Starting phenix.real_space_refine on Fri Jul 3 19:08:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28yn_56974/07_2026/28yn_56974.cif Found real_map, /net/cci-nas-00/data/ceres_data/28yn_56974/07_2026/28yn_56974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/28yn_56974/07_2026/28yn_56974.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28yn_56974/07_2026/28yn_56974.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28yn_56974/07_2026/28yn_56974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28yn_56974/07_2026/28yn_56974.map" } resolution = 2.63 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 48 5.16 5 C 9522 2.51 5 N 2781 2.21 5 O 2883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15234 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5078 Classifications: {'peptide': 642} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 606} Chain: "B" Number of atoms: 5078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5078 Classifications: {'peptide': 642} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 606} Chain: "C" Number of atoms: 5078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5078 Classifications: {'peptide': 642} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 606} Time building chain proxies: 3.14, per 1000 atoms: 0.21 Number of scatterers: 15234 At special positions: 0 Unit cell: (91.98, 91.25, 185.42, 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 48 16.00 O 2883 8.00 N 2781 7.00 C 9522 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: 1.30 Conformation dependent library (CDL) restraints added in 782.8 milliseconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3474 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 19 sheets defined 12.5% alpha, 28.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 114 through 125 removed outlier: 3.572A pdb=" N LEU A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 Processing helix chain 'A' and resid 264 through 281 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 625 through 637 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 114 through 125 removed outlier: 3.634A pdb=" N LEU B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 264 through 281 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 114 through 125 removed outlier: 3.568A pdb=" N LEU C 125 " --> pdb=" O VAL C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 264 through 281 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 625 through 636 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 7 through 10 current: chain 'A' and resid 34 through 41 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 34 through 41 current: chain 'A' and resid 67 through 80 removed outlier: 6.837A pdb=" N THR A 92 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS A 77 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN A 90 " --> pdb=" O CYS A 77 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLN A 79 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLY A 88 " --> pdb=" O GLN A 79 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 87 through 94 current: chain 'A' and resid 284 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 291 current: chain 'A' and resid 314 through 325 removed outlier: 6.601A pdb=" N ASP A 345 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA A 320 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU A 343 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR A 322 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU A 341 " --> pdb=" O TYR A 322 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 324 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN A 339 " --> pdb=" O VAL A 324 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 339 through 348 current: chain 'B' and resid 34 through 41 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 34 through 41 current: chain 'B' and resid 67 through 80 removed outlier: 5.306A pdb=" N VAL B 74 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG B 94 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 76 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 80 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLY B 88 " --> pdb=" O VAL B 80 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 87 through 94 current: chain 'B' and resid 284 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 291 current: chain 'B' and resid 314 through 325 removed outlier: 6.577A pdb=" N ASP B 345 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA B 320 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU B 343 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR B 322 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU B 341 " --> pdb=" O TYR B 322 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 341 through 348 current: chain 'C' and resid 34 through 41 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 34 through 41 current: chain 'C' and resid 67 through 80 removed outlier: 6.851A pdb=" N THR C 92 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS C 77 " --> pdb=" O GLN C 90 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN C 90 " --> pdb=" O CYS C 77 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLN C 79 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLY C 88 " --> pdb=" O GLN C 79 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 87 through 94 current: chain 'C' and resid 284 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 291 current: chain 'C' and resid 314 through 325 removed outlier: 5.394A pdb=" N VAL C 317 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 347 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 325 " --> pdb=" O GLN C 339 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 109 removed outlier: 7.082A pdb=" N ASP A 105 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A 148 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243 removed outlier: 6.451A pdb=" N SER A 223 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASP A 257 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 225 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 392 removed outlier: 4.572A pdb=" N LYS A 389 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU A 430 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ARG A 448 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 432 " --> pdb=" O THR A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 420 through 422 removed outlier: 6.262A pdb=" N ASP B 519 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N LEU C 514 " --> pdb=" O ASP B 519 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASN B 521 " --> pdb=" O LEU C 514 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL C 516 " --> pdb=" O ASN B 521 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER B 523 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N LEU A 529 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE B 524 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG A 531 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 545 " --> pdb=" O ARG C 538 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL C 540 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU B 547 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER A 553 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL B 548 " --> pdb=" O SER A 553 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER A 555 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS A 552 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLU C 563 " --> pdb=" O LYS A 552 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASP A 554 " --> pdb=" O GLU C 563 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN B 567 " --> pdb=" O TYR C 560 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE C 562 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 569 " --> pdb=" O ILE C 562 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA C 564 " --> pdb=" O ARG B 569 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 571 " --> pdb=" O ALA C 564 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR B 584 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE A 592 " --> pdb=" O ASN C 601 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP C 603 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 594 " --> pdb=" O ASP C 603 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 608 through 610 removed outlier: 7.023A pdb=" N ILE A 585 " --> pdb=" O ASN C 593 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N TYR C 595 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 587 " --> pdb=" O TYR C 595 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 584 " --> pdb=" O ASN A 580 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN A 567 " --> pdb=" O TYR B 560 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE B 562 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG A 569 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA B 564 " --> pdb=" O ARG A 569 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 571 " --> pdb=" O ALA B 564 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A 545 " --> pdb=" O ARG B 538 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N VAL B 540 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 547 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR B 537 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE C 532 " --> pdb=" O THR B 537 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ALA B 539 " --> pdb=" O ILE C 532 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASP A 519 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU B 514 " --> pdb=" O ASP A 519 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A 521 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL B 516 " --> pdb=" O ASN A 521 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER A 523 " --> pdb=" O VAL B 516 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP B 511 " --> pdb=" O GLN C 504 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN C 506 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER B 513 " --> pdb=" O ASN C 506 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL C 508 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER B 515 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 496 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU C 507 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE A 498 " --> pdb=" O LEU C 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.430A pdb=" N ASP A 511 " --> pdb=" O GLN B 504 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ASN B 506 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N SER A 513 " --> pdb=" O ASN B 506 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL B 508 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N SER A 515 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 529 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE C 524 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG B 531 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR A 537 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE B 532 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA A 539 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER B 553 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL C 548 " --> pdb=" O SER B 553 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER B 555 " --> pdb=" O VAL C 548 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR A 559 " --> pdb=" O LYS B 552 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASP B 554 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 561 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N VAL B 556 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU A 563 " --> pdb=" O VAL B 556 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 584 " --> pdb=" O ASN C 580 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 591 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE C 587 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASN B 593 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY C 589 " --> pdb=" O ASN B 593 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR B 595 " --> pdb=" O GLY C 589 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY A 600 " --> pdb=" O ASP C 609 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 104 through 109 removed outlier: 7.047A pdb=" N ASP B 105 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 148 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 112 through 113 Processing sheet with id=AB3, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.445A pdb=" N SER B 223 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASP B 257 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR B 225 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 389 through 392 removed outlier: 4.579A pdb=" N LYS B 389 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLU B 430 " --> pdb=" O ARG B 448 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG B 448 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 432 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 