Starting phenix.real_space_refine on Thu Sep 18 20:34:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3x_44159/09_2025/9b3x_44159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3x_44159/09_2025/9b3x_44159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b3x_44159/09_2025/9b3x_44159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3x_44159/09_2025/9b3x_44159.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b3x_44159/09_2025/9b3x_44159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3x_44159/09_2025/9b3x_44159.map" } resolution = 3.2 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= 0.005 sd= 0.058 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 112 5.16 5 B 4 2.79 5 C 13112 2.51 5 N 3328 2.21 5 O 3428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19988 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 619, 4945 Classifications: {'peptide': 619} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 595} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 4, 'TRP:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'FZ4': 1, 'PEX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.82, per 1000 atoms: 0.24 Number of scatterers: 19988 At special positions: 0 Unit cell: (138.61, 138.61, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 112 16.00 P 4 15.00 O 3428 8.00 N 3328 7.00 C 13112 6.00 B 4 5.00 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: 1.81 Conformation dependent library (CDL) restraints added in 877.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4688 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 4 sheets defined 66.6% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 90 through 93 removed outlier: 3.566A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.503A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.517A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 413 removed outlier: 4.767A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 460 through 463 removed outlier: 4.044A pdb=" N ILE A 463 " --> pdb=" O ARG A 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 460 through 463' Processing helix chain 'A' and resid 466 through 492 removed outlier: 5.912A pdb=" N PHE A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.879A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 Processing helix chain 'A' and resid 519 through 531 removed outlier: 4.812A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 559 removed outlier: 4.273A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.659A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 646 Processing helix chain 'A' and resid 646 through 651 removed outlier: 4.578A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 646 through 651' Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.772A pdb=" N SER A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.527A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 90 through 93 removed outlier: 3.566A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 93' Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.504A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.517A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 413 removed outlier: 4.767A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 460 through 463 removed outlier: 4.045A pdb=" N ILE B 463 " --> pdb=" O ARG B 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 466 through 492 removed outlier: 5.912A pdb=" N PHE B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.878A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 Processing helix chain 'B' and resid 519 through 531 removed outlier: 4.812A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 559 removed outlier: 4.274A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 removed outlier: 3.660A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 646 Processing helix chain 'B' and resid 646 through 651 removed outlier: 4.578A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 646 through 651' Processing helix chain 'B' and resid 652 through 672 removed outlier: 3.772A pdb=" N SER B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.527A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 90 through 93 removed outlier: 3.566A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 93' Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.503A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.517A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 413 removed outlier: 4.767A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 460 through 463 removed outlier: 4.044A pdb=" N ILE C 463 " --> pdb=" O ARG C 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 460 through 463' Processing helix chain 'C' and resid 466 through 492 removed outlier: 5.912A pdb=" N PHE C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.878A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 Processing helix chain 'C' and resid 519 through 531 removed outlier: 4.812A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 559 removed outlier: 4.273A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 603 removed outlier: 3.660A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 646 Processing helix chain 'C' and resid 646 through 651 removed outlier: 4.578A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 646 through 651' Processing helix chain 'C' and resid 652 through 672 removed outlier: 3.771A pdb=" N SER C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 removed outlier: 3.527A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 