Starting phenix.real_space_refine on Tue Nov 19 11:58:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjd_14745/11_2024/7zjd_14745.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjd_14745/11_2024/7zjd_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjd_14745/11_2024/7zjd_14745.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjd_14745/11_2024/7zjd_14745.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjd_14745/11_2024/7zjd_14745.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zjd_14745/11_2024/7zjd_14745.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Restraints were copied for chains: C, B, D Time building chain proxies: 10.60, per 1000 atoms: 0.55 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: 4.76 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.79 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: 4.95 Time building geometry restraints manager: 5.53 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 40.310 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.900 ------------------------------------------------------------------------------- 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= 0.168 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 : 5.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (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 TRP 0.011 0.001 TRP A 333 HIS 0.002 0.001 HIS A 251 PHE 0.027 0.001 PHE A 519 TYR 0.012 0.001 TYR D 525 ARG 0.001 0.000 ARG C 619 *********************** 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 : 2.211 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: 1.2100 time to fit residues: 321.2101 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 : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 184 optimal weight: 30.0000 chunk 71 optimal weight: 9.9990 chunk 112 optimal weight: 0.0000 chunk 137 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1323 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= 0.257 Angle : 0.596 6.985 26920 Z= 0.300 Chirality : 0.041 0.185 3052 Planarity : 0.003 0.038 3304 Dihedral : 4.113 20.471 2600 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.96 % Favored : 92.70 % Rotamer: Outliers : 1.25 % Allowed : 9.82 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2356 helix: 1.77 (0.14), residues: 1452 sheet: -2.56 (0.60), residues: 84 loop : -2.71 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 333 HIS 0.005 0.001 HIS D 251 PHE 0.020 0.002 PHE D 407 TYR 0.013 0.002 TYR D 471 ARG 0.002 0.000 ARG C 619 *********************** 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 202 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 2.278 Fit side-chains REVERT: A 179 CYS cc_start: 0.8227 (m) cc_final: 0.7696 (m) REVERT: A 272 ASP cc_start: 0.8296 (m-30) cc_final: 0.7994 (m-30) REVERT: A 708 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: A 711 ASN cc_start: 0.8978 (t0) cc_final: 0.8754 (t0) REVERT: C 179 CYS cc_start: 0.8221 (m) cc_final: 0.7693 (m) REVERT: C 272 ASP cc_start: 0.8292 (m-30) cc_final: 0.7990 (m-30) REVERT: C 277 MET cc_start: 0.8078 (ttm) cc_final: 0.7699 (ttm) REVERT: C 708 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: C 711 ASN cc_start: 0.8986 (t0) cc_final: 0.8760 (t0) REVERT: B 179 CYS cc_start: 0.8224 (m) cc_final: 0.7698 (m) REVERT: B 708 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: B 711 ASN cc_start: 0.8981 (t0) cc_final: 0.8755 (t0) REVERT: D 179 CYS cc_start: 0.8247 (m) cc_final: 0.7719 (m) REVERT: D 708 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: D 711 ASN cc_start: 0.8974 (t0) cc_final: 0.8748 (t0) outliers start: 26 outliers final: 12 residues processed: 192 average time/residue: 1.0953 time to fit residues: 243.5552 Evaluate side-chains 177 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 2.063 ------------------------------------------------------------------------------- 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 119 optimal weight: 0.0170 chunk 66 optimal weight: 0.3980 chunk 178 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 0.8980 chunk 231 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19844 Z= 0.152 Angle : 0.503 6.378 26920 Z= 0.256 Chirality : 0.038 0.182 3052 Planarity : 0.003 0.038 3304 Dihedral : 3.770 17.117 2600 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.11 % Favored : 93.55 % Rotamer: Outliers : 1.25 % Allowed : 11.97 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2356 helix: 2.07 (0.14), residues: 1460 sheet: -2.41 (0.60), residues: 84 loop : -2.52 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 333 HIS 0.002 0.001 HIS B 251 PHE 0.011 0.001 PHE C 519 TYR 0.013 0.001 TYR B 335 ARG 0.001 0.000 ARG B 684 *********************** 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 205 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 2.217 Fit side-chains REVERT: A 179 CYS cc_start: 0.8211 (m) cc_final: 0.7720 (m) REVERT: A 468 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7522 (tpt) REVERT: C 179 CYS cc_start: 0.8215 (m) cc_final: 0.7726 (m) REVERT: C 468 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7526 (tpt) REVERT: B 179 CYS cc_start: 0.8208 (m) cc_final: 0.7721 (m) REVERT: B 468 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7521 (tpt) REVERT: D 179 CYS cc_start: 0.8214 (m) cc_final: 0.7737 (m) REVERT: D 468 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7567 (tpt) outliers start: 26 outliers final: 4 residues processed: 194 average time/residue: 1.1050 time to fit residues: 248.7692 Evaluate side-chains 169 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 2.223 ------------------------------------------------------------------------------- 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 212 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 102 optimal weight: 0.8980 chunk 144 optimal weight: 0.0060 chunk 215 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5294 ------------------------------------------------------------------------------- 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 ** 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 639 ASN ** 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 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 711 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** D 711 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19844 Z= 0.141 Angle : 0.504 8.640 26920 Z= 0.250 Chirality : 0.037 0.191 3052 Planarity : 0.003 0.037 3304 Dihedral : 3.619 16.548 2600 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.58 % Favored : 93.08 % Rotamer: Outliers : 1.63 % Allowed : 14.18 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2356 helix: 2.21 (0.14), residues: 1456 sheet: -2.33 (0.61), residues: 84 loop : -2.50 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 333 HIS 0.002 0.001 HIS A 251 PHE 0.010 0.001 PHE C 519 TYR 0.009 0.001 TYR B 228 ARG 0.001 0.000 ARG B 684 *********************** 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 199 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 2.158 Fit side-chains REVERT: A 179 CYS cc_start: 0.8198 (m) cc_final: 0.7716 (m) REVERT: A 468 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7544 (tpt) REVERT: C 179 CYS cc_start: 0.8193 (m) cc_final: 0.7710 (m) REVERT: C 468 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7548 (tpt) REVERT: B 179 CYS cc_start: 0.8195 (m) cc_final: 0.7716 (m) REVERT: B 468 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7542 (tpt) REVERT: B 645 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6764 (tmt) REVERT: D 179 CYS cc_start: 0.8199 (m) cc_final: 0.7722 (m) REVERT: D 468 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7538 (tpt) REVERT: D 645 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6679 (tmt) outliers start: 34 outliers final: 12 residues processed: 185 average time/residue: 1.1220 time to fit residues: 240.3935 Evaluate side-chains 162 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 2.294 ------------------------------------------------------------------------------- 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 529 ILE Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain B residue 529 ILE 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 468 MET 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 189 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 chunk 3 optimal weight: 0.0870 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1848 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= 0.204 Angle : 0.536 7.388 26920 Z= 0.269 Chirality : 0.039 0.201 3052 Planarity : 0.003 0.039 3304 Dihedral : 3.809 18.963 2600 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.79 % Favored : 92.87 % Rotamer: Outliers : 2.01 % Allowed : 15.37 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2356 helix: 2.14 (0.14), residues: 1456 sheet: -2.34 (0.61), residues: 84 loop : -2.49 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 509 HIS 0.004 0.001 HIS C 251 PHE 0.015 0.001 PHE D 519 TYR 0.010 0.001 TYR A 471 ARG 0.001 0.000 ARG C 369 *********************** 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 192 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 2.183 Fit side-chains REVERT: A 179 CYS cc_start: 0.8186 (m) cc_final: 0.7700 (m) REVERT: A 392 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6736 (ttp-170) REVERT: C 179 CYS cc_start: 0.8180 (m) cc_final: 0.7697 (m) REVERT: C 392 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6733 (ttp-170) REVERT: B 179 CYS cc_start: 0.8193 (m) cc_final: 0.7707 (m) REVERT: B 392 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6727 (ttp-170) REVERT: B 645 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6905 (tmt) REVERT: D 179 CYS cc_start: 0.8209 (m) cc_final: 0.7734 (m) REVERT: D 392 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.6738 (ttp-170) REVERT: D 645 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6874 (tmt) outliers start: 42 outliers final: 16 residues processed: 176 average time/residue: 1.2258 time to fit residues: 247.2328 Evaluate side-chains 171 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 435 LEU 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 392 ARG 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 392 ARG Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 645 MET Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain D residue 392 ARG Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 645 MET 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 76 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 228 optimal weight: 0.5980 chunk 189 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 119 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19844 Z= 0.152 Angle : 0.499 7.559 26920 Z= 0.251 Chirality : 0.037 0.214 3052 Planarity : 0.003 0.039 3304 Dihedral : 3.629 17.312 2600 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.54 % Favored : 93.12 % Rotamer: Outliers : 2.11 % Allowed : 15.37 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2356 helix: 2.27 (0.14), residues: 1456 sheet: -2.32 (0.61), residues: 84 loop : -2.44 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 333 HIS 0.003 0.001 HIS C 251 PHE 0.011 0.001 PHE A 519 TYR 0.009 0.001 TYR B 525 ARG 0.001 0.000 ARG C 684 *********************** 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 212 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 2.009 Fit side-chains REVERT: A 179 CYS cc_start: 0.8183 (m) cc_final: 0.7676 (m) REVERT: A 392 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6698 (ttp-170) REVERT: A 468 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7536 (tpt) REVERT: A 516 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8307 (m) REVERT: A 612 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7143 (m-80) REVERT: A 661 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8133 (mtpp) REVERT: C 179 CYS cc_start: 0.8179 (m) cc_final: 0.7670 (m) REVERT: C 392 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.6722 (ttp-170) REVERT: C 468 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7544 (tpt) REVERT: C 516 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8313 (m) REVERT: C 612 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7176 (m-80) REVERT: C 661 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: B 179 CYS cc_start: 0.8179 (m) cc_final: 0.7678 (m) REVERT: B 392 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.6699 (ttp-170) REVERT: B 468 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.7538 (tpt) REVERT: B 516 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8315 (m) REVERT: B 612 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: B 645 MET cc_start: 0.6978 (tmm) cc_final: 0.6709 (tmt) REVERT: B 661 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8204 (mtpp) REVERT: D 179 CYS cc_start: 0.8205 (m) cc_final: 0.7707 (m) REVERT: D 392 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6701 (ttp-170) REVERT: D 468 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7545 (tpt) REVERT: D 516 THR cc_start: 0.8561 (OUTLIER) cc_final: 0.8313 (m) REVERT: D 612 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.7149 (m-80) REVERT: D 661 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8199 (mtpp) outliers start: 44 outliers final: 8 residues processed: 197 average time/residue: 1.1305 time to fit residues: 256.9188 Evaluate side-chains 174 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 468 MET Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 529 ILE 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 C residue 392 ARG Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 516 THR 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 B residue 345 LEU Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain B residue 516 THR 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 D residue 392 ARG Chi-restraints excluded: chain D residue 468 MET Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 612 PHE Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 259 ASN A 613 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B 613 GLN ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN ** D 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19844 Z= 0.309 Angle : 0.589 7.865 26920 Z= 0.296 Chirality : 0.041 0.226 3052 Planarity : 0.003 0.041 3304 Dihedral : 4.074 22.538 2600 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.51 % Favored : 92.15 % Rotamer: Outliers : 2.39 % Allowed : 15.85 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.18), residues: 2356 helix: 2.01 (0.14), residues: 1452 sheet: -2.46 (0.60), residues: 84 loop : -2.56 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 677 HIS 0.006 0.001 HIS A 251 PHE 0.019 0.002 PHE D 519 TYR 0.015 0.002 TYR C 471 ARG 0.001 0.000 ARG C 591 *********************** 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 