104 through 109 removed outlier: 7.082A pdb=" N ASP C 105 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 148 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AB9, first strand: chain 'C' and resid 240 through 243 removed outlier: 6.464A pdb=" N SER C 223 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ASP C 257 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR C 225 " --> pdb=" O ASP C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 389 through 392 removed outlier: 4.563A pdb=" N LYS C 389 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLU C 430 " --> pdb=" O ARG C 448 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG C 448 " --> pdb=" O GLU C 430 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 432 " --> pdb=" O THR C 446 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1002 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: 2.74 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5301 1.34 - 1.46: 3438 1.46 - 1.58: 6780 1.58 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 15594 Sorted by residual: bond pdb=" CG LEU A 39 " pdb=" CD2 LEU A 39 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.09e+00 bond pdb=" CG ARG A 289 " pdb=" CD ARG A 289 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" CA ASN B 243 " pdb=" CB ASN B 243 " ideal model delta sigma weight residual 1.533 1.553 -0.020 2.29e-02 1.91e+03 7.26e-01 bond pdb=" CG ARG A 26 " pdb=" CD ARG A 26 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.72e-01 bond pdb=" CB PRO B 97 " pdb=" CG PRO B 97 " ideal model delta sigma weight residual 1.492 1.452 0.040 5.00e-02 4.00e+02 6.42e-01 ... (remaining 15589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 20870 1.89 - 3.78: 241 3.78 - 5.67: 15 5.67 - 7.56: 4 7.56 - 9.44: 2 Bond angle restraints: 21132 Sorted by residual: angle pdb=" CG ARG A 289 " pdb=" CD ARG A 289 " pdb=" NE ARG A 289 " ideal model delta sigma weight residual 112.00 118.56 -6.56 2.20e+00 2.07e-01 8.90e+00 angle pdb=" CB LEU A 18 " pdb=" CG LEU A 18 " pdb=" CD2 LEU A 18 " ideal model delta sigma weight residual 110.70 119.56 -8.86 3.00e+00 1.11e-01 8.72e+00 angle pdb=" CA LEU A 18 " pdb=" CB LEU A 18 " pdb=" CG LEU A 18 " ideal model delta sigma weight residual 116.30 125.74 -9.44 3.50e+00 8.16e-02 7.28e+00 angle pdb=" CB ARG A 289 " pdb=" CG ARG A 289 " pdb=" CD ARG A 289 " ideal model delta sigma weight residual 111.30 117.23 -5.93 2.30e+00 1.89e-01 6.65e+00 angle pdb=" CA GLN C 90 " pdb=" CB GLN C 90 " pdb=" CG GLN C 90 " ideal model delta sigma weight residual 114.10 118.78 -4.68 2.00e+00 2.50e-01 5.47e+00 ... (remaining 21127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 8126 17.84 - 35.67: 789 35.67 - 53.51: 265 53.51 - 71.35: 68 71.35 - 89.18: 37 Dihedral angle restraints: 9285 sinusoidal: 3807 harmonic: 5478 Sorted by residual: dihedral pdb=" CA PHE C 482 " pdb=" C PHE C 482 " pdb=" N ASN C 483 " pdb=" CA ASN C 483 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PHE A 482 " pdb=" C PHE A 482 " pdb=" N ASN A 483 " pdb=" CA ASN A 483 " ideal model delta harmonic sigma weight residual 180.00 160.71 19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PHE B 482 " pdb=" C PHE B 482 " pdb=" N ASN B 483 " pdb=" CA ASN B 483 " ideal model delta harmonic sigma weight residual 180.00 161.16 18.84 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 9282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2041 0.095 - 0.190: 142 0.190 - 0.284: 0 0.284 - 0.379: 0 0.379 - 0.474: 1 Chirality restraints: 2184 Sorted by residual: chirality pdb=" CG LEU A 18 " pdb=" CB LEU A 18 " pdb=" CD1 LEU A 18 " pdb=" CD2 LEU A 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CG LEU A 39 " pdb=" CB LEU A 39 " pdb=" CD1 LEU A 39 " pdb=" CD2 LEU A 39 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA LEU A 18 " pdb=" N LEU A 18 " pdb=" C LEU A 18 " pdb=" CB LEU A 18 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 2181 not shown) Planarity restraints: 2853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 289 " -0.168 9.50e-02 1.11e+02 7.60e-02 4.90e+00 pdb=" NE ARG A 289 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 289 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 289 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 289 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 479 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 478 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.35e+00 pdb=" N PRO C 479 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.026 5.00e-02 4.00e+02 ... (remaining 2850 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 7873 3.01 - 3.48: 14036 3.48 - 3.95: 26114 3.95 - 4.43: 30810 4.43 - 4.90: 51112 Nonbonded interactions: 129945 Sorted by model distance: nonbonded pdb=" N ASP A 252 " pdb=" OD1 ASP A 252 " model vdw 2.534 3.120 nonbonded pdb=" N ASN A 243 " pdb=" OD1 ASN A 243 " model vdw 2.551 3.120 nonbonded pdb=" N ASN C 243 " pdb=" OD1 ASN C 243 " model vdw 2.560 3.120 nonbonded pdb=" N ASP B 252 " pdb=" OD1 ASP B 252 " model vdw 2.563 3.120 nonbonded pdb=" N ASN B 243 " pdb=" OD1 ASN B 243 " model vdw 2.564 3.120 ... (remaining 129940 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 12.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.680 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15594 Z= 0.121 Angle : 0.521 9.444 21132 Z= 0.280 Chirality : 0.045 0.474 2184 Planarity : 0.004 0.076 2853 Dihedral : 17.236 89.182 5811 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.68 % Allowed : 19.50 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 1920 helix: 2.46 (0.40), residues: 177 sheet: -0.30 (0.22), residues: 570 loop : 0.14 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG A 289 TYR 0.015 0.001 TYR C 89 PHE 0.010 0.001 PHE A 211 TRP 0.012 0.001 TRP C 96 HIS 0.003 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15594) covalent geometry : angle 0.52108 / 0.28 (21132) hydrogen bonds : bond 0.12125 / 8.07 ( 394) hydrogen bonds : angle 6.81895 / 4.90 ( 1002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.534 Fit side-chains REVERT: A 21 GLN cc_start: 0.7278 (tt0) cc_final: 0.6425 (tm-30) REVERT: A 38 HIS cc_start: 0.6749 (t-90) cc_final: 0.5406 (m90) REVERT: A 67 ARG cc_start: 0.7330 (mtp85) cc_final: 0.6615 (mtt-85) REVERT: A 131 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7592 (mm-30) REVERT: A 237 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7304 (ttp80) REVERT: A 261 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7782 (mt-10) REVERT: A 341 GLU