Starting phenix.real_space_refine on Tue Jun 17 12:47:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3x_44159/06_2025/9b3x_44159.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3x_44159/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3x_44159/06_2025/9b3x_44159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3x_44159/06_2025/9b3x_44159.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3x_44159/06_2025/9b3x_44159.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3x_44159/06_2025/9b3x_44159.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} 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: C, B, D Time building chain proxies: 11.53, per 1000 atoms: 0.58 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: 4.80 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.97 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: 5.98 Time building geometry restraints manager: 5.70 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.640 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.031 0.001 TRP D 509 HIS 0.005 0.001 HIS C 521 PHE 0.014 0.001 PHE D 75 TYR 0.023 0.001 TYR B 228 ARG 0.005 0.001 ARG D 619 Details of bonding type rmsd hydrogen bonds : bond 0.22967 ( 1128) hydrogen bonds : angle 6.49692 ( 3240) covalent geometry : bond 0.00224 (20488) covalent geometry : angle 0.54273 (27796) *********************** 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 : 2.117 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: 0.3838 time to fit residues: 167.6582 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 : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9990 chunk 184 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 221 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 186 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 269 HIS C 165 HIS C 269 HIS D 165 HIS D 186 ASN D 269 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.158942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117965 restraints weight = 23355.458| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.21 r_work: 0.3172 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 20488 Z= 0.319 Angle : 0.678 8.906 27796 Z= 0.346 Chirality : 0.043 0.144 3136 Planarity : 0.005 0.044 3428 Dihedral : 7.986 97.169 2832 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.54 % Allowed : 12.19 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.17), residues: 2436 helix: 1.12 (0.13), residues: 1448 sheet: -1.08 (0.50), residues: 112 loop : -0.07 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 333 HIS 0.007 0.002 HIS B 169 PHE 0.017 0.002 PHE B 319 TYR 0.019 0.002 TYR B 471 ARG 0.004 0.001 ARG A 702 Details of bonding type rmsd hydrogen bonds : bond 0.05598 ( 1128) hydrogen bonds : angle 4.37709 ( 3240) covalent geometry : bond 0.00769 (20488) covalent geometry : angle 0.67793 (27796) *********************** 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 363 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 289 time to evaluate : 3.311 Fit side-chains REVERT: A 263 ASN cc_start: 0.8524 (t0) cc_final: 0.8217 (t0) REVERT: A 612 PHE cc_start: 0.7059 (OUTLIER) cc_final: 0.6343 (m-10) REVERT: A 616 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5748 (mt) REVERT: A 683 HIS cc_start: 0.7676 (t-170) cc_final: 0.7298 (t-170) REVERT: B 263 ASN cc_start: 0.8498 (t0) cc_final: 0.8212 (t0) REVERT: B 612 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6085 (m-10) REVERT: B 616 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5726 (mt) REVERT: B 683 HIS cc_start: 0.7748 (t-170) cc_final: 0.7346 (t-170) REVERT: C 182 LEU cc_start: 0.8397 (tt) cc_final: 0.8067 (tp) REVERT: C 186 ASN cc_start: 0.7926 (m-40) cc_final: 0.7638 (m110) REVERT: C 263 ASN cc_start: 0.8483 (t0) cc_final: 0.8199 (t0) REVERT: C 612 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6144 (m-10) REVERT: C 616 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5721 (mt) REVERT: C 683 HIS cc_start: 0.7731 (t-170) cc_final: 0.7345 (t-170) REVERT: D 612 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6099 (m-10) REVERT: D 616 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5757 (mt) outliers start: 74 outliers final: 43 residues processed: 332 average time/residue: 0.4821 time to fit residues: 238.1088 Evaluate side-chains 329 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 278 time to evaluate : 2.744 ------------------------------------------------------------------------------- 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 180 VAL Chi-restraints excluded: chain A residue 212 LEU 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 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 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 