Starting phenix.real_space_refine on Thu Mar 5 04:51:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zjd_14745/03_2026/7zjd_14745.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zjd_14745/03_2026/7zjd_14745.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zjd_14745/03_2026/7zjd_14745.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zjd_14745/03_2026/7zjd_14745.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zjd_14745/03_2026/7zjd_14745.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zjd_14745/03_2026/7zjd_14745.map" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12712 2.51 5 N 3232 2.21 5 O 3304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19360 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4840 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 18, 'TRANS': 578} Chain breaks: 3 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 35 Restraints were copied for chains: C, B, D Time building chain proxies: 3.96, per 1000 atoms: 0.20 Number of scatterers: 19360 At special positions: 0 Unit cell: (168.434, 168.434, 113.418, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3304 8.00 N 3232 7.00 C 12712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 847.7 milliseconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 4 sheets defined 63.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 Processing helix chain 'A' and resid 88 through 98 removed outlier: 4.181A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 removed outlier: 3.560A pdb=" N ASP A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.911A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.967A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.689A pdb=" N GLU A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.649A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.928A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 413 removed outlier: 3.603A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.332A 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 459 through 466 removed outlier: 3.797A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.613A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.055A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.897A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 534 removed outlier: 3.631A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 560 removed outlier: 3.523A pdb=" N PHE A 540 " --> pdb=" O ASP A 536 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 605 removed outlier: 3.608A pdb=" N ALA A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 646 removed outlier: 3.541A pdb=" N VAL A 622 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 672 removed outlier: 3.548A pdb=" N ILE A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 88 through 98 removed outlier: 4.181A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 removed outlier: 3.559A pdb=" N ASP C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.912A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.968A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.688A pdb=" N GLU C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.648A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 286 through 290' Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.927A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 413 removed outlier: 3.604A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.332A 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 459 through 466 removed outlier: 3.797A pdb=" N ILE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 470 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.614A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.055A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.897A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.632A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 560 removed outlier: 3.523A pdb=" N PHE C 540 " --> pdb=" O ASP C 536 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 553 " --> pdb=" O PHE C 549 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG C 560 " --> pdb=" O VAL C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 removed outlier: 3.608A pdb=" N ALA C 596 " --> pdb=" O SER C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 646 removed outlier: 3.541A pdb=" N VAL C 622 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 672 removed outlier: 3.548A pdb=" N ILE C 659 " --> pdb=" O ASN C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 718 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 88 through 98 removed outlier: 4.182A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR B 93 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.559A pdb=" N ASP B 145 " --> pdb=" O GLN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.911A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.967A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.689A pdb=" N GLU