cc_start: 0.8613 (mm-30) cc_final: 0.7510 (tm-30) REVERT: A 345 ASP cc_start: 0.7683 (t70) cc_final: 0.7319 (t0) REVERT: A 459 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7635 (tm-30) REVERT: A 490 LYS cc_start: 0.7891 (tttt) cc_final: 0.7561 (tptm) REVERT: B 8 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.5760 (mt0) REVERT: B 38 HIS cc_start: 0.6844 (t-90) cc_final: 0.5627 (m90) REVERT: B 90 GLN cc_start: 0.7768 (mp10) cc_final: 0.7556 (mp10) REVERT: B 124 ASN cc_start: 0.8276 (m-40) cc_final: 0.7732 (t0) REVERT: B 261 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6886 (mm-30) REVERT: B 341 GLU cc_start: 0.8618 (mm-30) cc_final: 0.7468 (tm-30) REVERT: B 345 ASP cc_start: 0.7789 (t70) cc_final: 0.7248 (t0) REVERT: B 490 LYS cc_start: 0.7791 (tttt) cc_final: 0.7473 (tptm) REVERT: C 38 HIS cc_start: 0.6963 (t-90) cc_final: 0.5677 (m90) REVERT: C 172 GLN cc_start: 0.7598 (tt0) cc_final: 0.7375 (tt0) REVERT: C 237 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7194 (ttp80) REVERT: C 261 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7744 (mt-10) REVERT: C 345 ASP cc_start: 0.7807 (t70) cc_final: 0.7274 (t0) REVERT: C 417 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8454 (ttpp) REVERT: C 459 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7601 (tm-30) REVERT: C 574 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7689 (mtmt) REVERT: C 618 VAL cc_start: 0.7888 (m) cc_final: 0.7593 (p) outliers start: 27 outliers final: 16 residues processed: 158 average time/residue: 0.8721 time to fit residues: 148.0366 Evaluate side-chains 157 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 351 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN C 21 GLN C 567 GLN C 580 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.093977 restraints weight = 19642.675| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.12 r_work: 0.3029 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15594 Z= 0.181 Angle : 0.521 6.859 21132 Z= 0.276 Chirality : 0.044 0.136 2184 Planarity : 0.004 0.044 2853 Dihedral : 5.740 49.107 2194 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.30 % Allowed : 17.63 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1920 helix: 2.36 (0.41), residues: 177 sheet: -0.44 (0.21), residues: 588 loop : 0.09 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.013 0.002 TYR B 306 PHE 0.014 0.002 PHE A 592 TRP 0.009 0.001 TRP B 96 HIS 0.004 0.001 HIS B 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (15594) covalent geometry : angle 0.52085 / 0.28 (21132) hydrogen bonds : bond 0.03461 / 2.34 ( 394) hydrogen bonds : angle 5.30484 / 3.83 ( 1002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 147 time to evaluate : 0.674 Fit side-chains REVERT: A 22 ARG cc_start: 0.7189 (ttm170) cc_final: 0.6542 (mtp85) REVERT: A 38 HIS cc_start: 0.6840 (t-90) cc_final: 0.5571 (m90) REVERT: A 39 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6229 (tt) REVERT: A 131 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7555 (mm-30) REVERT: A 341 GLU cc_start: 0.8651 (mm-30) cc_final: 0.7546 (tm-30) REVERT: A 345 ASP cc_start: 0.7777 (t70) cc_final: 0.7276 (t0) REVERT: A 459 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7608 (tm-30) REVERT: A 490 LYS cc_start: 0.7873 (tttt) cc_final: 0.7551 (tptm) REVERT: B 8 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.5963 (mt0) REVERT: B 38 HIS cc_start: 0.7194 (t-90) cc_final: 0.6046 (m90) REVERT: B 90 GLN cc_start: 0.7778 (mp10) cc_final: 0.7533 (mp10) REVERT: B 124 ASN cc_start: 0.8303 (m-40) cc_final: 0.7705 (t0) REVERT: B 136 ARG cc_start: 0.7280 (mtm110) cc_final: 0.6674 (ptt-90) REVERT: B 261 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6976 (mm-30) REVERT: B 341 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: B 345 ASP cc_start: 0.7891 (t70) cc_final: 0.7341 (t0) REVERT: B 490 LYS cc_start: 0.7841 (tttt) cc_final: 0.7519 (tptm) REVERT: B 634 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7859 (mp-120) REVERT: C 8 GLN cc_start: 0.6903 (OUTLIER) cc_final: 0.6011 (mt0) REVERT: C 38 HIS cc_start: 0.7237 (t-90) cc_final: 0.5963 (m90) REVERT: C 172 GLN cc_start: 0.7662 (tt0) cc_final: 0.7425 (tt0) REVERT: C 269 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: C 345 ASP cc_start: 0.7873 (t70) cc_final: 0.7359 (t0) REVERT: C 459 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7536 (tm-30) REVERT: C 574 LYS cc_start: 0.8329 (mtpt) cc_final: 0.7758 (mtmt) outliers start: 53 outliers final: 22 residues processed: 178 average time/residue: 0.8282 time to fit residues: 159.0732 Evaluate side-chains 167 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 634 GLN Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 542 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 156 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.124453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093048 restraints weight = 19831.700| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.13 r_work: 0.3016 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15594 Z= 0.201 Angle : 0.529 7.598 21132 Z= 0.280 Chirality : 0.045 0.133 2184 Planarity : 0.004 0.056 2853 Dihedral : 5.387 48.459 2177 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.68 % Allowed : 17.76 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.19), residues: 1920 helix: 2.22 (0.41), residues: 177 sheet: -0.45 (0.21), residues: 582 loop : -0.00 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 289 TYR 0.014 0.002 TYR B 306 PHE 0.014 0.002 PHE B 592 TRP 0.010 0.001 TRP B 96 HIS 0.004 0.001 HIS B 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (15594) covalent geometry : angle 0.52929 / 0.28 (21132) hydrogen bonds : bond 0.03570 / 2.43 ( 394) hydrogen bonds : angle 5.15990 / 3.72 ( 1002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 142 time to evaluate : 0.566 Fit side-chains REVERT: A 38 HIS cc_start: 0.6948 (t-90) cc_final: 0.5714 (m90) REVERT: A 131 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7470 (mm-30) REVERT: A 341 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7516 (tm-30) REVERT: A 345 ASP cc_start: 0.7819 (t70) cc_final: 0.7309 (t0) REVERT: A 459 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 490 LYS cc_start: 0.7871 (tttt) cc_final: 0.7575 (tptm) REVERT: B 8 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6043 (mt0) REVERT: B 38 HIS cc_start: 0.7221 (t-90) cc_final: 0.6073 (m90) REVERT: B 90 GLN cc_start: 0.7787 (mp10) cc_final: 0.7556 (mp10) REVERT: B 124 ASN cc_start: 0.8315 (m-40) cc_final: 