedral : 11.831 145.698 4350 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 2.34 % Allowed : 20.56 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.17), residues: 2496 helix: 1.97 (0.12), residues: 1794 sheet: None (None), residues: 0 loop : 0.04 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 570 TYR 0.012 0.001 TYR F 600 PHE 0.040 0.001 PHE B 442 TRP 0.033 0.001 TRP D 269 HIS 0.003 0.001 HIS J 473 Details of bonding type rmsd covalent geometry : bond 0.00229 (22842) covalent geometry : angle 0.55010 (31068) hydrogen bonds : bond 0.03053 ( 1314) hydrogen bonds : angle 3.85756 ( 3834) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8518.90 seconds wall clock time: 145 minutes 49.27 seconds (8749.27 seconds total)