90 through 93 removed outlier: 3.566A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 90 through 93' Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 232 Processing helix chain 'D' and resid 248 through 257 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.503A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.517A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 413 removed outlier: 4.767A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 460 through 463 removed outlier: 4.044A pdb=" N ILE D 463 " --> pdb=" O ARG D 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 460 through 463' Processing helix chain 'D' and resid 466 through 492 removed outlier: 5.912A pdb=" N PHE D 472 " --> pdb=" O MET D 468 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.879A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 519 through 531 removed outlier: 4.812A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 559 removed outlier: 4.273A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 603 removed outlier: 3.660A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 646 Processing helix chain 'D' and resid 646 through 651 removed outlier: 4.579A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 646 through 651' Processing helix chain 'D' and resid 652 through 672 removed outlier: 3.771A pdb=" N SER D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 removed outlier: 3.527A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.910A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.910A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.910A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.910A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3336 1.33 - 1.45: 5583 1.45 - 1.57: 11381 1.57 - 1.69: 16 1.69 - 1.81: 172 Bond restraints: 20488 Sorted by residual: bond pdb=" CE1 HIS C 521 " pdb=" NE2 HIS C 521 " ideal model delta sigma weight residual 1.321 1.337 -0.016 1.00e-02 1.00e+04 2.49e+00 bond pdb=" CE1 HIS A 521 " pdb=" NE2 HIS A 521 " ideal model delta sigma weight residual 1.321 1.336 -0.015 1.00e-02 1.00e+04 2.37e+00 bond pdb=" CE1 HIS B 521 " pdb=" NE2 HIS B 521 " ideal model delta sigma weight residual 1.321 1.336 -0.015 1.00e-02 1.00e+04 2.22e+00 bond pdb=" CE1 HIS D 521 " pdb=" NE2 HIS D 521 " ideal model delta sigma weight residual 1.321 1.336 -0.015 1.00e-02 1.00e+04 2.22e+00 bond pdb=" CG PRO D 261 " pdb=" CD PRO D 261 " ideal model delta sigma weight residual 1.503 1.551 -0.048 3.40e-02 8.65e+02 2.02e+00 ... (remaining 20483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 27200 1.51 - 3.02: 460 3.02 - 4.53: 96 4.53 - 6.04: 32 6.04 - 7.55: 8 Bond angle restraints: 27796 Sorted by residual: angle pdb=" C PHE D 612 " pdb=" N GLN D 613 " pdb=" CA GLN D 613 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.34e+00 angle pdb=" C PHE C 612 " pdb=" N GLN C 613 " pdb=" CA GLN C 613 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.34e+00 angle pdb=" C PHE A 612 " pdb=" N GLN A 613 " pdb=" CA GLN A 613 " ideal model delta sigma weight residual 121.54 126.68 -5.14 1.91e+00 2.74e-01 7.23e+00 angle pdb=" C PHE B 612 " pdb=" N GLN B 613 " pdb=" CA GLN B 613 " ideal model delta sigma weight residual 121.54 126.63 -5.09 1.91e+00 2.74e-01 7.11e+00 angle pdb=" N ILE D 605 " pdb=" CA ILE D 605 " pdb=" C ILE D 605 " ideal model delta sigma weight residual 111.91 109.70 2.21 8.90e-01 1.26e+00 6.18e+00 ... (remaining 27791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 11153 23.90 - 47.81: 774 47.81 - 71.71: 81 71.71 - 95.62: 24 95.62 - 119.52: 4 Dihedral angle restraints: 12036 sinusoidal: 4792 harmonic: 7244 Sorted by residual: dihedral pdb=" CA PHE B 209 " pdb=" C PHE B 209 " pdb=" N GLY B 210 " pdb=" CA GLY B 210 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE D 209 " pdb=" C PHE D 209 " pdb=" N GLY D 210 " pdb=" CA GLY D 210 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PHE A 209 " pdb=" C PHE A 209 " pdb=" N GLY A 210 " pdb=" CA GLY A 210 " ideal model delta harmonic sigma weight residual -180.00 -156.73 -23.27 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 12033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2126 0.029 - 0.058: 658 0.058 - 0.086: 282 0.086 - 0.115: 62 0.115 - 0.144: 8 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CA PRO D 261 " pdb=" N PRO D 261 " pdb=" C PRO D 261 " pdb=" CB PRO D 261 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA PRO C 261 " pdb=" N PRO C 261 " pdb=" C PRO C 261 " pdb=" CB PRO C 261 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA PRO A 261 " pdb=" N PRO A 261 " pdb=" C PRO A 261 " pdb=" CB PRO A 261 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.08e-01 ... (remaining 3133 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 260 " -0.035 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO C 261 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 261 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 261 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 260 " -0.035 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 261 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 260 " 0.035 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 261 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " 0.029 5.00e-02 4.00e+02 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5216 2.80 - 3.33: 19271 3.33 - 3.85: 32707 3.85 - 4.38: 40089 4.38 - 4.90: 68153 Nonbonded interactions: 165436 Sorted by model distance: nonbonded pdb=" O PRO C 325 " pdb=" NH2 ARG C 702 " model vdw 2.276 3.120 nonbonded pdb=" O