B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.649A pdb=" N GLU B 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 290' Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.928A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 413 removed outlier: 3.604A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.331A 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 459 through 466 removed outlier: 3.798A pdb=" N ILE B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 470 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.613A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.055A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.897A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 534 removed outlier: 3.631A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 560 removed outlier: 3.523A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 560 " --> pdb=" O VAL B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 605 removed outlier: 3.608A pdb=" N ALA B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 646 removed outlier: 3.541A pdb=" N VAL B 622 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B 624 " --> pdb=" O GLY B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 672 removed outlier: 3.548A pdb=" N ILE B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 718 Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 88 through 98 removed outlier: 4.180A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 removed outlier: 3.560A pdb=" N ASP D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.911A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.966A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.688A pdb=" N GLU D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.650A pdb=" N GLU D 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 286 through 290' Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.928A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 413 removed outlier: 3.603A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.332A 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 459 through 466 removed outlier: 3.798A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 470 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.614A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.055A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.897A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 removed outlier: 3.631A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 560 removed outlier: 3.523A pdb=" N PHE D 540 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL D 553 " --> pdb=" O PHE D 549 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG D 560 " --> pdb=" O VAL D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 605 removed outlier: 3.608A pdb=" N ALA D 596 " --> pdb=" O SER D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 646 removed outlier: 3.541A pdb=" N VAL D 622 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 623 " --> pdb=" O ARG D 619 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU D 624 " --> pdb=" O GLY D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 672 removed outlier: 3.549A pdb=" N ILE D 659 " --> pdb=" O ASN D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 718 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 334 removed outlier: 7.255A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 329 through 334 removed outlier: 7.254A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 329 through 334 removed outlier: 7.255A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 334 removed outlier: 7.255A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) 1009 hydrogen bonds defined for protein. 2979 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4648 1.33 - 1.45: 4104 1.45 - 1.57: 10920 1.57 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 19844 Sorted by residual: bond pdb=" CA MET B 137 " pdb=" C MET B 137 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.15e-01 bond pdb=" CA MET D 137 " pdb=" C MET D 137 " ideal model delta sigma weight residual 1.522 1.534 -0.012 1.26e-02 6.30e+03 9.15e-01 bond pdb=" C ASN A 148 " pdb=" N PRO A 149 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.58e-01 bond pdb=" CA MET C 137 " pdb=" C MET C 137 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.26e-02 6.30e+03 8.12e-01 bond pdb=" CA MET A 137 " pdb=" C MET A 137 " ideal model delta sigma weight residual 1.522 1.533 -0.011 1.26e-02 6.30e+03 8.11e-01 ... (remaining 19839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 26425 1.79 - 3.58: 422 3.58 - 5.36: 65 5.36 - 7.15: 4 7.15 - 8.94: 4 Bond angle restraints: 26920 Sorted by residual: angle pdb=" N ASN B 186 " pdb=" CA ASN B 186 " pdb=" C ASN B 186 " ideal model delta sigma weight residual 107.80 112.75 -4.95 1.73e+00 3.34e-01 8.19e+00 angle pdb=" N ASN A 186 " pdb=" CA ASN A 186 " pdb=" C ASN A 186 " ideal model delta sigma weight residual 107.80 112.72 -4.92 1.73e+00 3.34e-01 