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 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 183 optimal weight: 0.0040 chunk 73 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 239 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS B 269 HIS C 269 HIS D 269 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.165384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124226 restraints weight = 22898.923| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.29 r_work: 0.3264 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20488 Z= 0.106 Angle : 0.491 8.510 27796 Z= 0.253 Chirality : 0.037 0.142 3136 Planarity : 0.004 0.037 3428 Dihedral : 7.251 89.914 2832 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.10 % Allowed : 12.81 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2436 helix: 1.64 (0.14), residues: 1448 sheet: -0.74 (0.52), residues: 112 loop : 0.03 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 509 HIS 0.004 0.001 HIS D 269 PHE 0.010 0.001 PHE A 75 TYR 0.010 0.001 TYR D 514 ARG 0.007 0.001 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 1128) hydrogen bonds : angle 3.86254 ( 3240) covalent geometry : bond 0.00232 (20488) covalent geometry : angle 0.49083 (27796) *********************** 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 330 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.8242 (t0) cc_final: 0.7885 (t0) REVERT: A 277 MET cc_start: 0.7092 (mtm) cc_final: 0.6844 (mtt) REVERT: A 308 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7877 (mt) REVERT: A 612 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.6159 (m-10) REVERT: A 683 HIS cc_start: 0.7537 (t-170) cc_final: 0.7227 (t-170) REVERT: B 145 ASP cc_start: 0.7359 (m-30) cc_final: 0.7065 (p0) REVERT: B 263 ASN cc_start: 0.8266 (t0) cc_final: 0.7919 (t0) REVERT: B 308 ILE cc_start: 0.8099 (OUTLIER) cc_final: 0.7850 (mt) REVERT: B 612 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6096 (m-10) REVERT: B 683 HIS cc_start: 0.7563 (t-170) cc_final: 0.7228 (t-170) REVERT: C 145 ASP cc_start: 0.7347 (m-30) cc_final: 0.7035 (p0) REVERT: C 182 LEU cc_start: 0.8485 (tt) cc_final: 0.8205 (tt) REVERT: C 186 ASN cc_start: 0.7806 (m-40) cc_final: 0.7584 (m110) REVERT: C 263 ASN cc_start: 0.8260 (t0) cc_final: 0.7916 (t0) REVERT: C 277 MET cc_start: 0.7118 (mtm) cc_final: 0.6868 (mtt) REVERT: C 308 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7841 (mt) REVERT: C 612 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6084 (m-10) REVERT: C 683 HIS cc_start: 0.7561 (t-170) cc_final: 0.7216 (t-170) REVERT: D 145 ASP cc_start: 0.7347 (m-30) cc_final: 0.7078 (p0) REVERT: D 277 MET cc_start: 0.7090 (mtm) cc_final: 0.6838 (mtt) REVERT: D 308 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7841 (mt) REVERT: D 612 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.6110 (m-10) REVERT: D 683 HIS cc_start: 0.7598 (t-170) cc_final: 0.7337 (t-170) outliers start: 44 outliers final: 27 residues processed: 313 average time/residue: 0.3961 time to fit residues: 183.5684 Evaluate side-chains 295 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 2.351 ------------------------------------------------------------------------------- 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 308 ILE Chi-restraints excluded: chain A residue 352 GLU 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 308 ILE Chi-restraints excluded: chain B residue 352 GLU 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 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 528 MET 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 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 5 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN B 186 ASN D 186 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.120475 restraints weight = 23271.165| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.34 r_work: 0.3210 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20488 Z= 0.174 Angle : 0.527 8.465 27796 Z= 0.266 Chirality : 0.038 0.119 3136 Planarity : 0.004 0.040 3428 Dihedral : 7.401 87.512 2832 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.49 % Allowed : 14.01 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.17), residues: 2436 helix: 1.66 (0.14), residues: 1448 sheet: -0.68 (0.52), residues: 112 loop : -0.13 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 351 HIS 0.005 0.001 HIS D 313 PHE 0.009 0.001 PHE A 75 TYR 0.015 0.001 TYR A 471 ARG 0.006 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 1128) hydrogen bonds : angle 3.85782 ( 3240) covalent geometry : bond 0.00415 (20488) covalent geometry : angle 0.52718 (27796) *********************** 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 325 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 273 