0.7713 (t0) REVERT: B 161 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: B 261 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7037 (mm-30) REVERT: B 341 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: B 345 ASP cc_start: 0.7884 (t70) cc_final: 0.7339 (t0) REVERT: B 433 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8812 (t) REVERT: B 490 LYS cc_start: 0.7872 (tttt) cc_final: 0.7553 (tptm) REVERT: C 8 GLN cc_start: 0.6982 (OUTLIER) cc_final: 0.6115 (mt0) REVERT: C 38 HIS cc_start: 0.7167 (t-90) cc_final: 0.5992 (m90) REVERT: C 261 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7299 (mm-30) REVERT: C 345 ASP cc_start: 0.7927 (t70) cc_final: 0.7422 (t0) REVERT: C 417 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8522 (ttpp) REVERT: C 433 VAL cc_start: 0.8993 (OUTLIER) cc_final: 0.8784 (t) REVERT: C 459 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7508 (tm-30) REVERT: C 490 LYS cc_start: 0.7880 (tttt) cc_final: 0.7506 (tptm) REVERT: C 574 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7753 (mtmt) REVERT: C 618 VAL cc_start: 0.8027 (m) cc_final: 0.7771 (p) outliers start: 59 outliers final: 25 residues processed: 177 average time/residue: 0.8162 time to fit residues: 156.0611 Evaluate side-chains 172 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 542 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 170 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.124913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.093623 restraints weight = 19702.335| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.12 r_work: 0.3023 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15594 Z= 0.163 Angle : 0.501 6.956 21132 Z= 0.266 Chirality : 0.044 0.134 2184 Planarity : 0.004 0.045 2853 Dihedral : 5.276 48.271 2177 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.68 % Allowed : 17.76 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % 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: 0.04 (0.19), residues: 1920 helix: 2.31 (0.41), residues: 177 sheet: -0.48 (0.21), residues: 579 loop : 0.04 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 136 TYR 0.013 0.001 TYR B 306 PHE 0.012 0.002 PHE B 592 TRP 0.009 0.001 TRP B 96 HIS 0.003 0.001 HIS B 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (15594) covalent geometry : angle 0.50129 / 0.27 (21132) hydrogen bonds : bond 0.03178 / 2.16 ( 394) hydrogen bonds : angle 4.93372 / 3.57 ( 1002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 148 time to evaluate : 0.783 Fit side-chains REVERT: A 38 HIS cc_start: 0.6993 (t-90) cc_final: 0.5679 (m90) REVERT: A 89 TYR cc_start: 0.7831 (m-80) cc_final: 0.7535 (m-80) REVERT: A 90 GLN cc_start: 0.7887 (mp10) cc_final: 0.7509 (mt0) REVERT: A 94 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7725 (mtt-85) REVERT: A 131 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7437 (mm-30) REVERT: A 261 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: A 341 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: A 345 ASP cc_start: 0.7806 (t70) cc_final: 0.7298 (t0) REVERT: A 459 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 490 LYS cc_start: 0.7896 (tttt) cc_final: 0.7558 (tptm) REVERT: B 8 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6067 (mt0) REVERT: B 38 HIS cc_start: 0.7217 (t-90) cc_final: 0.6128 (m90) REVERT: B 90 GLN cc_start: 0.7787 (mp10) cc_final: 0.7560 (mp10) REVERT: B 124 ASN cc_start: 0.8308 (m-40) cc_final: 0.7720 (t0) REVERT: B 136 ARG cc_start: 0.7414 (mtm110) cc_final: 0.7042 (ptt-90) REVERT: B 161 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8494 (tt0) REVERT: B 261 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6993 (mm-30) REVERT: B 341 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: B 345 ASP cc_start: 0.7938 (t70) cc_final: 0.7358 (t0) REVERT: B 490 LYS cc_start: 0.7877 (tttt) cc_final: 0.7552 (tptm) REVERT: C 8 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6173 (mt0) REVERT: C 38 HIS cc_start: 0.7240 (t-90) cc_final: 0.6069 (m90) REVERT: C 261 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: C 269 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: C 345 ASP cc_start: 0.7937 (t70) cc_final: 0.7441 (t0) REVERT: C 459 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7506 (tm-30) REVERT: C 490 LYS cc_start: 0.7863 (tttt) cc_final: 0.7559 (tptm) REVERT: C 491 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8365 (tptt) REVERT: C 574 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7751 (mtmt) REVERT: C 618 VAL cc_start: 0.8038 (m) cc_final: 0.7776 (p) outliers start: 59 outliers final: 26 residues processed: 183 average time/residue: 0.8125 time to fit residues: 160.6931 Evaluate side-chains 177 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 140 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 491 LYS Chi-restraints excluded: chain C residue 542 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 61 optimal weight: 0.0060 chunk 11 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 280 GLN A 580 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094900 restraints weight = 19701.342| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.13 r_work: 0.3054 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15594 Z= 0.113 Angle : 0.465 6.369 21132 Z= 0.247 Chirality : 0.043 0.201 2184 Planarity : 0.004 0.044 2853 Dihedral : 5.006 45.910 2175 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.99 % Allowed : 18.38 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 1920 helix: 2.46 (0.41), residues: 177 sheet: -0.48 (0.22), residues: 582 loop : 0.13 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 136 TYR 0.011 0.001 TYR B 306 PHE 0.010 0.001 PHE C 231 TRP 0.009 0.001 TRP B 96 HIS 0.003 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (15594) covalent geometry : angle 0.46531 / 0.25 (21132) hydrogen bonds : bond 0.02793 / 1.90 ( 394) hydrogen bonds : angle 4.72061 / 3.41 ( 1002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 0.581 Fit side-chains REVERT: A 38 HIS cc_start: 0.6936 (t-90) cc_final: 0.5643 (m90) REVERT: A 90 GLN cc_start: 0.7837 (mp10) cc_final: 0.7461 (mt0) REVERT: A 131 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7390 (mm-30) REVERT: A 136 ARG cc_start: 0.7164 (mtm110) cc_final: 0.6685 (ptt-90) REVERT: A 341 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: A 345 ASP cc_start: 0.7783 (t70) cc_final: 0.7239 (t0) REVERT: A 459 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7600 (tm-30) REVERT: A 490 LYS cc_start: 0.7884 (tttt) cc_final: 0.7532 (tptm) REVERT: B 8 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6155 (mt0) REVERT: B 38 HIS cc_start: 0.7152 (t-90) cc_final: 0.6073 (m90) REVERT: B 90 GLN cc_start: 0.7852 (mp10) cc_final: 0.7618 (mp10) REVERT: B 124 ASN cc_start: 0.8283 (m-40) cc_final: 0.7701 (t0) REVERT: B 161 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: B 261 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: B 341 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7523 (tm-30) REVERT: B 345 ASP cc_start: 0.7883 (t70) cc_final: 0.7280 (t0) REVERT: B 490 LYS cc_start: 0.7857 (tttt) cc_final: 0.7534 (tptm) REVERT: C 8 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6143 (mt0) REVERT: C 38 HIS cc_start: 0.7229 (t-90) cc_final: 0.6069 (m90) REVERT: C 261 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7266 (mm-30) REVERT: C 345 ASP cc_start: 0.7889 (t70) cc_final: 0.7372 (t0) REVERT: C 417 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8543 (ttpp) REVERT: C 459 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7536 (tm-30) REVERT: C 574 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7708 (mtmt) REVERT: C 618 VAL cc_start: 0.7960 (m) cc_final: 0.7673 (p) outliers start: 48 outliers final: 21 residues processed: 177 average time/residue: 0.7762 time to fit residues: 148.2061 Evaluate side-chains 172 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 181 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.125884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094587 restraints weight = 19698.513| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.13 r_work: 0.3048 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15594 Z= 0.129 Angle : 0.473 6.479 21132 Z= 0.251 Chirality : 0.043 0.153 2184 Planarity : 0.004 0.043 2853 Dihedral : 4.944 45.251 2174 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.80 % Allowed : 18.38 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % 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: 0.12 (0.19), residues: 1920 helix: 2.46 (0.41), residues: 177 sheet: -0.43 (0.22), residues: 579 loop : 0.09 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 289 TYR 0.012 0.001 TYR A 306 PHE 0.011 0.002 PHE A 33 TRP 0.009 0.001 TRP B 96 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (15594) covalent geometry : angle 0.47346 / 0.25 (21132) hydrogen bonds : bond 0.02867 / 1.95 ( 394) hydrogen bonds : angle 4.66524 / 3.38 ( 1002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.552 Fit side-chains REVERT: A 38 HIS cc_start: 0.7006 (t-90) cc_final: 0.5666 (m90) REVERT: A 90 GLN cc_start: 0.7811 (mp10) cc_final: 0.7471 (mt0) REVERT: A 131 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7357 (mm-30) REVERT: A 136 ARG cc_start: 0.7152 (mtm110) cc_final: 0.6701 (ptt-90) REVERT: A 266 GLN cc_start: 0.7711 (mp10) cc_final: 0.7409 (mp10) REVERT: A 341 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.7547 (tm-30) REVERT: A 345 ASP cc_start: 0.7785 (t70) cc_final: 0.7245 (t0) REVERT: A 459 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 490 LYS cc_start: 0.7866 (tttt) cc_final: 0.7514 (tptm) REVERT: B 8 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6186 (mt0) REVERT: B 38 HIS cc_start: 0.7167 (t-90) cc_final: 0.6073 (m90) REVERT: B 90 GLN cc_start: 0.7844 (mp10) cc_final: 0.7547 (mt0) REVERT: B 124 ASN cc_start: 0.8285 (m-40) cc_final: 0.7703 (t0) REVERT: B 261 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.6989 (mm-30) REVERT: B 341 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: B 345 ASP cc_start: 0.7920 (t70) cc_final: 0.7328 (t0) REVERT: B 490 LYS cc_start: 0.7849 (tttt) cc_final: 0.7526 (tptm) REVERT: B 528 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: C 8 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6174 (mt0) REVERT: C 38 HIS cc_start: 0.7245 (t-90) cc_final: 0.6106 (m90) REVERT: C 89 TYR cc_start: 0.7788 (m-80) cc_final: 0.7509 (m-80) REVERT: C 237 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7623 (mtp85) REVERT: C 261 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: C 345 ASP cc_start: 0.7885 (t70) cc_final: 0.7372 (t0) REVERT: C 417 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8524 (ttpp) REVERT: C 459 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7528 (tm-30) REVERT: C 574 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7705 (mtmt) outliers start: 45 outliers final: 21 residues processed: 170 average time/residue: 0.7534 time to fit residues: 138.3823 Evaluate side-chains 172 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 528 GLU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 61 optimal weight: 0.0060 chunk 169 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 481 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.092028 restraints weight = 19625.289| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.12 r_work: 0.3012 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15594 Z= 0.222 Angle : 0.542 7.465 21132 Z= 0.287 Chirality : 0.045 0.201 2184 Planarity : 0.004 0.043 2853 Dihedral : 5.267 46.570 2174 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.87 % Allowed : 18.13 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % 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: -0.02 (0.19), residues: 1920 helix: 2.19 (0.41), residues: 177 sheet: -0.48 (0.21), residues: 588 loop : -0.00 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.015 0.002 TYR A 306 PHE 0.016 0.002 PHE C 592 TRP 0.010 0.001 TRP B 213 HIS 0.005 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (15594) covalent geometry : angle 0.54180 / 0.29 (21132) hydrogen bonds : bond 0.03520 / 2.39 ( 394) hydrogen bonds : angle 4.90708 / 3.55 ( 1002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.468 Fit side-chains REVERT: A 38 HIS cc_start: 0.7077 (t-90) cc_final: 0.5720 (m90) REVERT: A 90 GLN cc_start: 0.7846 (mp10) cc_final: 0.7475 (mt0) REVERT: A 131 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7409 (mm-30) REVERT: A 136 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6720 (ptt-90) REVERT: A 261 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: A 341 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7568 (tm-30) REVERT: A 345 ASP cc_start: 0.7844 (t70) cc_final: 0.7431 (t0) REVERT: A 459 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7485 (tm-30) REVERT: A 490 LYS cc_start: 0.7901 (tttt) cc_final: 0.7542 (tptm) REVERT: B 8 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6241 (mt0) REVERT: B 38 HIS cc_start: 0.7222 (t-90) cc_final: 