8.08e+00 angle pdb=" N ASN C 186 " pdb=" CA ASN C 186 " pdb=" C ASN C 186 " ideal model delta sigma weight residual 107.80 112.71 -4.91 1.73e+00 3.34e-01 8.06e+00 angle pdb=" N ASN D 186 " pdb=" CA ASN D 186 " pdb=" C ASN D 186 " ideal model delta sigma weight residual 107.80 112.70 -4.90 1.73e+00 3.34e-01 8.02e+00 angle pdb=" CA MET A 137 " pdb=" CB MET A 137 " pdb=" CG MET A 137 " ideal model delta sigma weight residual 114.10 119.28 -5.18 2.00e+00 2.50e-01 6.72e+00 ... (remaining 26915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 10392 17.24 - 34.48: 984 34.48 - 51.72: 196 51.72 - 68.95: 32 68.95 - 86.19: 20 Dihedral angle restraints: 11624 sinusoidal: 4640 harmonic: 6984 Sorted by residual: dihedral pdb=" CA LEU A 375 " pdb=" C LEU A 375 " pdb=" N GLU A 376 " pdb=" CA GLU A 376 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LEU D 375 " pdb=" C LEU D 375 " pdb=" N GLU D 376 " pdb=" CA GLU D 376 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LEU B 375 " pdb=" C LEU B 375 " pdb=" N GLU B 376 " pdb=" CA GLU B 376 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 11621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2264 0.042 - 0.083: 632 0.083 - 0.125: 145 0.125 - 0.166: 7 0.166 - 0.208: 4 Chirality restraints: 3052 Sorted by residual: chirality pdb=" CA MET D 137 " pdb=" N MET D 137 " pdb=" C MET D 137 " pdb=" CB MET D 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA MET C 137 " pdb=" N MET C 137 " pdb=" C MET C 137 " pdb=" CB MET C 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA MET A 137 " pdb=" N MET A 137 " pdb=" C MET A 137 " pdb=" CB MET A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3049 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 481 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C LEU A 481 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU A 481 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 482 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 481 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C LEU C 481 " 0.036 2.00e-02 2.50e+03 pdb=" O LEU C 481 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 482 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 481 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C LEU D 481 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU D 481 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU D 482 " 0.012 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5808 2.83 - 3.35: 18721 3.35 - 3.86: 29848 3.86 - 4.38: 33085 4.38 - 4.90: 57987 Nonbonded interactions: 145449 Sorted by model distance: nonbonded pdb=" OD1 ASP B 159 " pdb=" NE2 GLN B 163 " model vdw 2.311 3.120 nonbonded pdb=" OD1 ASP D 159 " pdb=" NE2 GLN D 163 " model vdw 2.311 3.120 nonbonded pdb=" OD1 ASP A 159 " pdb=" NE2 GLN A 163 " model vdw 2.311 3.120 nonbonded pdb=" OD1 ASP C 159 " pdb=" NE2 GLN C 163 " model vdw 2.312 3.120 nonbonded pdb=" OD1 ASN C 368 " pdb=" NH2 ARG C 371 " model vdw 2.343 3.120 ... (remaining 145444 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: 0.05 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19844 Z= 0.122 Angle : 0.560 8.938 26920 Z= 0.294 Chirality : 0.039 0.208 3052 Planarity : 0.004 0.033 3304 Dihedral : 14.117 86.194 7112 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.58 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.18), residues: 2356 helix: 1.50 (0.14), residues: 1412 sheet: -2.61 (0.60), residues: 84 loop : -2.39 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 619 TYR 0.012 0.001 TYR D 525 PHE 0.027 0.001 PHE A 519 TRP 0.011 0.001 TRP A 333 HIS 0.002 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00256 (19844) covalent geometry : angle 0.56041 (26920) hydrogen bonds : bond 0.14410 ( 1009) hydrogen bonds : angle 5.42958 ( 2979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.730 Fit side-chains REVERT: A 179 CYS cc_start: 0.8187 (m) cc_final: 0.7691 (m) REVERT: C 179 CYS cc_start: 0.8163 (m) cc_final: 0.7664 (m) REVERT: B 179 CYS cc_start: 0.8169 (m) cc_final: 0.7677 (m) REVERT: D 179 CYS cc_start: 0.8189 (m) cc_final: 0.7693 (m) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.5871 time to fit residues: 155.2179 Evaluate side-chains 165 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.179156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.108975 restraints weight = 23609.375| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.59 r_work: 0.3118 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19844 Z= 0.151 Angle : 0.580 6.969 26920 Z= 0.292 Chirality : 0.040 0.187 3052 Planarity : 0.003 0.038 3304 Dihedral : 4.042 19.650 2600 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.79 % Favored : 92.87 % Rotamer: Outliers : 1.25 % Allowed : 9.67 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.18), residues: 2356 helix: 1.82 (0.14), residues: 1452 sheet: -2.58 (0.60), residues: 84 loop : -2.69 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 371 TYR 0.013 0.001 