time to evaluate : 3.268 Fit side-chains REVERT: A 263 ASN cc_start: 0.8284 (t0) cc_final: 0.7934 (t0) REVERT: A 280 ARG cc_start: 0.6827 (mtm110) cc_final: 0.6399 (mtm180) REVERT: A 308 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7933 (mt) REVERT: A 612 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6267 (m-10) REVERT: A 683 HIS cc_start: 0.7581 (t-170) cc_final: 0.7282 (t-170) REVERT: B 223 TRP cc_start: 0.4907 (m100) cc_final: 0.4636 (t60) REVERT: B 263 ASN cc_start: 0.8292 (t0) cc_final: 0.7948 (t0) REVERT: B 280 ARG cc_start: 0.6654 (mtm110) cc_final: 0.6229 (mtm180) REVERT: B 308 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7943 (mt) REVERT: B 612 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.6150 (m-10) REVERT: B 683 HIS cc_start: 0.7586 (t-170) cc_final: 0.7240 (t-170) REVERT: C 186 ASN cc_start: 0.7816 (m-40) cc_final: 0.7601 (m110) REVERT: C 263 ASN cc_start: 0.8282 (t0) cc_final: 0.7939 (t0) REVERT: C 280 ARG cc_start: 0.6758 (mtm110) cc_final: 0.6252 (mtm180) REVERT: C 308 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7942 (mt) REVERT: C 612 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.6138 (m-10) REVERT: C 683 HIS cc_start: 0.7567 (t-170) cc_final: 0.7231 (t-170) REVERT: D 280 ARG cc_start: 0.6795 (mtm110) cc_final: 0.6357 (mtm180) REVERT: D 308 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7945 (mt) REVERT: D 612 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6185 (m-10) REVERT: D 683 HIS cc_start: 0.7695 (t-170) cc_final: 0.7433 (t-170) outliers start: 52 outliers final: 33 residues processed: 305 average time/residue: 0.4344 time to fit residues: 197.2720 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 : 2.247 ------------------------------------------------------------------------------- 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 528 MET 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 153 VAL Chi-restraints excluded: chain B residue 212 LEU 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 528 MET 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 153 VAL Chi-restraints excluded: chain C residue 212 LEU 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 528 MET 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 612 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 210 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 231 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 193 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 ASN C 186 ASN C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.164612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123325 restraints weight = 23041.850| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.31 r_work: 0.3239 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20488 Z= 0.106 Angle : 0.467 8.327 27796 Z= 0.238 Chirality : 0.036 0.113 3136 Planarity : 0.004 0.040 3428 Dihedral : 7.089 83.361 2832 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.15 % Allowed : 13.43 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.17), residues: 2436 helix: 1.90 (0.14), residues: 1452 sheet: -0.58 (0.51), residues: 112 loop : -0.04 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 351 HIS 0.003 0.001 HIS D 313 PHE 0.009 0.001 PHE C 75 TYR 0.012 0.001 TYR D 514 ARG 0.005 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 1128) hydrogen bonds : angle 3.66414 ( 3240) covalent geometry : bond 0.00240 (20488) covalent geometry : angle 0.46666 (27796) *********************** 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 346 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 280 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.7711 (ttp80) cc_final: 0.7334 (ttp80) REVERT: A 186 ASN cc_start: 0.8134 (m-40) cc_final: 0.7886 (m110) REVERT: A 263 ASN cc_start: 0.8239 (t0) cc_final: 0.7861 (t0) REVERT: A 280 ARG cc_start: 0.6760 (mtm110) cc_final: 0.6281 (mtm180) REVERT: A 308 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7805 (mt) REVERT: A 333 TRP cc_start: 0.8624 (p-90) cc_final: 0.8132 (p-90) REVERT: A 485 LEU cc_start: 0.7866 (mt) cc_final: 0.7610 (mp) REVERT: A 612 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: A 683 HIS cc_start: 0.7575 (t-170) cc_final: 0.7266 (t-170) REVERT: B 79 ARG cc_start: 0.7695 (ttp80) cc_final: 0.7339 (ttp80) REVERT: B 127 ASN cc_start: 0.8167 (m110) cc_final: 0.7773 (m110) REVERT: B 223 TRP cc_start: 0.5026 (m100) cc_final: 0.4683 (t60) REVERT: B 263 ASN cc_start: 0.8217 (t0) cc_final: 0.7849 (t0) REVERT: B 280 ARG cc_start: 0.6714 (mtm110) cc_final: 0.6301 (mtm180) REVERT: B 308 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7833 (mt) REVERT: B 485 LEU cc_start: 0.7881 (mt) cc_final: 0.7650 (mp) REVERT: B 612 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6170 (m-10) REVERT: B 683 HIS cc_start: 0.7548 (t-170) cc_final: 0.7218 (t-170) REVERT: C 127 ASN cc_start: 0.8153 (m110) cc_final: 0.7757 (m110) REVERT: C 182 LEU cc_start: 0.8455 (tt) cc_final: 0.8183 (tp) REVERT: C 263 ASN cc_start: 0.8227 (t0) cc_final: 0.7866 (t0) REVERT: C 280 ARG cc_start: 0.6750 (mtm110) cc_final: 0.6261 (mtm180) REVERT: C 308 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7829 (mt) REVERT: C 333 TRP cc_start: 0.8627 (p-90) cc_final: 0.8136 (p-90) REVERT: C 612 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: C 683 HIS cc_start: 0.7561 (t-170) cc_final: 0.7084 (t-170) REVERT: D 280 ARG cc_start: 0.6775 (mtm110) cc_final: 0.6290 (mtm180) REVERT: D 308 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7820 (mt) REVERT: D 333 TRP cc_start: 0.8644 (p-90) cc_final: 0.8155 (p-90) REVERT: D 612 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6195 (m-10) REVERT: D 683 HIS cc_start: 0.7659 (t-170) cc_final: 0.7408 (t-170) outliers start: 66 outliers final: 38 residues processed: 326 average time/residue: 0.4084 time to fit residues: 200.6711 Evaluate side-chains 312 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 2.321 ------------------------------------------------------------------------------- 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 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 528 MET Chi-restraints excluded: chain A residue 545 LEU 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 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 528 MET 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 212 LEU 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 528 MET 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 110 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117925 restraints weight = 23235.943| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.32 r_work: 0.3186 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20488 Z= 0.241 Angle : 0.588 8.438 27796 Z= 0.295 Chirality : 0.040 0.212 3136 Planarity : 0.004 0.047 3428 Dihedral : 7.708 83.358 2832 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.54 % Allowed : 13.15 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.17), residues: 2436 helix: 1.60 (0.14), residues: 1448 sheet: -0.62 (0.52), residues: 112 loop : -0.36 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 351 HIS 0.006 0.001 HIS B 313 PHE 0.013 0.002 PHE D 472 TYR 0.018 0.002 TYR A 471 ARG 0.004 0.001 ARG A 86 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 1128) hydrogen bonds : angle 3.91530 ( 3240) covalent geometry : bond 0.00577 (20488) covalent geometry : angle 0.58806 (27796) *********************** 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 338 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 264 time to evaluate : 2.151 Fit side-chains REVERT: A 79 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7544 (ttt90) REVERT: A 186 ASN cc_start: 0.8147 (m-40) cc_final: 0.7891 (m110) REVERT: A 263 ASN cc_start: 0.8332 (t0) cc_final: 0.7982 (t0) REVERT: A 280 ARG cc_start: 0.6757 (mtm110) cc_final: 0.6399 (mtm180) REVERT: A 308 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7883 (mt) REVERT: A 612 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: A 616 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5904 (mt) REVERT: A 683 HIS cc_start: 0.7655 (t-170) cc_final: 0.7310 (t-170) REVERT: B 79 ARG cc_start: 0.7778 (ttp80) cc_final: 0.7552 (ttt90) REVERT: B 263 ASN cc_start: 0.8351 (t0) cc_final: 0.7978 (t0) REVERT: B 280 ARG cc_start: 0.6802 (mtm110) cc_final: 0.6434 (mtm180) REVERT: B 308 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7886 (mt) REVERT: B 612 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.6538 (m-80) REVERT: B 616 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5866 (mt) REVERT: B 683 HIS cc_start: 0.7676 (t-170) cc_final: 0.7321 (t-170) REVERT: C 228 TYR cc_start: 0.7506 (t80) cc_final: 0.7108 (t80) REVERT: C 263 ASN cc_start: 0.8340 (t0) cc_final: 0.7977 (t0) REVERT: C 280 ARG cc_start: 0.6741 (mtm110) cc_final: 0.6379 (mtm180) REVERT: C 308 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7893 (mt) REVERT: C 612 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6575 (m-80) REVERT: C 616 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5830 (mt) REVERT: C 683 HIS cc_start: 0.7649 (t-170) cc_final: 0.7297 (t-170) REVERT: D 79 ARG cc_start: 0.7786 (ttp80) cc_final: 0.7513 (ttt90) REVERT: D 280 ARG cc_start: 0.6770 (mtm110) cc_final: 0.6396 (mtm180) REVERT: D 308 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7890 (mt) REVERT: D 612 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6543 (m-80) REVERT: D 616 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5865 (mt) REVERT: D 683 