0.6169 (m90) REVERT: B 90 GLN cc_start: 0.7838 (mp10) cc_final: 0.7588 (mt0) REVERT: B 124 ASN cc_start: 0.8310 (m-40) cc_final: 0.7728 (t0) REVERT: B 261 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: B 341 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: B 345 ASP cc_start: 0.7982 (t70) cc_final: 0.7444 (t0) REVERT: B 490 LYS cc_start: 0.7885 (tttt) cc_final: 0.7582 (tptm) REVERT: C 8 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6255 (mt0) REVERT: C 38 HIS cc_start: 0.7305 (t-90) cc_final: 0.6177 (m90) REVERT: C 89 TYR cc_start: 0.7855 (m-80) cc_final: 0.7569 (m-80) REVERT: C 237 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7575 (mtp85) REVERT: C 261 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: C 345 ASP cc_start: 0.7970 (t70) cc_final: 0.7495 (t0) REVERT: C 417 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8540 (ttpp) REVERT: C 459 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 490 LYS cc_start: 0.7880 (tttt) cc_final: 0.7578 (tptm) REVERT: C 574 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7731 (mtmt) REVERT: C 618 VAL cc_start: 0.8067 (m) cc_final: 0.7798 (p) outliers start: 46 outliers final: 28 residues processed: 165 average time/residue: 0.6839 time to fit residues: 121.8881 Evaluate side-chains 174 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 542 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 481 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 580 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.125425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.094267 restraints weight = 19725.510| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.13 r_work: 0.3035 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15594 Z= 0.114 Angle : 0.481 7.565 21132 Z= 0.254 Chirality : 0.044 0.389 2184 Planarity : 0.004 0.044 2853 Dihedral : 5.015 45.683 2174 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.24 % Allowed : 18.88 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.19), residues: 1920 helix: 2.41 (0.41), residues: 177 sheet: -0.51 (0.22), residues: 579 loop : 0.08 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.011 0.001 TYR B 306 PHE 0.010 0.001 PHE C 231 TRP 0.009 0.001 TRP B 96 HIS 0.003 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (15594) covalent geometry : angle 0.48057 / 0.25 (21132) hydrogen bonds : bond 0.02864 / 1.94 ( 394) hydrogen bonds : angle 4.67719 / 3.39 ( 1002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 145 time to evaluate : 0.614 Fit side-chains REVERT: A 38 HIS cc_start: 0.6926 (t-90) cc_final: 0.5602 (m90) REVERT: A 90 GLN cc_start: 0.7795 (mp10) cc_final: 0.7415 (mt0) REVERT: A 131 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7385 (mm-30) REVERT: A 136 ARG cc_start: 0.7190 (mtm110) cc_final: 0.6737 (ptt-90) REVERT: A 261 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: A 341 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: A 345 ASP cc_start: 0.7795 (t70) cc_final: 0.7248 (t0) REVERT: A 459 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7566 (tm-30) REVERT: A 490 LYS cc_start: 0.7883 (tttt) cc_final: 0.7531 (tptm) REVERT: B 8 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6272 (mt0) REVERT: B 38 HIS cc_start: 0.7171 (t-90) cc_final: 0.6113 (m90) REVERT: B 90 GLN cc_start: 0.7783 (mp10) cc_final: 0.7520 (mt0) REVERT: B 124 ASN cc_start: 0.8286 (m-40) cc_final: 0.7699 (t0) REVERT: B 261 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7021 (mm-30) REVERT: B 341 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: B 345 ASP cc_start: 0.7943 (t70) cc_final: 0.7386 (t0) REVERT: B 490 LYS cc_start: 0.7848 (tttt) cc_final: 0.7528 (tptm) REVERT: C 8 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6198 (mt0) REVERT: C 38 HIS cc_start: 0.7305 (t-90) cc_final: 0.6180 (m90) REVERT: C 89 TYR cc_start: 0.7780 (m-80) cc_final: 0.7542 (m-80) REVERT: C 205 ARG cc_start: 0.6089 (mmp-170) cc_final: 0.5872 (mmp-170) REVERT: C 237 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7651 (mtp85) REVERT: C 261 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: C 269 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: C 345 ASP cc_start: 0.7897 (t70) cc_final: 0.7431 (t0) REVERT: C 417 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8552 (ttpp) REVERT: C 459 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7501 (tm-30) REVERT: C 490 LYS cc_start: 0.7855 (tttt) cc_final: 0.7547 (tptm) REVERT: C 574 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7705 (mtmt) REVERT: C 618 VAL cc_start: 0.7968 (m) cc_final: 0.7681 (p) outliers start: 36 outliers final: 22 residues processed: 163 average time/residue: 0.7207 time to fit residues: 126.3695 Evaluate side-chains 173 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 542 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 82 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 481 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.093842 restraints weight = 19546.613| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.10 r_work: 0.3037 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15594 Z= 0.147 Angle : 0.497 8.759 21132 Z= 0.261 Chirality : 0.045 0.477 2184 Planarity : 0.004 0.044 2853 Dihedral : 5.022 45.178 2174 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.18 % Allowed : 19.00 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1920 helix: 2.37 (0.41), residues: 177 sheet: -0.53 (0.21), residues: 579 loop : 0.07 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 187 TYR 0.012 0.001 TYR A 306 PHE 0.012 0.002 PHE B 592 TRP 0.009 0.001 TRP B 96 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (15594) covalent geometry : angle 0.49674 / 0.26 (21132) hydrogen bonds : bond 0.02988 / 2.03 ( 394) hydrogen bonds : angle 4.68422 / 3.39 ( 1002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 141 time to evaluate : 0.411 Fit side-chains REVERT: A 38 HIS cc_start: 0.6884 (t-90) cc_final: 0.5588 (m90) REVERT: A 90 GLN cc_start: 0.7807 (mp10) cc_final: 0.7454 (mt0) REVERT: A 131 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7413 (mm-30) REVERT: A 136 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6741 (ptt-90) REVERT: A 261 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: A 341 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: A 345 ASP cc_start: 0.7807 (t70) cc_final: 0.7294 (t0) REVERT: A 459 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 490 LYS cc_start: 0.7897 (tttt) cc_final: 0.7547 (tptm) REVERT: B 8 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6218 (mt0) REVERT: B 38 HIS cc_start: 0.7206 (t-90) cc_final: 0.6147 (m90) REVERT: B 90 GLN cc_start: 0.7795 (mp10) cc_final: 0.7564 (mt0) REVERT: B 124 ASN cc_start: 0.8291 (m-40) cc_final: 0.7707 (t0) REVERT: B 187 ARG cc_start: 0.7234 (mmp-170) cc_final: 0.6861 (mmp80) REVERT: B 261 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7039 (mm-30) REVERT: B 341 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: B 345 ASP cc_start: 0.7927 (t70) cc_final: 0.7354 (t0) REVERT: B 490 LYS cc_start: 0.7862 (tttt) cc_final: 0.7545 (tptm) REVERT: C 8 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6246 (mt0) REVERT: C 38 HIS cc_start: 0.7353 (t-90) cc_final: 0.6258 (m90) REVERT: C 89 TYR cc_start: 0.7835 (m-80) cc_final: 0.7609 (m-80) REVERT: C 205 ARG cc_start: 0.6144 (mmp-170) cc_final: 0.5923 (mmp-170) REVERT: C 237 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7653 (mtp85) REVERT: C 261 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7264 (mm-30) REVERT: C 345 ASP cc_start: 0.7913 (t70) cc_final: 0.7421 (t0) REVERT: C 417 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8542 (ttpp) REVERT: C 459 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7490 (tm-30) REVERT: C 490 LYS cc_start: 0.7863 (tttt) cc_final: 0.7554 (tptm) REVERT: C 574 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7704 (mtmt) REVERT: C 618 VAL cc_start: 0.7973 (m) cc_final: 0.7681 (p) outliers start: 35 outliers final: 24 residues processed: 157 average time/residue: 0.7628 time to fit residues: 129.3704 Evaluate side-chains 173 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 243 ASN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 449 VAL Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 111 optimal weight: 0.1980 chunk 59 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 280 GLN A 481 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.125773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.094716 restraints weight = 19686.474| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.12 r_work: 0.3067 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15594 Z= 0.118 Angle : 0.473 7.427 21132 Z= 0.250 Chirality : 0.043 0.133 2184 Planarity : 0.004 0.045 2853 Dihedral : 4.915 45.784 2174 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.99 % Allowed : 19.31 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % 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: 0.11 (0.19), residues: 1920 helix: 2.46 (0.41), residues: 177 sheet: -0.50 (0.21), residues: 579 loop : 0.11 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 187 TYR 0.010 0.001 TYR A 306 PHE 0.010 0.001 PHE C 231 TRP 0.009 0.001 TRP B 96 HIS 0.004 0.001 HIS C 526 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15594) covalent geometry : angle 0.47318 / 0.25 (21132) hydrogen bonds : bond 0.02774 / 1.88 ( 394) hydrogen bonds : angle 4.58432 / 3.32 ( 1002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.620 Fit side-chains REVERT: A 38 HIS cc_start: 0.6822 (t-90) cc_final: 0.5591 (m90) REVERT: A 90 GLN cc_start: 0.7813 (mp10) cc_final: 0.7477 (mt0) REVERT: A 131 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7418 (mm-30) REVERT: A 136 ARG cc_start: 0.7186 (mtm110) cc_final: 0.6775 (ptt-90) REVERT: A 261 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: A 266 GLN cc_start: 0.7737 (mp10) cc_final: 0.7429 (mp10) REVERT: A 341 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: A 345 ASP cc_start: 0.7816 (t70) cc_final: 0.7286 (t0) REVERT: A 459 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7601 (tm-30) REVERT: A 490 LYS cc_start: 0.7936 (tttt) cc_final: 0.7592 (tptm) REVERT: B 8 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6263 (mt0) REVERT: B 38 HIS cc_start: 0.7261 (t-90) cc_final: 0.6222 (m90) REVERT: B 90 GLN cc_start: 0.7817 (mp10) cc_final: 0.7559 (mt0) REVERT: B 124 ASN cc_start: 0.8304 (m-40) cc_final: 0.7717 (t0) REVERT: B 187 ARG cc_start: 0.7147 (mmp-170) cc_final: 0.6808 (mmp80) REVERT: B 261 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7018 (mm-30) REVERT: B 341 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: B 345 ASP cc_start: 0.7943 (t70) cc_final: 0.7400 (t0) REVERT: B 490 LYS cc_start: 0.7895 (tttt) cc_final: 0.7585 (tptm) REVERT: C 8 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6274 (mt0) REVERT: C 38 HIS cc_start: 0.7381 (t-90) cc_final: 0.6309 (m90) REVERT: C 89 TYR cc_start: 0.7848 (m-80) cc_final: 0.7629 (m-80) REVERT: C 205 ARG cc_start: 0.6136 (mmp-170) cc_final: 0.5911 (mmp-170) REVERT: C 237 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7644 (mtp85) REVERT: C 261 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: C 345 ASP cc_start: 0.7898 (t70) cc_final: 0.7440 (t0) REVERT: C 417 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8570 (ttpp) REVERT: C 459 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7546 (tm-30) REVERT: C 490 LYS cc_start: 0.7901 (tttt) cc_final: 0.7595 (tptm) REVERT: C 574 LYS cc_start: 0.8334 (mtpt) cc_final: 0.7742 (mtmt) REVERT: C 618 VAL cc_start: 0.7947 (m) cc_final: 0.7640 (p) outliers start: 32 outliers final: 21 residues processed: 156 average time/residue: 0.8240 time to fit residues: 138.6743 Evaluate side-chains 168 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 449 VAL Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 542 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 61 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 481 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.093294 restraints weight = 19529.818| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.11 r_work: 0.3029 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15594 Z= 0.169 Angle : 0.506 7.250 21132 Z= 0.267 Chirality : 0.044 0.132 2184 Planarity : 0.004 0.043 2853 Dihedral : 5.031 46.699 2173 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.24 % Allowed : 19.13 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1920 helix: 2.34 (0.41), residues: 177 sheet: -0.53 (0.21), residues: 579 loop : 0.08 (0.19), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 187 TYR 0.013 0.001 TYR A 306 PHE 0.013 0.002 PHE B 592 TRP 0.009 0.001 TRP B 96 HIS 0.004 0.001 HIS C 518 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (15594) covalent geometry : angle 0.50555 / 0.27 (21132) hydrogen bonds : bond 0.03139 / 2.13 ( 394) hydrogen bonds : angle 4.70020 / 3.41 ( 1002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5432.84 seconds wall clock time: 93 minutes 23.49 seconds (5603.49 seconds total)