TYR A 471 PHE 0.018 0.001 PHE A 407 TRP 0.011 0.001 TRP C 333 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00360 (19844) covalent geometry : angle 0.58023 (26920) hydrogen bonds : bond 0.05408 ( 1009) hydrogen bonds : angle 3.64928 ( 2979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.641 Fit side-chains REVERT: A 179 CYS cc_start: 0.8427 (m) cc_final: 0.7941 (m) REVERT: A 272 ASP cc_start: 0.8295 (m-30) cc_final: 0.7959 (m-30) REVERT: A 708 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: A 711 ASN cc_start: 0.8798 (t0) cc_final: 0.8560 (t0) REVERT: C 179 CYS cc_start: 0.8422 (m) cc_final: 0.7939 (m) REVERT: C 708 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: C 711 ASN cc_start: 0.8799 (t0) cc_final: 0.8560 (t0) REVERT: B 179 CYS cc_start: 0.8457 (m) cc_final: 0.7988 (m) REVERT: B 708 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 711 ASN cc_start: 0.8810 (t0) cc_final: 0.8567 (t0) REVERT: D 179 CYS cc_start: 0.8449 (m) cc_final: 0.7967 (m) REVERT: D 708 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: D 711 ASN cc_start: 0.8787 (t0) cc_final: 0.8547 (t0) outliers start: 26 outliers final: 12 residues processed: 184 average time/residue: 0.4886 time to fit residues: 105.1532 Evaluate side-chains 175 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 678 CYS Chi-restraints excluded: chain D residue 708 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 28 optimal weight: 1.9990 chunk 200 optimal weight: 0.0770 chunk 136 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 71 optimal weight: 0.0670 chunk 6 optimal weight: 40.0000 chunk 38 optimal weight: 1.9990 chunk 119 optimal weight: 0.0770 chunk 75 optimal weight: 0.4980 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.184998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116217 restraints weight = 23971.819| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.61 r_work: 0.3204 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19844 Z= 0.098 Angle : 0.494 6.365 26920 Z= 0.250 Chirality : 0.037 0.184 3052 Planarity : 0.003 0.037 3304 Dihedral : 3.674 16.947 2600 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.07 % Favored : 93.59 % Rotamer: Outliers : 1.20 % Allowed : 11.93 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2356 helix: 2.14 (0.14), residues: 1456 sheet: -2.40 (0.60), residues: 84 loop : -2.51 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 687 TYR 0.011 0.001 TYR C 335 PHE 0.008 0.001 PHE D 519 TRP 0.010 0.001 TRP A 333 HIS 0.002 0.000 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00207 (19844) covalent geometry : angle 0.49401 (26920) hydrogen bonds : bond 0.03505 ( 1009) hydrogen bonds : angle 3.26955 ( 2979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.811 Fit side-chains REVERT: A 179 CYS cc_start: 0.8387 (m) cc_final: 0.7924 (m) REVERT: A 468 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7914 (tpt) REVERT: C 179 CYS cc_start: 0.8382 (m) cc_final: 0.7916 (m) REVERT: C 468 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.7915 (tpt) REVERT: B 179 CYS cc_start: 0.8394 (m) cc_final: 0.7918 (m) REVERT: B 468 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7922 (tpt) REVERT: D 179 CYS cc_start: 0.8362 (m) cc_final: 0.7920 (m) REVERT: D 468 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.7979 (tpt) outliers start: 25 outliers final: 4 residues processed: 195 average time/residue: 0.5391 time to fit residues: 121.2279 Evaluate side-chains 167 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain D residue 534 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 184 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 230 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 75 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 711 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.180360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.110121 restraints weight = 23832.038| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.61 r_work: 0.3145 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19844 Z= 0.117 Angle : 0.529 9.154 26920 Z= 0.263 Chirality : 0.038 0.191 3052 Planarity : 0.003 0.039 3304 Dihedral : 3.734 17.798 2600 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.75 % Favored : 92.91 % Rotamer: Outliers : 1.44 % Allowed : 13.70 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2356 helix: 2.14 (0.14), residues: 1456 sheet: -2.34 (0.60), residues: 84 loop : -2.49 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 679 TYR 0.010 0.001 TYR A 335 PHE 0.012 0.001 PHE C 519 TRP 0.008 0.001 TRP B 509 HIS 0.004 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00271 (19844) covalent geometry : angle 0.52912 (26920) hydrogen bonds : bond 0.04449 ( 1009) hydrogen bonds : angle 3.26060 ( 2979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.776 Fit side-chains REVERT: A 179 CYS cc_start: 0.8413 (m) cc_final: 0.7944 (m) REVERT: A 468 