HIS cc_start: 0.7803 (t-170) cc_final: 0.7530 (t-170) outliers start: 74 outliers final: 45 residues processed: 311 average time/residue: 0.3507 time to fit residues: 161.5402 Evaluate side-chains 318 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 2.113 ------------------------------------------------------------------------------- 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 401 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 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 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 401 LEU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 637 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 401 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 637 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 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 401 LEU 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 612 PHE Chi-restraints excluded: chain D residue 616 LEU Chi-restraints excluded: chain D residue 637 LEU Chi-restraints excluded: chain D residue 641 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 155 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 232 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 188 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.164004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122992 restraints weight = 22900.190| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.29 r_work: 0.3189 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20488 Z= 0.103 Angle : 0.479 8.423 27796 Z= 0.244 Chirality : 0.037 0.201 3136 Planarity : 0.004 0.042 3428 Dihedral : 7.280 79.522 2832 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.44 % Allowed : 14.34 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.17), residues: 2436 helix: 1.90 (0.14), residues: 1452 sheet: -0.54 (0.52), residues: 112 loop : -0.22 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 351 HIS 0.002 0.001 HIS B 313 PHE 0.009 0.001 PHE D 75 TYR 0.015 0.001 TYR C 228 ARG 0.005 0.000 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 1128) hydrogen bonds : angle 3.65524 ( 3240) covalent geometry : bond 0.00234 (20488) covalent geometry : angle 0.47946 (27796) *********************** 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: 51 poor density : 260 time to evaluate : 2.375 Fit side-chains REVERT: A 186 ASN cc_start: 0.8133 (m-40) cc_final: 0.7874 (m110) REVERT: A 263 ASN cc_start: 0.8228 (t0) cc_final: 0.7845 (t0) REVERT: A 280 ARG cc_start: 0.6687 (mtm110) cc_final: 0.6332 (mtm180) REVERT: A 308 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7797 (mt) REVERT: A 612 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: A 683 HIS cc_start: 0.7612 (t-170) cc_final: 0.7286 (t-170) REVERT: B 127 ASN cc_start: 0.8121 (m110) cc_final: 0.7626 (m110) REVERT: B 263 ASN cc_start: 0.8225 (t0) cc_final: 0.7849 (t0) REVERT: B 269 HIS cc_start: 0.8000 (t-90) cc_final: 0.7506 (t70) REVERT: B 280 ARG cc_start: 0.6754 (mtm110) cc_final: 0.6445 (mtm180) REVERT: B 308 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7802 (mt) REVERT: B 612 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: B 616 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5715 (mt) REVERT: B 683 HIS cc_start: 0.7590 (t-170) cc_final: 0.7248 (t-170) REVERT: C 79 ARG cc_start: 0.7889 (ttt90) cc_final: 0.7684 (ttp80) REVERT: C 127 ASN cc_start: 0.8107 (m110) cc_final: 0.7615 (m110) REVERT: C 263 ASN cc_start: 0.8237 (t0) cc_final: 0.7862 (t0) REVERT: C 280 ARG cc_start: 0.6708 (mtm110) cc_final: 0.6355 (mtm180) REVERT: C 308 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7811 (mt) REVERT: C 537 LEU cc_start: 0.5877 (OUTLIER) cc_final: 0.5549 (mm) REVERT: C 612 PHE cc_start: 0.6724 (OUTLIER) cc_final: 0.6505 (m-80) REVERT: C 683 HIS cc_start: 0.7582 (t-170) cc_final: 0.7248 (t-170) REVERT: D 186 ASN cc_start: 0.8166 (m-40) cc_final: 0.7886 (m110) REVERT: D 280 ARG cc_start: 0.6709 (mtm110) cc_final: 0.6354 (mtm180) REVERT: D 308 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7805 (mt) REVERT: D 612 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: D 616 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5728 (mt) REVERT: D 683 HIS cc_start: 0.7691 (t-170) cc_final: 0.7419 (t-170) outliers start: 51 outliers final: 26 residues processed: 293 average time/residue: 0.3663 time to fit residues: 158.3492 Evaluate side-chains 288 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE 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 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 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 616 LEU Chi-restraints excluded: chain C residue 91 GLU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 125 