PRO D 325 " pdb=" NH2 ARG D 702 " model vdw 2.276 3.120 nonbonded pdb=" O PRO B 325 " pdb=" NH2 ARG B 702 " model vdw 2.276 3.120 nonbonded pdb=" O PRO A 325 " pdb=" NH2 ARG A 702 " model vdw 2.276 3.120 nonbonded pdb=" OG SER A 37 " pdb=" OE2 GLU D 332 " model vdw 2.302 3.040 ... (remaining 165431 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.220 Find NCS groups from input model: 0.180 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.002 0.048 20488 Z= 0.116 Angle : 0.543 7.548 27796 Z= 0.297 Chirality : 0.035 0.144 3136 Planarity : 0.004 0.051 3428 Dihedral : 15.776 119.522 7348 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.17), residues: 2436 helix: 1.04 (0.13), residues: 1412 sheet: -1.09 (0.54), residues: 112 loop : 0.32 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 619 TYR 0.023 0.001 TYR B 228 PHE 0.014 0.001 PHE D 75 TRP 0.031 0.001 TRP D 509 HIS 0.005 0.001 HIS C 521 Details of bonding type rmsd covalent geometry : bond 0.00224 (20488) covalent geometry : angle 0.54273 (27796) hydrogen bonds : bond 0.22967 ( 1128) hydrogen bonds : angle 6.49692 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.870 Fit side-chains REVERT: A 263 ASN cc_start: 0.8562 (t0) cc_final: 0.8361 (t0) REVERT: A 683 HIS cc_start: 0.7464 (t-170) cc_final: 0.7066 (t-170) REVERT: B 263 ASN cc_start: 0.8542 (t0) cc_final: 0.8335 (t0) REVERT: B 683 HIS cc_start: 0.7510 (t-170) cc_final: 0.7059 (t-170) REVERT: C 263 ASN cc_start: 0.8518 (t0) cc_final: 0.8307 (t0) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1846 time to fit residues: 80.4803 Evaluate side-chains 282 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 186 ASN B 165 HIS B 186 ASN C 165 HIS D 165 HIS D 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117848 restraints weight = 23316.925| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.32 r_work: 0.3165 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 20488 Z= 0.289 Angle : 0.656 8.802 27796 Z= 0.333 Chirality : 0.042 0.144 3136 Planarity : 0.005 0.044 3428 Dihedral : 7.833 96.895 2832 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.73 % Allowed : 11.90 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.17), residues: 2436 helix: 1.22 (0.13), residues: 1448 sheet: -1.05 (0.50), residues: 112 loop : 0.01 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 79 TYR 0.018 0.002 TYR C 471 PHE 0.016 0.002 PHE B 319 TRP 0.016 0.002 TRP D 333 HIS 0.007 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00696 (20488) covalent geometry : angle 0.65611 (27796) hydrogen bonds : bond 0.05398 ( 1128) hydrogen bonds : angle 4.31716 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 287 time to evaluate : 0.697 Fit side-chains REVERT: A 263 ASN cc_start: 0.8440 (t0) cc_final: 0.8151 (t0) REVERT: A 612 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.6177 (m-10) REVERT: A 616 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5723 (mt) REVERT: A 683 HIS cc_start: 0.7580 (t-170) cc_final: 0.7243 (t-170) REVERT: B 263 ASN cc_start: 0.8443 (t0) cc_final: 0.8144 (t0) REVERT: B 612 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6018 (m-10) REVERT: B 616 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5696 (mt) REVERT: B 683 HIS cc_start: 0.7644 (t-170) cc_final: 0.7290 (t-170) REVERT: C 182 LEU cc_start: 0.8479 (tt) cc_final: 0.8096 (mp) REVERT: C 263 ASN cc_start: 0.8437 (t0) cc_final: 0.8148 (t0) REVERT: C 612 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6058 (m-10) REVERT: C 616 LEU cc_start: 0.6115 (OUTLIER) cc_final: 0.5726 (mt) REVERT: C 683 HIS cc_start: 0.7622 (t-170) cc_final: 0.7278 (t-170) REVERT: D 612 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6034 (m-10) REVERT: D 616 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5722 (mt) REVERT: D 683 HIS cc_start: 0.7641 (t-170) cc_final: 0.7288 (t-170) outliers start: 78 outliers final: 48 residues processed: 336 average time/residue: 0.1813 time to fit residues: 88.7250 Evaluate side-chains 332 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 616 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 156 optimal weight: 0.6980 chunk 184 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 229 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.163927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122421 restraints weight = 23107.159| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.32 r_work: 0.3231 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20488 Z= 0.129 Angle : 0.500 8.584 27796 Z= 0.258 Chirality : 0.037 0.139 3136 Planarity : 0.004 0.040 3428 Dihedral : 7.341 90.814 2832 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.49 % Allowed : 12.91 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.17), residues: 2436 helix: 1.59 (0.13), residues: 1448 sheet: -0.78 (0.51), residues: 112 loop : -0.01 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.012 0.001 TYR D 471 PHE 0.010 0.001 PHE A 75 TRP 0.010 0.001 TRP B 509 HIS 0.003 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00297 (20488) covalent geometry : angle 0.50040 (27796) hydrogen bonds : bond 0.03938 ( 1128) hydrogen bonds : angle 3.90087 ( 3240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 282 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.8221 (t0) cc_final: 0.7892 (t0) REVERT: A 308 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7894 (mt) REVERT: A 612 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6149 (m-10) REVERT: A 683 HIS cc_start: 0.7545 (t-170) cc_final: 0.7230 (t-170) REVERT: B 145 ASP