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.7954 (tpt) REVERT: C 179 CYS cc_start: 0.8386 (m) cc_final: 0.7908 (m) REVERT: C 468 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.7948 (tpt) REVERT: B 179 CYS cc_start: 0.8381 (m) cc_final: 0.7903 (m) REVERT: B 468 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7945 (tpt) REVERT: B 645 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6933 (tmt) REVERT: D 179 CYS cc_start: 0.8399 (m) cc_final: 0.7942 (m) REVERT: D 645 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6923 (tmt) outliers start: 30 outliers final: 10 residues processed: 184 average time/residue: 0.5134 time to fit residues: 109.9035 Evaluate side-chains 166 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 128 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 123 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 613 GLN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.177361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107234 restraints weight = 23881.587| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.57 r_work: 0.3052 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19844 Z= 0.143 Angle : 0.551 7.285 26920 Z= 0.276 Chirality : 0.039 0.208 3052 Planarity : 0.003 0.039 3304 Dihedral : 3.954 20.299 2600 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.79 % Favored : 92.87 % Rotamer: Outliers : 1.77 % Allowed : 15.33 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 2356 helix: 2.07 (0.14), residues: 1452 sheet: -2.38 (0.60), residues: 84 loop : -2.50 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 684 TYR 0.012 0.001 TYR C 335 PHE 0.016 0.001 PHE D 519 TRP 0.008 0.001 TRP D 509 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00343 (19844) covalent geometry : angle 0.55053 (26920) hydrogen bonds : bond 0.05156 ( 1009) hydrogen bonds : angle 3.33076 ( 2979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 152 time to evaluate : 0.497 Fit side-chains REVERT: A 179 CYS cc_start: 0.8393 (m) cc_final: 0.7919 (m) REVERT: A 528 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.6218 (mmt) REVERT: C 179 CYS cc_start: 0.8397 (m) cc_final: 0.7896 (m) REVERT: B 179 CYS cc_start: 0.8395 (m) cc_final: 0.7915 (m) REVERT: B 645 MET cc_start: 0.7394 (tmm) cc_final: 0.7135 (tmt) REVERT: D 179 CYS cc_start: 0.8419 (m) cc_final: 0.7944 (m) REVERT: D 645 MET cc_start: 0.7400 (tmm) cc_final: 0.6979 (tmt) outliers start: 37 outliers final: 14 residues processed: 172 average time/residue: 0.5485 time to fit residues: 107.6895 Evaluate side-chains 161 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 224 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.179019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.109212 restraints weight = 23888.445| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.60 r_work: 0.3083 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19844 Z= 0.115 Angle : 0.510 7.637 26920 Z= 0.257 Chirality : 0.038 0.213 3052 Planarity : 0.003 0.039 3304 Dihedral : 3.757 18.729 2600 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.62 % Favored : 93.04 % Rotamer: Outliers : 2.16 % Allowed : 15.76 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 2356 helix: 2.16 (0.14), residues: 1452 sheet: -2.40 (0.60), residues: 84 loop : -2.48 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 684 TYR 0.010 0.001 TYR C 228 PHE 0.012 0.001 PHE A 519 TRP 0.008 0.001 TRP A 333 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00267 (19844) covalent geometry : angle 0.50987 (26920) hydrogen bonds : bond 0.04324 ( 1009) hydrogen bonds : angle 3.22801 ( 2979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.768 Fit side-chains REVERT: A 179 CYS cc_start: 0.8383 (m) cc_final: 0.7881 (m) REVERT: A 516 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8358 (m) REVERT: A 612 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7253 (m-80) REVERT: A 661 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8329 (mtpp) REVERT: A 708 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: C 179 CYS cc_start: 0.8396 (m) cc_final: 0.7908 (m) REVERT: C 516 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8356 (m) REVERT: C 612 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7354 (m-80) REVERT: C 661 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8323 (mtpp) REVERT: C 708 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8054 (mt-10) REVERT: B 179 CYS cc_start: 0.8366 (m) cc_final: 0.7866 (m) REVERT: B 516 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8356 (m) REVERT: B 612 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: B 645 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6913 (tmt) REVERT: B 661 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8327 (mtpp) REVERT: B 708 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: D 179 CYS cc_start: 0.8403 (m) cc_final: 0.7910 (m) REVERT: D 516 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8361 (m) REVERT: D 612 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: D 645 MET cc_start: 0.7192 (tmm) cc_final: 0.6924 (tmt) REVERT: D 661 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8327 (mtpp) REVERT: D 708 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8072 (mt-10) outliers start: 45 outliers final: 13 residues processed: 199 average time/residue: 0.4917 time to fit residues: 113.6086 Evaluate side-chains 176 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 678 CYS Chi-restraints excluded: chain D residue 708 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 59 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 186 optimal weight: 0.0370 chunk 55 optimal weight: 0.4980 chunk 198 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.177761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107857 restraints weight = 23933.467| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.58 r_work: 0.3115 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19844 Z= 0.129 Angle : 0.532 7.925 26920 Z= 0.268 Chirality : 0.038 0.221 3052 Planarity : 0.003 0.040 3304 Dihedral : 3.829 19.705 2600 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.05 % Favored : 92.61 % Rotamer: Outliers : 2.35 % Allowed : 16.33 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2356 helix: 2.14 (0.14), residues: 1452 sheet: -2.48 (0.59), residues: 84 loop : -2.50 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 684 TYR 0.010 0.001 TYR C 228 PHE 0.015 0.001 PHE A 519 TRP 0.007 0.001 TRP A 333 HIS 0.004 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00305 (19844) covalent geometry : angle 0.53169 (26920) hydrogen bonds : bond 0.04761 ( 1009) hydrogen bonds : angle 3.28220 ( 2979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 0.733 Fit side-chains REVERT: A 179 CYS cc_start: 0.8384 (m) cc_final: 0.7875 (m) REVERT: A 516 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8330 (m) REVERT: A 612 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7025 (m-80) REVERT: A 708 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8108 (mt-10) REVERT: C 179 CYS cc_start: 0.8296 (m) cc_final: 0.7814 (m) REVERT: C 516 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8328 (m) REVERT: C 612 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7133 (m-80) REVERT: C 708 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: B 179 CYS cc_start: 0.8375 (m) cc_final: 0.7874 (m) REVERT: B 516 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8325 (m) REVERT: B 612 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: B 645 MET cc_start: 0.7196 (OUTLIER) cc_final: 0.6986 (tmt) REVERT: B 708 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: D 179 CYS cc_start: 0.8411 (m) cc_final: 0.7920 (m) REVERT: D 516 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8332 (m) REVERT: D 612 PHE cc_start: 0.7532 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: D 645 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6888 (tmt) REVERT: D 708 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8120 (mt-10) outliers start: 49 outliers final: 19 residues processed: 187 average time/residue: 0.5321 time to fit residues: 115.1433 Evaluate side-chains 178 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 678 CYS Chi-restraints excluded: chain D residue 708 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 126 optimal weight: 0.6980 chunk 211 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 181 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 GLN B 165 HIS ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.180756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111558 restraints weight = 23945.661| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.60 r_work: 0.3152 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19844 Z= 0.106 Angle : 0.508 7.880 26920 Z= 0.256 Chirality : 0.038 0.241 3052 Planarity : 0.003 0.039 3304 Dihedral : 3.672 17.772 2600 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.37 % Favored : 93.29 % Rotamer: Outliers : 2.30 % Allowed : 16.52 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.18), residues: 2356 helix: 2.25 (0.14), residues: 1452 sheet: -2.42 (0.59), residues: 84 loop : -2.46 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 684 TYR 0.011 0.001 TYR A 525 PHE 0.011 0.001 PHE A 519 TRP 0.007 0.001 TRP C 333 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00238 (19844) covalent geometry : angle 0.50759 (26920) hydrogen bonds : bond 0.03998 ( 1009) hydrogen bonds : angle 3.19049 ( 2979) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.8378 (m) cc_final: 0.7868 (m) REVERT: A 516 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8301 (m) REVERT: A 528 MET cc_start: 0.6323 (OUTLIER) cc_final: 0.6103 (mmt) REVERT: A 612 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.7100 (m-80) REVERT: A 661 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8245 (mtpp) REVERT: A 708 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: C 179 CYS cc_start: 0.8322 (m) cc_final: 0.7841 (m) REVERT: C 516 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8302 (m) REVERT: C 612 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: C 661 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8234 (mtpp) REVERT: C 708 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: B 179 CYS cc_start: 0.8347 (m) cc_final: 0.7873 (m) REVERT: B 516 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8296 (m) REVERT: B 612 PHE cc_start: 0.7412 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: B 645 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6548 (tmt) REVERT: B 661 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8255 (mtpp) REVERT: B 708 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: D 179 CYS cc_start: 0.8364 (m) cc_final: 0.7883 (m) REVERT: D 516 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8299 (m) REVERT: D 612 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: D 645 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6804 (tmt) REVERT: D 661 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8249 (mtpp) REVERT: D 708 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8072 (mt-10) outliers start: 48 outliers final: 12 residues processed: 183 average time/residue: 0.5716 time to fit residues: 119.5794 Evaluate side-chains 172 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 678 CYS Chi-restraints excluded: chain D residue 708 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 208 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 232 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 171 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 530 GLN D 530 GLN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.178293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.108185 restraints weight = 23712.376| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.59 r_work: 0.3120 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19844 Z= 0.127 Angle : 0.530 8.204 26920 Z= 0.269 Chirality : 0.039 0.253 3052 Planarity : 0.003 0.040 3304 Dihedral : 3.768 19.257 2600 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.09 % Favored : 92.57 % Rotamer: Outliers : 2.16 % Allowed : 17.00 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.18), residues: 2356 helix: 2.17 (0.14), residues: 1452 sheet: -2.43 (0.59), residues: 84 loop : -2.45 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 175 TYR 0.010 0.001 TYR C 544 PHE 0.014 0.001 PHE C 519 TRP 0.008 0.001 TRP C 677 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00300 (19844) covalent geometry : angle 0.53028 (26920) hydrogen bonds : bond 0.04672 ( 1009) hydrogen bonds : angle 3.26490 ( 2979) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 179 CYS cc_start: 0.8382 (m) cc_final: 0.7889 (m) REVERT: A 516 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8323 (m) REVERT: A 528 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.6178 (mmt) REVERT: A 612 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7041 (m-80) REVERT: A 661 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8265 (mtpp) REVERT: A 708 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: C 179 CYS cc_start: 0.8301 (m) cc_final: 0.7841 (m) REVERT: C 516 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8323 (m) REVERT: C 530 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6288 (mm110) REVERT: C 612 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: C 661 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8259 (mtpp) REVERT: C 708 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: B 179 CYS cc_start: 0.8312 (m) cc_final: 0.7864 (m) REVERT: B 516 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8321 (m) REVERT: B 612 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7212 (m-80) REVERT: B 645 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6747 (tmt) REVERT: B 661 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8262 (mtpp) REVERT: B 708 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: D 179 CYS cc_start: 0.8355 (m) cc_final: 0.7896 (m) REVERT: D 516 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8323 (m) REVERT: D 530 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.6263 (mm110) REVERT: D 612 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: D 645 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6799 (tmt) REVERT: D 661 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8269 (mtpp) REVERT: D 708 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8091 (mt-10) outliers start: 45 outliers final: 16 residues processed: 182 average time/residue: 0.5822 time to fit residues: 121.1596 Evaluate side-chains 179 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 678 CYS Chi-restraints excluded: chain D residue 708 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 192 optimal weight: 0.0670 chunk 165 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 