206 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 2.256 Fit side-chains REVERT: A 179 CYS cc_start: 0.8159 (m) cc_final: 0.7649 (m) REVERT: A 392 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6663 (ttp-170) REVERT: A 516 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8318 (m) REVERT: A 612 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: C 179 CYS cc_start: 0.8157 (m) cc_final: 0.7649 (m) REVERT: C 277 MET cc_start: 0.8045 (ttm) cc_final: 0.7719 (ttm) REVERT: C 392 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.6664 (ttp-170) REVERT: C 516 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8320 (m) REVERT: C 612 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: B 179 CYS cc_start: 0.8158 (m) cc_final: 0.7651 (m) REVERT: B 392 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6664 (ttp-170) REVERT: B 516 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8324 (m) REVERT: B 612 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: B 645 MET cc_start: 0.7217 (tmm) cc_final: 0.6911 (tmt) REVERT: D 179 CYS cc_start: 0.8175 (m) cc_final: 0.7673 (m) REVERT: D 392 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.6664 (ttp-170) REVERT: D 516 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8319 (m) REVERT: D 612 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.7349 (m-80) outliers start: 50 outliers final: 14 residues processed: 194 average time/residue: 1.1666 time to fit residues: 261.1935 Evaluate side-chains 176 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 516 THR 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 C residue 392 ARG Chi-restraints excluded: chain C residue 435 LEU 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 B residue 392 ARG 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 678 CYS Chi-restraints excluded: chain D residue 392 ARG 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 678 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 0.0570 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 21 optimal weight: 0.0570 chunk 178 optimal weight: 0.0770 chunk 206 optimal weight: 5.9990 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS ** D 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19844 Z= 0.132 Angle : 0.500 7.795 26920 Z= 0.252 Chirality : 0.037 0.231 3052 Planarity : 0.003 0.038 3304 Dihedral : 3.584 17.852 2600 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.75 % Favored : 92.91 % Rotamer: Outliers : 1.48 % Allowed : 16.91 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2356 helix: 2.31 (0.14), residues: 1452 sheet: -2.30 (0.60), residues: 84 loop : -2.50 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 333 HIS 0.001 0.000 HIS C 521 PHE 0.010 0.001 PHE B 519 TYR 0.013 0.001 TYR A 525 ARG 0.001 0.000 ARG B 684 *********************** 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 181 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.8136 (m) cc_final: 0.7668 (m) REVERT: A 392 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6694 (ttp-170) REVERT: A 516 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8295 (m) REVERT: A 661 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8211 (mtpp) REVERT: C 179 CYS cc_start: 0.8130 (m) cc_final: 0.7662 (m) REVERT: C 392 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6695 (ttp-170) REVERT: C 516 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8297 (m) REVERT: C 661 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8220 (mtpp) REVERT: B 179 CYS cc_start: 0.8126 (m) cc_final: 0.7660 (m) REVERT: B 392 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6673 (ttp-170) REVERT: B 516 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8298 (m) REVERT: B 661 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8196 (mtpp) REVERT: D 179 CYS cc_start: 0.8142 (m) cc_final: 0.7666 (m) REVERT: D 392 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6696 (ttp-170) REVERT: D 516 THR cc_start: 0.8558 (OUTLIER) cc_final: 0.8298 (m) REVERT: D 661 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8214 (mtpp) outliers start: 31 outliers final: 5 residues processed: 178 average time/residue: 1.2727 time to fit residues: 261.0308 Evaluate side-chains 151 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain D residue 392 ARG Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 211 optimal weight: 9.9990 chunk 127 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 530 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19844 Z= 0.180 Angle : 0.526 8.172 26920 Z= 0.265 Chirality : 0.038 0.231 3052 Planarity : 0.003 0.039 3304 Dihedral : 3.685 18.080 2600 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.66 % Favored : 93.00 % Rotamer: Outliers : 1.48 % Allowed : 17.15 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 2356 helix: 2.28 (0.14), residues: 1452 sheet: -2.30 (0.60), residues: 84 loop : -2.47 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 