cc_start: 0.7331 (m-30) cc_final: 0.7054 (p0) REVERT: B 263 ASN cc_start: 0.8264 (t0) cc_final: 0.7926 (t0) REVERT: B 308 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7906 (mt) REVERT: B 612 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6088 (m-10) REVERT: B 683 HIS cc_start: 0.7572 (t-170) cc_final: 0.7217 (t-170) REVERT: C 145 ASP cc_start: 0.7360 (m-30) cc_final: 0.7036 (p0) REVERT: C 263 ASN cc_start: 0.8292 (t0) cc_final: 0.7943 (t0) REVERT: C 308 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7911 (mt) REVERT: C 612 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.6086 (m-10) REVERT: C 683 HIS cc_start: 0.7557 (t-170) cc_final: 0.7207 (t-170) REVERT: D 145 ASP cc_start: 0.7341 (m-30) cc_final: 0.7065 (p0) REVERT: D 308 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7905 (mt) REVERT: D 612 PHE cc_start: 0.6841 (OUTLIER) cc_final: 0.6083 (m-10) REVERT: D 683 HIS cc_start: 0.7564 (t-170) cc_final: 0.7189 (t-170) outliers start: 52 outliers final: 36 residues processed: 314 average time/residue: 0.1830 time to fit residues: 83.7659 Evaluate side-chains 305 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 163 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 186 ASN A 521 HIS B 156 GLN B 186 ASN C 156 GLN C 521 HIS D 156 GLN D 186 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.156481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115672 restraints weight = 23598.819| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.21 r_work: 0.3095 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.064 20488 Z= 0.360 Angle : 0.696 9.141 27796 Z= 0.349 Chirality : 0.044 0.144 3136 Planarity : 0.005 0.052 3428 Dihedral : 8.345 89.605 2832 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.15 % Allowed : 14.20 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2436 helix: 1.14 (0.14), residues: 1448 sheet: -1.03 (0.49), residues: 112 loop : -0.52 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 371 TYR 0.024 0.002 TYR A 471 PHE 0.017 0.002 PHE C 472 TRP 0.011 0.002 TRP D 454 HIS 0.007 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00866 (20488) covalent geometry : angle 0.69613 (27796) hydrogen bonds : bond 0.04953 ( 1128) hydrogen bonds : angle 4.27971 ( 3240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 279 time to evaluate : 0.712 Fit side-chains REVERT: A 263 ASN cc_start: 0.8409 (t0) cc_final: 0.8098 (t0) REVERT: A 280 ARG cc_start: 0.6721 (mtm110) cc_final: 0.6217 (mtm180) REVERT: A 308 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8083 (mt) REVERT: A 384 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: A 435 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6477 (pp) REVERT: A 599 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6382 (mm-30) REVERT: A 612 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6535 (m-80) REVERT: A 616 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5968 (mt) REVERT: B 263 ASN cc_start: 0.8386 (t0) cc_final: 0.8062 (t0) REVERT: B 308 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8077 (mt) REVERT: B 435 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6593 (pp) REVERT: B 599 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6441 (mm-30) REVERT: B 612 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6533 (m-80) REVERT: B 616 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5952 (mt) REVERT: C 263 ASN cc_start: 0.8384 (t0) cc_final: 0.8059 (t0) REVERT: C 308 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.8079 (mt) REVERT: C 384 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: C 435 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6565 (pp) REVERT: C 599 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6418 (mm-30) REVERT: C 612 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: C 616 LEU cc_start: 0.6302 (OUTLIER) cc_final: 0.5939 (mt) REVERT: C 685 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8854 (mm-30) REVERT: D 280 ARG cc_start: 0.6721 (mtm110) cc_final: 0.6215 (mtm180) REVERT: D 308 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8090 (mt) REVERT: D 435 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6584 (pp) REVERT: D 599 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6432 (mm-30) REVERT: D 612 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: D 616 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5965 (mt) REVERT: D 683 HIS cc_start: 0.7729 (t-170) cc_final: 0.7136 (t-170) outliers start: 66 outliers final: 36 residues processed: 325 average time/residue: 0.1663 time to fit residues: 80.3416 Evaluate side-chains 323 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 269 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 161 optimal weight: 9.9990 chunk 238 optimal weight: 0.0010 chunk 181 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 217 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 214 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122525 restraints weight = 22881.117| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.29 r_work: 0.3245 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20488 Z= 0.102 Angle : 0.490 8.959 27796 Z= 0.250 Chirality : 0.036 0.117 3136 Planarity : 0.004 0.042 3428 Dihedral : 7.568 82.821 2832 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.25 % Allowed : 14.77 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.17), residues: 2436 helix: 1.69 (0.14), residues: 1452 sheet: -0.70 (0.52), residues: 112 loop : -0.20 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 86 TYR 0.014 0.001 TYR D 514 PHE 0.009 0.001 PHE C 75 TRP 0.008 0.001 TRP B 660 HIS 0.002 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00228 (20488) covalent geometry : angle 0.48995 (27796) hydrogen bonds : bond 0.03410 ( 1128) hydrogen bonds : angle 3.78852 ( 3240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 0.592 Fit side-chains REVERT: A 263 ASN cc_start: 0.8198 (t0) cc_final: 0.7829 (t0) REVERT: A 280 ARG cc_start: 0.6705 (mtm110) cc_final: 0.6278 (mtm180) REVERT: A 612 PHE cc_start: 0.6829 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: A 683 HIS cc_start: 0.7579 (t-170) cc_final: 0.7328 (t-170) REVERT: B 223 TRP cc_start: 0.5048 (m100) cc_final: 0.4714 (t60) REVERT: B 263 ASN cc_start: 0.8195 (t0) cc_final: 0.7841 (t0) REVERT: B 277 MET cc_start: 0.7129 (mtm) cc_final: 0.6912 (mtt) REVERT: B 308 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7826 (mt) REVERT: B 612 PHE cc_start: 0.6769 (OUTLIER) cc_final: 0.6413 (m-80) REVERT: B 683 HIS cc_start: 0.7516 (t-170) cc_final: 0.7275 (t-170) REVERT: C 263 ASN cc_start: 0.8226 (t0) cc_final: 0.7857 (t0) REVERT: C 308 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7821 (mt) REVERT: C 612 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6451 (m-80) REVERT: C 683 HIS cc_start: 0.7529 (t-170) cc_final: 0.7277 (t-170) REVERT: D 223 TRP cc_start: 0.5045 (m100) cc_final: 0.4706 (t60) REVERT: D 280 ARG cc_start: 0.6689 (mtm110) cc_final: 0.6315 (mtm180) REVERT: D 308 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7828 (mt) REVERT: D 612 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6425 (m-80) REVERT: D 685 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8507 (mm-30) outliers start: 47 outliers final: 23 residues processed: 295 average time/residue: 0.1555 time to fit residues: 68.3259 Evaluate side-chains 287 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 612 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 189 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116342 restraints weight = 23249.263| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.30 r_work: 0.3141 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 20488 Z= 0.286 Angle : 0.621 8.903 27796 Z= 0.313 Chirality : 0.042 0.212 3136 Planarity : 0.004 0.052 3428 Dihedral : 8.154 84.600 2832 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.35 % Allowed : 13.77 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.17), residues: 2436 helix: 1.43 (0.14), residues: 1448 sheet: -0.91 (0.51), residues: 112 loop : -0.57 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 86 TYR 0.020 0.002 TYR C 471 PHE 0.015 0.002 PHE C 472 TRP 0.010 0.002 TRP B 351 HIS 0.007 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00687 (20488) covalent geometry : angle 0.62120 (27796) hydrogen bonds : bond 0.04319 ( 1128) hydrogen bonds : angle 4.05364 ( 3240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 265 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7432 (ttt90) REVERT: A 263 ASN cc_start: 0.8367 (t0) cc_final: 0.8031 (t0) REVERT: A 280 ARG cc_start: 0.6809 (mtm110) cc_final: 0.6394 (mtm180) REVERT: A 308 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8007 (mt) REVERT: A 384 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: A 435 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6497 (pp) REVERT: A 612 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: A 616 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5952 (mt) REVERT: A 683 HIS cc_start: 0.7763 (t-170) cc_final: 0.7481 (t-170) REVERT: B 79 ARG cc_start: 0.7704 (ttp80) cc_final: 0.7421 (ttt90) REVERT: B 182 LEU cc_start: 0.8401 (tt) cc_final: 0.8128 (tp) REVERT: B 186 ASN cc_start: 0.8042 (m-40) cc_final: 0.7742 (m110) REVERT: B 263 ASN cc_start: 0.8348 (t0) cc_final: 0.8023 (t0) REVERT: B 308 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8007 (mt) REVERT: B 435 LEU cc_start: 0.6743 (OUTLIER) cc_final: 0.6537 (pp) REVERT: B 537 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5673 (mm) REVERT: B 612 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6592 (m-80) REVERT: B 616 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5931 (mt) REVERT: B 683 HIS cc_start: 0.7790 (t-170) cc_final: 0.7527 (t-170) REVERT: C 228 TYR cc_start: 0.7480 (t80) cc_final: 0.7062 (t80) REVERT: C 263 ASN cc_start: 0.8346 (t0) cc_final: 0.8014 (t0) REVERT: C 308 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8017 (mt) REVERT: C 384 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: C 435 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6552 (pp) REVERT: C 537 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5664 (mm) REVERT: C 612 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6611 (m-80) REVERT: C 616 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.5942 (mt) REVERT: C 683 HIS cc_start: 0.7739 (t-170) cc_final: 0.7486 (t-170) REVERT: C 685 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8805 (mm-30) REVERT: D 79 ARG cc_start: 0.7712 (ttp80) cc_final: 0.7441 (ttt90) REVERT: D 280 ARG cc_start: 0.6821 (mtm110) cc_final: 0.6401 (mtm180) REVERT: D 308 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.8008 (mt) REVERT: D 537 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5652 (mm) REVERT: D 612 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.6594 (m-80) REVERT: D 616 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5949 (mt) REVERT: D 683 HIS cc_start: 0.7826 (t-170) cc_final: 0.7476 (t-170) outliers start: 70 outliers final: 33 residues processed: 319 average time/residue: 