530 GLN B 530 GLN D 530 GLN ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.180267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110965 restraints weight = 23860.166| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.59 r_work: 0.3138 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19844 Z= 0.115 Angle : 0.528 8.454 26920 Z= 0.267 Chirality : 0.038 0.267 3052 Planarity : 0.003 0.039 3304 Dihedral : 3.723 18.306 2600 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.45 % Favored : 93.21 % Rotamer: Outliers : 1.96 % Allowed : 17.39 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2356 helix: 2.23 (0.14), residues: 1452 sheet: -2.37 (0.60), residues: 84 loop : -2.39 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 77 TYR 0.012 0.001 TYR A 525 PHE 0.012 0.001 PHE A 519 TRP 0.009 0.001 TRP C 677 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00265 (19844) covalent geometry : angle 0.52817 (26920) hydrogen bonds : bond 0.04251 ( 1009) hydrogen bonds : angle 3.24291 ( 2979) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.894 Fit side-chains REVERT: A 179 CYS cc_start: 0.8347 (m) cc_final: 0.7881 (m) REVERT: A 516 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8305 (m) REVERT: A 528 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6177 (mmt) REVERT: A 612 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7056 (m-80) REVERT: A 661 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8241 (mtpp) REVERT: A 708 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: C 179 CYS cc_start: 0.8313 (m) cc_final: 0.7854 (m) REVERT: C 516 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8307 (m) REVERT: C 530 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6308 (mm110) REVERT: C 612 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: C 661 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8241 (mtpp) REVERT: C 708 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: B 179 CYS cc_start: 0.8347 (m) cc_final: 0.7900 (m) REVERT: B 516 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8301 (m) REVERT: B 530 GLN cc_start: 0.7219 (OUTLIER) cc_final: 0.6253 (mm110) REVERT: B 612 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: B 645 MET cc_start: 0.7177 (tmm) cc_final: 0.6775 (tmt) REVERT: B 661 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8259 (mtpp) REVERT: B 708 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: D 179 CYS cc_start: 0.8368 (m) cc_final: 0.7916 (m) REVERT: D 516 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8300 (m) REVERT: D 530 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6252 (mm110) REVERT: D 612 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7150 (m-80) REVERT: D 645 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6853 (tmt) REVERT: D 661 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8259 (mtpp) REVERT: D 708 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8075 (mt-10) outliers start: 41 outliers final: 15 residues processed: 177 average time/residue: 0.5667 time to fit residues: 114.9232 Evaluate side-chains 175 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 559 SER Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 530 GLN Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 612 PHE Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 530 GLN Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 645 MET Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 678 CYS Chi-restraints excluded: chain D residue 708 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 152 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 124 optimal weight: 0.0370 chunk 132 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 189 optimal weight: 20.0000 chunk 136 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 197 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.180341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110867 restraints weight = 23836.087| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.60 r_work: 0.3137 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.285 19844 Z= 0.247 Angle : 0.906 59.188 26920 Z= 0.539 Chirality : 0.039 0.378 3052 Planarity : 0.005 0.184 3304 Dihedral : 3.740 18.251 2600 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.49 % Favored : 93.17 % Rotamer: Outliers : 1.68 % Allowed : 17.62 % Favored : 80.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2356 helix: 2.21 (0.14), residues: 1452 sheet: -2.37 (0.60), residues: 84 loop : -2.39 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 684 TYR 0.010 0.001 TYR C 525 PHE 0.013 0.001 PHE A 519 TRP 0.009 0.001 TRP C 677 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00499 (19844) covalent geometry : angle 0.90605 (26920) hydrogen bonds : bond 0.04253 ( 1009) hydrogen bonds : angle 3.23863 ( 2979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7021.40 seconds wall clock time: 120 minutes 17.28 seconds (7217.28 seconds total)