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.157075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115575 restraints weight = 23356.956| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.31 r_work: 0.3144 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 20488 Z= 0.345 Angle : 0.676 8.741 27796 Z= 0.338 Chirality : 0.043 0.180 3136 Planarity : 0.005 0.053 3428 Dihedral : 8.190 86.309 2832 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.11 % Allowed : 13.77 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2436 helix: 1.35 (0.14), residues: 1452 sheet: -0.90 (0.50), residues: 112 loop : -0.65 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 351 HIS 0.007 0.001 HIS A 313 PHE 0.020 0.002 PHE B 472 TYR 0.022 0.002 TYR A 471 ARG 0.007 0.001 ARG A 79 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 1128) hydrogen bonds : angle 4.09210 ( 3240) covalent geometry : bond 0.00828 (20488) covalent geometry : angle 0.67575 (27796) *********************** 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: 65 poor density : 267 time to evaluate : 2.098 Fit side-chains REVERT: A 79 ARG cc_start: 0.7891 (ttt90) cc_final: 0.7654 (ttp80) REVERT: A 186 ASN cc_start: 0.8196 (m-40) cc_final: 0.7973 (m110) REVERT: A 263 ASN cc_start: 0.8413 (t0) cc_final: 0.8055 (t0) REVERT: A 280 ARG cc_start: 0.6754 (mtm110) cc_final: 0.6445 (mtm180) REVERT: A 308 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7915 (mt) REVERT: A 599 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6284 (mm-30) REVERT: A 612 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: A 616 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6034 (mt) REVERT: A 683 HIS cc_start: 0.7663 (t-170) cc_final: 0.7291 (t-170) REVERT: B 79 ARG cc_start: 0.7947 (ttt90) cc_final: 0.7724 (ttp80) REVERT: B 280 ARG cc_start: 0.6916 (mtm110) cc_final: 0.6575 (mtm180) REVERT: B 308 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7907 (mt) REVERT: B 537 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5878 (mm) REVERT: B 599 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6264 (mm-30) REVERT: B 612 PHE cc_start: 0.7029 (OUTLIER) cc_final: 0.6638 (m-80) REVERT: B 616 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5994 (mt) REVERT: B 683 HIS cc_start: 0.7690 (t-170) cc_final: 0.7308 (t-170) REVERT: C 280 ARG cc_start: 0.6754 (mtm110) cc_final: 0.6451 (mtm180) REVERT: C 308 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7914 (mt) REVERT: C 537 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5865 (mm) REVERT: C 599 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6282 (mm-30) REVERT: C 612 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: C 616 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6028 (mt) REVERT: C 683 HIS cc_start: 0.7673 (t-170) cc_final: 0.7293 (t-170) REVERT: D 79 ARG cc_start: 0.7945 (ttt90) cc_final: 0.7737 (ttp80) REVERT: D 186 ASN cc_start: 0.8215 (m-40) cc_final: 0.7966 (m110) REVERT: D 280 ARG cc_start: 0.6766 (mtm110) cc_final: 0.6455 (mtm180) REVERT: D 308 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7918 (mt) REVERT: D 537 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5866 (mm) REVERT: D 599 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6284 (mm-30) REVERT: D 612 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6654 (m-80) REVERT: D 616 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6003 (mt) REVERT: D 683 HIS cc_start: 0.7815 (t-170) cc_final: 0.7536 (t-170) outliers start: 65 outliers final: 32 residues processed: 313 average time/residue: 0.3505 time to fit residues: 160.4539 Evaluate side-chains 309 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 262 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 308 ILE Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 409 VAL 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 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 409 VAL 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 C residue 75 PHE 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 409 VAL 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 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 409 VAL Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 534 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 55 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 153 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 234 optimal weight: 0.0270 chunk 81 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.163700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122425 restraints weight = 22938.174| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.33 r_work: 0.3241 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2292 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= 0.107 Angle : 0.508 10.303 27796 Z= 0.255 Chirality : 0.037 0.165 3136 Planarity : 0.004 0.044 3428 Dihedral : 7.519 82.369 2832 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.06 % Allowed : 14.67 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2436 helix: 1.78 (0.14), residues: 1452 sheet: -0.87 (0.49), residues: 112 loop : -0.32 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 660 HIS 0.003 0.001 HIS A 521 PHE 0.008 0.001 PHE C 394 TYR 0.013 0.001 TYR C 228 ARG 0.005 0.001 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.03234 ( 1128) hydrogen bonds : angle 3.69686 ( 3240) covalent geometry : bond 0.00246 (20488) covalent geometry : angle 0.50813 (27796) *********************** 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 301 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 2.732 Fit side-chains REVERT: A 182 LEU cc_start: 0.8487 (tt) cc_final: 0.8208 (tp) REVERT: A 186 ASN cc_start: 0.8166 (m-40) cc_final: 0.7913 (m110) REVERT: A 228 TYR cc_start: 0.7524 (t80) cc_final: 0.7184 (t80) REVERT: A 263 ASN cc_start: 0.8232 (t0) cc_final: 0.7866 (t0) REVERT: A 280 ARG cc_start: 0.6671 (mtm110) cc_final: 0.6375 (mtm180) REVERT: A 308 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7810 (mt) REVERT: A 612 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6603 (m-80) REVERT: A 616 LEU cc_start: 0.6251 (OUTLIER) cc_final: 0.5872 (mt) REVERT: A 683 HIS cc_start: 0.7612 (t-170) cc_final: 0.7251 (t-170) REVERT: B 127 ASN cc_start: 0.8084 (m110) cc_final: 0.7553 (m110) REVERT: B 228 TYR cc_start: 0.7593 (t80) cc_final: 0.7274 (t80) REVERT: B 247 ASN cc_start: 0.8681 (m110) cc_final: 0.8405 (m-40) REVERT: B 263 ASN cc_start: 0.8230 (t0) cc_final: 0.7851 (t0) REVERT: B 269 HIS cc_start: 0.8020 (t-90) cc_final: 0.7589 (t70) REVERT: B 280 ARG cc_start: 0.6754 (mtm110) cc_final: 0.6463 (mtm180) REVERT: B 308 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7821 (mt) REVERT: B 612 PHE cc_start: 0.6840 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: B 616 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5759 (mt) REVERT: B 683 HIS cc_start: 0.7616 (t-170) cc_final: 0.7255 (t-170) REVERT: C 127 ASN cc_start: 0.8076 (m110) cc_final: 0.7545 (m110) REVERT: C 247 ASN cc_start: 0.8682 (m110) cc_final: 0.8407 (m-40) REVERT: C 263 ASN cc_start: 0.8252 (t0) cc_final: 0.7878 (t0) REVERT: C 280 ARG cc_start: 0.6679 (mtm110) cc_final: 0.6384 (mtm180) REVERT: C 308 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7815 (mt) REVERT: C 612 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6620 (m-80) REVERT: C 683 HIS cc_start: 0.7595 (t-170) cc_final: 0.7242 (t-170) REVERT: D 127 ASN cc_start: 0.8088 (m110) cc_final: 0.7558 (m110) REVERT: D 186 ASN cc_start: 0.8192 (m-40) cc_final: 0.7945 (m110) REVERT: D 228 TYR cc_start: 0.7560 (t80) cc_final: 0.7231 (t80) REVERT: D 280 ARG cc_start: 0.6688 (mtm110) cc_final: 0.6408 (mtm180) REVERT: D 308 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7822 (mt) REVERT: D 612 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: D 616 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5787 (mt) REVERT: D 683 HIS cc_start: 0.7766 (t-170) cc_final: 0.7485 (t-170) outliers start: 43 outliers final: 23 residues processed: 287 average time/residue: 0.5285 time to fit residues: 230.5843 Evaluate side-chains 282 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 2.846 ------------------------------------------------------------------------------- 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 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 612 PHE Chi-restraints excluded: chain A residue 616 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 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 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 446 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 75 PHE 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 612 PHE Chi-restraints excluded: chain D residue 616 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 222 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 120 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 0.0970 chunk 5 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.162252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.121017 restraints weight = 23007.831| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.32 r_work: 0.3221 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2319 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= 0.146 Angle : 0.527 9.122 27796 Z= 0.263 Chirality : 0.038 0.174 3136 Planarity : 0.004 0.044 3428 Dihedral : 7.490 83.997 2832 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.96 % Allowed : 14.77 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.17), residues: 2436 helix: 1.81 (0.14), residues: 1452 sheet: -0.84 (0.49), residues: 112 loop : -0.31 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 333 HIS 0.004 0.001 HIS A 313 PHE 0.009 0.001 PHE A 75 TYR 0.014 0.001 TYR D 471 ARG 0.007 0.000 ARG C 79 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 1128) hydrogen bonds : angle 3.73598 ( 3240) covalent geometry : bond 0.00346 (20488) covalent geometry : angle 0.52674 (27796) ********************** 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 293 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 2.303 Fit side-chains REVERT: A 182 LEU cc_start: 0.8505 (tt) cc_final: 0.8209 (tp) REVERT: A 186 ASN cc_start: 0.8190 (m-40) cc_final: 0.7925 (m110) REVERT: A 228 TYR cc_start: 0.7559 (t80) cc_final: 0.7214 (t80) REVERT: A 263 ASN cc_start: 0.8257 (t0) cc_final: 0.7894 (t0) REVERT: A 280 ARG cc_start: 0.6734 (mtm110) cc_final: 0.6428 (mtm180) REVERT: A 308 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7834 (mt) REVERT: A 612 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: A 616 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5882 (mt) REVERT: A 683 HIS cc_start: 0.7620 (t-170) cc_final: 0.7256 (t-170) REVERT: B 127 ASN cc_start: 0.8094 (m110) cc_final: 0.7559 (m110) REVERT: B 228 TYR cc_start: 0.7625 (t80) cc_final: 0.7301 (t80) REVERT: B 247 ASN cc_start: 0.8680 (m110) cc_final: 0.8416 (m-40) REVERT: B 263 ASN cc_start: 0.8254 (t0) cc_final: 0.7895 (t0) REVERT: B 280 ARG cc_start: 0.6782 (mtm110) cc_final: 0.6489 (mtm180) REVERT: B 308 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7847 (mt) REVERT: B 537 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5628 (mm) REVERT: B 616 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5825 (mt) REVERT: B 683 HIS cc_start: 0.7620 (t-170) cc_final: 0.7260 (t-170) REVERT: C 127 ASN cc_start: 0.8125 (m110) cc_final: 0.7606 (m110) REVERT: C 247 ASN cc_start: 0.8676 (m110) cc_final: 0.8410 (m-40) REVERT: C 263 ASN cc_start: 0.8268 (t0) cc_final: 0.7911 (t0) REVERT: C 280 ARG cc_start: 0.6724 (mtm110) cc_final: 0.6429 (mtm180) REVERT: C 308 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7837 (mt) REVERT: C 616 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5801 (mt) REVERT: C 683 HIS cc_start: 0.7604 (t-170) cc_final: 0.7245 (t-170) REVERT: D 127 ASN cc_start: 0.8105 (m110) cc_final: 0.7574 (m110) REVERT: D 186 ASN cc_start: 0.8209 (m-40) cc_final: 0.7973 (m110) REVERT: D 228 TYR cc_start: 0.7603 (t80) cc_final: 0.7263 (t80) REVERT: D 280 ARG cc_start: 0.6744 (mtm110) cc_final: 0.6434 (mtm180) REVERT: D 308 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7841 (mt) REVERT: D 616 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5827 (mt) REVERT: D 683 HIS cc_start: 0.7805 (t-170) cc_final: 0.7511 (t-170) outliers start: 41 outliers final: 24 residues processed: 281 average time/residue: 0.3907 time to fit residues: 162.3911 Evaluate side-chains 288 residues out of total 2216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 1.819 ------------------------------------------------------------------------------- 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 612 PHE Chi-restraints excluded: chain A residue 616 LEU 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 616 LEU 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 446 ILE Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 616 LEU 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 409 VAL Chi-restraints excluded: chain D residue 446 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 616 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.8980 chunk 65 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 32 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.161699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120216 restraints weight = 23193.130| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.33 r_work: 0.3226 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20488 Z= 0.169 Angle : 0.543 9.757 27796 Z= 0.270 Chirality : 0.039 0.168 3136 Planarity : 0.004 0.045 3428 Dihedral : 7.603 87.386 2832 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.86 % Allowed : 15.11 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.17), residues: 2436 helix: 1.76 (0.14), residues: 1448 sheet: -0.86 (0.49), residues: 112 loop : -0.38 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 333 HIS 0.004 0.001 HIS B 313 PHE 0.009 0.001 PHE C 472 TYR 0.014 0.001 TYR C 471 ARG 0.007 0.000 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 1128) hydrogen bonds : angle 3.76497 ( 3240) covalent geometry : bond 0.00404 (20488) covalent geometry : angle 0.54300 (27796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9641.88 seconds wall clock time: 173 minutes 31.43 seconds (10411.43 seconds total)