0.1730 time to fit residues: 80.4673 Evaluate side-chains 315 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 262 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 616 LEU Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 616 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 179 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.163237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122346 restraints weight = 23008.497| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.29 r_work: 0.3253 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20488 Z= 0.107 Angle : 0.485 9.981 27796 Z= 0.247 Chirality : 0.037 0.182 3136 Planarity : 0.004 0.044 3428 Dihedral : 7.570 82.677 2832 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.49 % Allowed : 14.87 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.17), residues: 2436 helix: 1.80 (0.14), residues: 1452 sheet: -0.92 (0.49), residues: 112 loop : -0.31 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 86 TYR 0.015 0.001 TYR D 514 PHE 0.009 0.001 PHE C 75 TRP 0.009 0.001 TRP D 660 HIS 0.002 0.001 HIS D 683 Details of bonding type rmsd covalent geometry : bond 0.00245 (20488) covalent geometry : angle 0.48477 (27796) hydrogen bonds : bond 0.03254 ( 1128) hydrogen bonds : angle 3.69518 ( 3240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.798 Fit side-chains REVERT: A 79 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7525 (ttt90) REVERT: A 186 ASN cc_start: 0.8179 (m-40) cc_final: 0.7922 (m110) REVERT: A 228 TYR cc_start: 0.7619 (t80) cc_final: 0.7327 (t80) REVERT: A 263 ASN cc_start: 0.8244 (t0) cc_final: 0.7888 (t0) REVERT: A 280 ARG cc_start: 0.6742 (mtm110) cc_final: 0.6421 (mtm180) REVERT: A 308 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7787 (mt) REVERT: A 612 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.6545 (m-80) REVERT: A 683 HIS cc_start: 0.7685 (t-170) cc_final: 0.7449 (t-170) REVERT: B 79 ARG cc_start: 0.7745 (ttp80) cc_final: 0.7520 (ttt90) REVERT: B 127 ASN cc_start: 0.8143 (m110) cc_final: 0.7611 (m110) REVERT: B 182 LEU cc_start: 0.8484 (tt) cc_final: 0.8213 (tp) REVERT: B 186 ASN cc_start: 0.8049 (m-40) cc_final: 0.7785 (m110) REVERT: B 228 TYR cc_start: 0.7666 (t80) cc_final: 0.7358 (t80) REVERT: B 263 ASN cc_start: 0.8220 (t0) cc_final: 0.7841 (t0) REVERT: B 308 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7802 (mt) REVERT: B 537 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5649 (mm) REVERT: B 612 PHE cc_start: 0.6804 (OUTLIER) cc_final: 0.6577 (m-80) REVERT: B 683 HIS cc_start: 0.7694 (t-170) cc_final: 0.7460 (t-170) REVERT: C 79 ARG cc_start: 0.7824 (ttp80) cc_final: 0.7543 (ttt90) REVERT: C 127 ASN cc_start: 0.8142 (m110) cc_final: 0.7611 (m110) REVERT: C 186 ASN cc_start: 0.8121 (m-40) cc_final: 0.7890 (m110) REVERT: C 263 ASN cc_start: 0.8229 (t0) cc_final: 0.7854 (t0) REVERT: C 308 ILE cc_start: 0.8048 (OUTLIER) cc_final: 0.7797 (mt) REVERT: C 612 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: C 683 HIS cc_start: 0.7672 (t-170) cc_final: 0.7188 (t-170) REVERT: D 79 ARG cc_start: 0.7747 (ttp80) cc_final: 0.7520 (ttt90) REVERT: D 228 TYR cc_start: 0.7639 (t80) cc_final: 0.7342 (t80) REVERT: D 280 ARG cc_start: 0.6728 (mtm110) cc_final: 0.6426 (mtm180) REVERT: D 308 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7795 (mt) REVERT: D 612 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6590 (m-80) REVERT: D 683 HIS cc_start: 0.7711 (t-170) cc_final: 0.7407 (t-170) outliers start: 52 outliers final: 26 residues processed: 299 average time/residue: 0.1665 time to fit residues: 73.9795 Evaluate side-chains 288 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 612 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 127 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 26 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 179 optimal weight: 0.0040 chunk 152 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 0.0370 overall best weight: 1.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.162898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121872 restraints weight = 23072.081| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.29 r_work: 0.3246 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20488 Z= 0.126 Angle : 0.502 8.586 27796 Z= 0.253 Chirality : 0.037 0.179 3136 Planarity : 0.004 0.043 3428 Dihedral : 7.469 84.723 2832 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.87 % Allowed : 14.72 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.17), residues: 2436 helix: 1.88 (0.14), residues: 1452 sheet: -0.88 (0.49), residues: 112 loop : -0.29 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 86 TYR 0.022 0.001 TYR C 228 PHE 0.008 0.001 PHE C 75 TRP 0.014 0.001 TRP C 333 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00296 (20488) covalent geometry : angle 0.50241 (27796) hydrogen bonds : bond 0.03298 ( 1128) hydrogen bonds : angle 3.69136 ( 3240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.802 Fit side-chains REVERT: A 79 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7578 (ttt90) REVERT: A 123 LYS cc_start: 0.8057 (tptm) cc_final: 0.7740 (tptm) REVERT: A 127 ASN cc_start: 0.8180 (m110) cc_final: 0.7634 (m110) REVERT: A 186 ASN cc_start: 0.8170 (m-40) cc_final: 0.7941 (m110) REVERT: A 228 TYR cc_start: 0.7682 (t80) cc_final: 0.7385 (t80) REVERT: A 263 ASN cc_start: 0.8254 (t0) cc_final: 0.7883 (t0) REVERT: A 280 ARG cc_start: 0.6742 (mtm110) cc_final: 0.6456 (mtm180) REVERT: A 308 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7822 (mt) REVERT: A 612 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.6562 (m-80) REVERT: A 683 HIS cc_start: 0.7707 (t-170) cc_final: 0.7503 (t-170) REVERT: B 79 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7537 (ttt90) REVERT: B 127 ASN cc_start: 0.8169 (m110) cc_final: 0.7663 (m110) REVERT: B 182 LEU cc_start: 0.8496 (tt) cc_final: 0.8220 (tp) REVERT: B 186 ASN cc_start: 0.8125 (m-40) cc_final: 0.7864 (m110) REVERT: B 228 TYR cc_start: 0.7645 (t80) cc_final: 0.7354 (t80) REVERT: B 263 ASN cc_start: 0.8281 (t0) cc_final: 0.7913 (t0) REVERT: B 308 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7825 (mt) REVERT: B 537 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5666 (mm) REVERT: B 683 HIS cc_start: 0.7698 (t-170) cc_final: 0.7462 (t-170) REVERT: C 127 ASN cc_start: 0.8167 (m110) cc_final: 0.7665 (m110) REVERT: C 182 LEU cc_start: 0.8483 (tt) cc_final: 0.8179 (tp) REVERT: C 186 ASN cc_start: 0.8138 (m-40) cc_final: 0.7858 (m110) REVERT: C 228 TYR cc_start: 0.7330 (t80) cc_final: 0.7091 (t80) REVERT: C 263 ASN cc_start: 0.8282 (t0) cc_final: 0.7923 (t0) REVERT: C 308 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7821 (mt) REVERT: C 537 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5647 (mm) REVERT: C 612 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6609 (m-80) REVERT: C 683 HIS cc_start: 0.7674 (t-170) cc_final: 0.7462 (t-170) REVERT: D 228 TYR cc_start: 0.7658 (t80) cc_final: 0.7386 (t80) REVERT: D 269 HIS cc_start: 0.8040 (t-90) cc_final: 0.7564 (t70) REVERT: D 280 ARG cc_start: 0.6776 (mtm110) cc_final: 0.6459 (mtm180) REVERT: D 308 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7806 (mt) REVERT: D 537 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5657 (mm) REVERT: D 683 HIS cc_start: 0.7696 (t-170) cc_final: 0.7381 (t-170) outliers start: 60 outliers final: 30 residues processed: 321 average time/residue: 0.1738 time to fit residues: 81.5326 Evaluate side-chains 296 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 257 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 701 GLU Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 604 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 116 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 122 optimal weight: 0.0270 chunk 65 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN D 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.121155 restraints weight = 22899.172| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.26 r_work: 0.3238 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20488 Z= 0.148 Angle : 0.518 8.581 27796 Z= 0.261 Chirality : 0.038 0.170 3136 Planarity : 0.004 0.044 3428 Dihedral : 7.516 87.879 2832 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.10 % Allowed : 15.44 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.17), residues: 2436 helix: 1.84 (0.14), residues: 1452 sheet: -0.90 (0.49), residues: 112 loop : -0.31 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 79 TYR 0.020 0.001 TYR C 228 PHE 0.008 0.001 PHE A 75 TRP 0.014 0.001 TRP C 333 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00354 (20488) covalent geometry : angle 0.51751 (27796) hydrogen bonds : bond 0.03408 ( 1128) hydrogen bonds : angle 3.70370 ( 3240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 0.617 Fit side-chains REVERT: A 79 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7497 (ttt90) REVERT: A 123 LYS cc_start: 0.8076 (tptm) cc_final: 0.7758 (tptm) REVERT: A 127 ASN cc_start: 0.8166 (m110) cc_final: 0.7602 (m110) REVERT: A 228 TYR cc_start: 0.7538 (t80) cc_final: 0.7248 (t80) REVERT: A 263 ASN cc_start: 0.8281 (t0) cc_final: 0.7931 (t0) REVERT: A 280 ARG cc_start: 0.6807 (mtm110) cc_final: 0.6485 (mtm180) REVERT: A 308 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7967 (mt) REVERT: A 612 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: A 683 HIS cc_start: 0.7835 (t-170) cc_final: 0.7605 (t-170) REVERT: B 79 ARG cc_start: 0.7662 (ttp80) cc_final: 0.7450 (ttt90) REVERT: B 127 ASN cc_start: 0.8117 (m110) cc_final: 0.7542 (m110) REVERT: B 182 LEU cc_start: 0.8419 (tt) cc_final: 0.8152 (tp) REVERT: B 186 ASN cc_start: 0.8047 (m-40) cc_final: 0.7794 (m110) REVERT: B 228 TYR cc_start: 0.7543 (t80) cc_final: 0.7259 (t80) REVERT: B 263 ASN cc_start: 0.8293 (t0) cc_final: 0.7929 (t0) REVERT: B 269 HIS cc_start: 0.8111 (t-90) cc_final: 0.7624 (t70) REVERT: B 308 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7984 (mt) REVERT: B 537 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5590 (mm) REVERT: B 683 HIS cc_start: 0.7821 (t-170) cc_final: 0.7576 (t-170) REVERT: C 79 ARG cc_start: 0.7709 (ttp80) cc_final: 0.7384 (ttt90) REVERT: C 127 ASN cc_start: 0.8116 (m110) cc_final: 0.7528 (m110) REVERT: C 182 LEU cc_start: 0.8393 (tt) cc_final: 0.8092 (tp) REVERT: C 186 ASN cc_start: 0.8090 (m-40) cc_final: 0.7781 (m110) REVERT: C 228 TYR cc_start: 0.7298 (t80) cc_final: 0.7029 (t80) REVERT: C 263 ASN cc_start: 0.8322 (t0) cc_final: 0.7964 (t0) REVERT: C 308 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7965 (mt) REVERT: C 537 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5555 (mm) REVERT: C 683 HIS cc_start: 0.7781 (t-170) cc_final: 0.7552 (t-170) REVERT: D 186 ASN cc_start: 0.7958 (m-40) cc_final: 0.7740 (m110) REVERT: D 228 TYR cc_start: 0.7532 (t80) cc_final: 0.7255 (t80) REVERT: D 269 HIS cc_start: 0.8094 (t-90) cc_final: 0.7609 (t70) REVERT: D 280 ARG cc_start: 0.6807 (mtm110) cc_final: 0.6459 (mtm180) REVERT: D 308 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7954 (mt) REVERT: D 537 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5554 (mm) REVERT: D 683 HIS cc_start: 0.7785 (t-170) cc_final: 0.7446 (t-170) outliers start: 44 outliers final: 29 residues processed: 298 average time/residue: 0.1718 time to fit residues: 75.3101 Evaluate side-chains 297 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 159 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 229 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 222 optimal weight: 0.1980 chunk 210 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120725 restraints weight = 23109.964| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.32 r_work: 0.3207 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20488 Z= 0.148 Angle : 0.520 9.619 27796 Z= 0.260 Chirality : 0.038 0.170 3136 Planarity : 0.004 0.043 3428 Dihedral : 7.535 89.848 2832 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.96 % Allowed : 15.30 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.17), residues: 2436 helix: 1.84 (0.14), residues: 1452 sheet: -0.83 (0.49), residues: 112 loop : -0.33 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.019 0.001 TYR C 228 PHE 0.008 0.001 PHE A 75 TRP 0.013 0.001 TRP C 333 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00353 (20488) covalent geometry : angle 0.51983 (27796) hydrogen bonds : bond 0.03395 ( 1128) hydrogen bonds : angle 3.69827 ( 3240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 267 time to evaluate : 0.794 Fit side-chains REVERT: A 123 LYS cc_start: 0.8077 (tptm) cc_final: 0.7741 (tptm) REVERT: A 127 ASN cc_start: 0.8160 (m110) cc_final: 0.7593 (m110) REVERT: A 228 TYR cc_start: 0.7637 (t80) cc_final: 0.7359 (t80) REVERT: A 247 ASN cc_start: 0.8691 (m110) cc_final: 0.8451 (m-40) REVERT: A 263 ASN cc_start: 0.8261 (t0) cc_final: 0.7905 (t0) REVERT: A 269 HIS cc_start: 0.8043 (t-90) cc_final: 0.7557 (t70) REVERT: A 280 ARG cc_start: 0.6815 (mtm110) cc_final: 0.6510 (mtm180) REVERT: A 308 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7826 (mt) REVERT: A 612 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.6593 (m-80) REVERT: A 683 HIS cc_start: 0.7769 (t-170) cc_final: 0.7258 (t-170) REVERT: B 79 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7537 (ttt90) REVERT: B 127 ASN cc_start: 0.8157 (m110) cc_final: 0.7646 (m110) REVERT: B 182 LEU cc_start: 0.8512 (tt) cc_final: 0.8252 (tp) REVERT: B 186 ASN cc_start: 0.8104 (m-40) cc_final: 0.7850 (m110) REVERT: B 228 TYR cc_start: 0.7662 (t80) cc_final: 0.7391 (t80) REVERT: B 263 ASN cc_start: 0.8270 (t0) cc_final: 0.7907 (t0) REVERT: B 269 HIS cc_start: 0.8034 (t-90) cc_final: 0.7558 (t70) REVERT: B 308 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7861 (mt) REVERT: B 537 LEU cc_start: 0.5972 (OUTLIER) cc_final: 0.5675 (mm) REVERT: B 683 HIS cc_start: 0.7773 (t-170) cc_final: 0.7541 (t-170) REVERT: C 79 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7445 (ttt90) REVERT: C 127 ASN cc_start: 0.8163 (m110) cc_final: 0.7655 (m110) REVERT: C 182 LEU cc_start: 0.8478 (tt) cc_final: 0.8166 (tp) REVERT: C 186 ASN cc_start: 0.8150 (m-40) cc_final: 0.7829 (m110) REVERT: C 228 TYR cc_start: 0.7393 (t80) cc_final: 0.7109 (t80) REVERT: C 263 ASN cc_start: 0.8308 (t0) cc_final: 0.7959 (t0) REVERT: C 308 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7855 (mt) REVERT: C 537 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5671 (mm) REVERT: C 683 HIS cc_start: 0.7750 (t-170) cc_final: 0.7534 (t-170) REVERT: D 186 ASN cc_start: 0.8155 (m-40) cc_final: 0.7901 (m110) REVERT: D 228 TYR cc_start: 0.7635 (t80) cc_final: 0.7367 (t80) REVERT: D 269 HIS cc_start: 0.8012 (t-90) cc_final: 0.7482 (t70) REVERT: D 280 ARG cc_start: 0.6799 (mtm110) cc_final: 0.6488 (mtm180) REVERT: D 308 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7829 (mt) REVERT: D 537 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5679 (mm) REVERT: D 683 HIS cc_start: 0.7733 (t-170) cc_final: 0.7412 (t-170) outliers start: 41 outliers final: 30 residues processed: 300 average time/residue: 0.1798 time to fit residues: 79.6599 Evaluate side-chains 303 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 265 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain B residue 75 PHE Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain D residue 75 PHE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 604 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 202 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 241 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123972 restraints weight = 23074.869| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.28 r_work: 0.3272 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20488 Z= 0.098 Angle : 0.480 9.405 27796 Z= 0.242 Chirality : 0.036 0.165 3136 Planarity : 0.004 0.043 3428 Dihedral : 7.203 87.814 2832 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.53 % Allowed : 16.16 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.17), residues: 2436 helix: 2.01 (0.14), residues: 1452 sheet: -0.84 (0.47), residues: 112 loop : -0.20 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 79 TYR 0.016 0.001 TYR C 228 PHE 0.008 0.001 PHE B 75 TRP 0.009 0.001 TRP D 351 HIS 0.003 0.001 HIS D 413 Details of bonding type rmsd covalent geometry : bond 0.00221 (20488) covalent geometry : angle 0.48032 (27796) hydrogen bonds : bond 0.03008 ( 1128) hydrogen bonds : angle 3.55603 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4777.62 seconds wall clock time: 82 minutes 41.92 seconds (4961.92 seconds total)