677 HIS 0.003 0.001 HIS B 251 PHE 0.012 0.001 PHE C 519 TYR 0.011 0.001 TYR A 525 ARG 0.001 0.000 ARG B 175 *********************** 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 179 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 CYS cc_start: 0.8161 (m) cc_final: 0.7707 (m) REVERT: A 392 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6706 (ttp-170) REVERT: A 516 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8348 (m) REVERT: A 661 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8205 (mtpp) REVERT: C 179 CYS cc_start: 0.8120 (m) cc_final: 0.7667 (m) REVERT: C 392 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6709 (ttp-170) REVERT: C 516 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8353 (m) REVERT: C 530 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6492 (mm110) REVERT: C 661 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: B 179 CYS cc_start: 0.8147 (m) cc_final: 0.7688 (m) REVERT: B 392 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6743 (ttp-170) REVERT: B 516 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8356 (m) REVERT: B 661 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: D 179 CYS cc_start: 0.8165 (m) cc_final: 0.7709 (m) REVERT: D 392 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6709 (ttp-170) REVERT: D 516 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8350 (m) REVERT: D 645 MET cc_start: 0.6947 (tmm) cc_final: 0.6735 (tmt) REVERT: D 661 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8214 (mtpp) outliers start: 31 outliers final: 5 residues processed: 174 average time/residue: 1.3653 time to fit residues: 271.5859 Evaluate side-chains 160 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain D residue 392 ARG Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 3.9990 chunk 106 optimal weight: 0.0570 chunk 155 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 216 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 530 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19844 Z= 0.164 Angle : 0.548 12.284 26920 Z= 0.269 Chirality : 0.038 0.258 3052 Planarity : 0.003 0.039 3304 Dihedral : 3.661 17.563 2600 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.66 % Favored : 93.00 % Rotamer: Outliers : 1.05 % Allowed : 17.72 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.18), residues: 2356 helix: 2.30 (0.14), residues: 1452 sheet: -2.20 (0.61), residues: 84 loop : -2.44 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 677 HIS 0.003 0.001 HIS B 251 PHE 0.012 0.001 PHE C 519 TYR 0.013 0.001 TYR A 525 ARG 0.001 0.000 ARG C 535 ********************** 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 163 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 2.196 Fit side-chains REVERT: A 179 CYS cc_start: 0.8095 (m) cc_final: 0.7670 (m) REVERT: A 392 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6702 (ttp-170) REVERT: A 516 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8332 (m) REVERT: A 661 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8202 (mtpp) REVERT: C 179 CYS cc_start: 0.8125 (m) cc_final: 0.7685 (m) REVERT: C 392 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.6705 (ttp-170) REVERT: C 516 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8334 (m) REVERT: C 530 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6746 (mm110) REVERT: C 661 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8204 (mtpp) REVERT: B 179 CYS cc_start: 0.8087 (m) cc_final: 0.7664 (m) REVERT: B 392 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6710 (ttp-170) REVERT: B 516 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8344 (m) REVERT: B 645 MET cc_start: 0.7415 (tmt) cc_final: 0.7210 (tmt) REVERT: B 661 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8209 (mtpp) REVERT: D 179 CYS cc_start: 0.8143 (m) cc_final: 0.7710 (m) REVERT: D 392 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6705 (ttp-170) REVERT: D 516 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8335 (m) REVERT: D 661 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8204 (mtpp) outliers start: 22 outliers final: 5 residues processed: 162 average time/residue: 1.3323 time to fit residues: 246.4268 Evaluate side-chains 155 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain C residue 392 ARG Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 530 GLN Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain B residue 392 ARG Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain D residue 392 ARG Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 187 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 530 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.179617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110012 restraints weight = 23870.783| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.60 r_work: 0.3125 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2302 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: