Starting phenix.real_space_refine on Sat Sep 28 18:55:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/09_2024/6u88_20682_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/09_2024/6u88_20682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/09_2024/6u88_20682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/09_2024/6u88_20682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/09_2024/6u88_20682_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/09_2024/6u88_20682_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 13116 2.51 5 N 3328 2.21 5 O 3448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20004 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4978 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: C, B, D Time building chain proxies: 11.21, per 1000 atoms: 0.56 Number of scatterers: 20004 At special positions: 0 Unit cell: (124.02, 124.02, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3448 8.00 N 3328 7.00 C 13116 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: 4.91 Conformation dependent library (CDL) restraints added in 2.4 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4616 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 59.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.841A pdb=" N LEU A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.602A pdb=" N VAL A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.700A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.507A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.353A 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 463 through 467 removed outlier: 3.596A pdb=" N PHE A 467 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 492 Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.071A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.819A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 559 removed outlier: 3.608A pdb=" N LYS A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 606 removed outlier: 4.274A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 651 removed outlier: 4.031A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.841A pdb=" N LEU B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.603A pdb=" N VAL B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.701A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.506A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.354A 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 463 through 467 removed outlier: 3.596A pdb=" N PHE B 467 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 492 Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.071A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.819A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 519 through 559 removed outlier: 3.609A pdb=" N LYS B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 606 removed outlier: 4.274A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 651 removed outlier: 4.031A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.841A pdb=" N LEU C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.602A pdb=" N VAL C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.700A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.507A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.355A 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 463 through 467 removed outlier: 3.597A pdb=" N PHE C 467 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.071A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.819A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 519 through 559 removed outlier: 3.609A pdb=" N LYS C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 606 removed outlier: 4.274A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 651 removed outlier: 4.031A pdb=" N VAL C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N HIS C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.842A pdb=" N LEU D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.603A pdb=" N VAL D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.701A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.507A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.354A 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 463 through 467 removed outlier: 3.597A pdb=" N PHE D 467 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 492 Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.072A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.820A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 519 through 559 removed outlier: 3.608A pdb=" N LYS D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 606 removed outlier: 4.274A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 651 removed outlier: 4.030A pdb=" N VAL D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 672 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.755A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.756A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.756A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.756A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.62 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6127 1.34 - 1.46: 5154 1.46 - 1.59: 9059 1.59 - 1.71: 0 1.71 - 1.83: 172 Bond restraints: 20512 Sorted by residual: bond pdb=" C04 P0T C1001 " pdb=" C08 P0T C1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C04 P0T D1001 " pdb=" C08 P0T D1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C04 P0T B1001 " pdb=" C08 P0T B1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C15 P0T A1001 " pdb=" C18 P0T A1001 " ideal model delta sigma weight residual 1.503 1.552 -0.049 2.00e-02 2.50e+03 6.04e+00 ... (remaining 20507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26385 2.08 - 4.15: 1186 4.15 - 6.23: 171 6.23 - 8.31: 46 8.31 - 10.39: 28 Bond angle restraints: 27816 Sorted by residual: angle pdb=" N TYR A 634 " pdb=" CA TYR A 634 " pdb=" C TYR A 634 " ideal model delta sigma weight residual 111.14 106.84 4.30 1.08e+00 8.57e-01 1.58e+01 angle pdb=" N TYR C 634 " pdb=" CA TYR C 634 " pdb=" C TYR C 634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.58e+01 angle pdb=" N TYR B 634 " pdb=" CA TYR B 634 " pdb=" C TYR B 634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.58e+01 angle pdb=" N TYR D 634 " pdb=" CA TYR D 634 " pdb=" C TYR D 634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.58e+01 angle pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 111.12 120.59 -9.47 3.00e+00 1.11e-01 9.96e+00 ... (remaining 27811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.24: 10818 20.24 - 40.47: 1066 40.47 - 60.71: 156 60.71 - 80.94: 36 80.94 - 101.18: 12 Dihedral angle restraints: 12088 sinusoidal: 4944 harmonic: 7144 Sorted by residual: dihedral pdb=" CA VAL C 652 " pdb=" C VAL C 652 " pdb=" N ALA C 653 " pdb=" CA ALA C 653 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA VAL D 652 " pdb=" C VAL D 652 " pdb=" N ALA D 653 " pdb=" CA ALA D 653 " ideal model delta harmonic sigma weight residual -180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL B 652 " pdb=" C VAL B 652 " pdb=" N ALA B 653 " pdb=" CA ALA B 653 " ideal model delta harmonic sigma weight residual -180.00 -151.81 -28.19 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 12085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2047 0.053 - 0.105: 861 0.105 - 0.158: 140 0.158 - 0.210: 53 0.210 - 0.263: 15 Chirality restraints: 3116 Sorted by residual: chirality pdb=" CB VAL B 652 " pdb=" CA VAL B 652 " pdb=" CG1 VAL B 652 " pdb=" CG2 VAL B 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL A 652 " pdb=" CA VAL A 652 " pdb=" CG1 VAL A 652 " pdb=" CG2 VAL A 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL C 652 " pdb=" CA VAL C 652 " pdb=" CG1 VAL C 652 " pdb=" CG2 VAL C 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3113 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 725 " 0.063 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO A 726 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 726 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 726 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 725 " -0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO C 726 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 726 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 726 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 725 " -0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO B 726 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 726 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 726 " -0.051 5.00e-02 4.00e+02 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 6571 2.84 - 3.36: 17484 3.36 - 3.87: 34128 3.87 - 4.39: 38551 4.39 - 4.90: 66564 Nonbonded interactions: 163298 Sorted by model distance: nonbonded pdb=" O SER B 466 " pdb=" OG SER B 470 " model vdw 2.328 3.040 nonbonded pdb=" O SER C 466 " pdb=" OG SER C 470 " model vdw 2.329 3.040 nonbonded pdb=" O SER D 466 " pdb=" OG SER D 470 " model vdw 2.329 3.040 nonbonded pdb=" O SER A 466 " pdb=" OG SER A 470 " model vdw 2.329 3.040 nonbonded pdb=" O SER D 470 " pdb=" OG SER D 470 " model vdw 2.333 3.040 ... (remaining 163293 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 42.290 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.009 0.084 20512 Z= 0.575 Angle : 1.052 10.385 27816 Z= 0.553 Chirality : 0.059 0.263 3116 Planarity : 0.009 0.095 3428 Dihedral : 16.098 101.178 7472 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.74 % Allowed : 10.70 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -4.92 (0.11), residues: 2412 helix: -3.13 (0.08), residues: 1456 sheet: -3.31 (0.36), residues: 124 loop : -3.12 (0.14), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 454 HIS 0.011 0.002 HIS B 251 PHE 0.021 0.003 PHE A 209 TYR 0.017 0.003 TYR C 228 ARG 0.008 0.001 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 359 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 GLN cc_start: 0.7791 (tp40) cc_final: 0.7509 (tt0) REVERT: A 591 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7711 (mmt-90) REVERT: A 595 ASP cc_start: 0.7405 (m-30) cc_final: 0.6976 (t0) REVERT: A 632 LEU cc_start: 0.8830 (mt) cc_final: 0.8531 (mt) REVERT: A 634 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: B 148 ASN cc_start: 0.6492 (p0) cc_final: 0.6260 (p0) REVERT: B 383 GLN cc_start: 0.7765 (tp40) cc_final: 0.7479 (tt0) REVERT: B 405 PHE cc_start: 0.7520 (t80) cc_final: 0.7290 (m-10) REVERT: B 591 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7699 (mmt-90) REVERT: B 595 ASP cc_start: 0.7428 (m-30) cc_final: 0.6966 (t0) REVERT: B 617 ARG cc_start: 0.7719 (ttt180) cc_final: 0.7511 (ttt180) REVERT: B 632 LEU cc_start: 0.8839 (mt) cc_final: 0.8540 (mt) REVERT: B 634 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: C 148 ASN cc_start: 0.6514 (p0) cc_final: 0.6264 (p0) REVERT: C 383 GLN cc_start: 0.7757 (tp40) cc_final: 0.7465 (tt0) REVERT: C 405 PHE cc_start: 0.7523 (t80) cc_final: 0.7290 (m-10) REVERT: C 481 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8810 (mp) REVERT: C 591 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7700 (mmt-90) REVERT: C 595 ASP cc_start: 0.7425 (m-30) cc_final: 0.6967 (t0) REVERT: C 617 ARG cc_start: 0.7717 (ttt180) cc_final: 0.7512 (ttt180) REVERT: C 632 LEU cc_start: 0.8835 (mt) cc_final: 0.8536 (mt) REVERT: C 634 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: D 148 ASN cc_start: 0.6512 (p0) cc_final: 0.6282 (p0) REVERT: D 383 GLN cc_start: 0.7750 (tp40) cc_final: 0.7462 (tt0) REVERT: D 405 PHE cc_start: 0.7526 (t80) cc_final: 0.7286 (m-10) REVERT: D 481 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8812 (mp) REVERT: D 591 ARG cc_start: 0.8126 (ptm160) cc_final: 0.7715 (mmt-90) REVERT: D 595 ASP cc_start: 0.7376 (m-30) cc_final: 0.7016 (t0) REVERT: D 617 ARG cc_start: 0.7725 (ttt180) cc_final: 0.7515 (ttt180) REVERT: D 632 LEU cc_start: 0.8837 (mt) cc_final: 0.8540 (mt) REVERT: D 634 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7605 (m-80) outliers start: 16 outliers final: 4 residues processed: 367 average time/residue: 0.3728 time to fit residues: 198.0684 Evaluate side-chains 267 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 257 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 154 ASN A 186 ASN A 263 ASN A 414 GLN A 487 GLN B 127 ASN B 154 ASN B 186 ASN B 263 ASN B 414 GLN B 487 GLN C 127 ASN C 154 ASN C 186 ASN C 263 ASN C 414 GLN C 487 GLN D 127 ASN D 154 ASN D 186 ASN D 263 ASN D 414 GLN D 487 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20512 Z= 0.211 Angle : 0.560 6.403 27816 Z= 0.283 Chirality : 0.038 0.185 3116 Planarity : 0.006 0.077 3428 Dihedral : 8.598 59.864 2776 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.80 % Allowed : 12.36 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.15), residues: 2412 helix: -0.42 (0.12), residues: 1440 sheet: -2.93 (0.39), residues: 124 loop : -2.55 (0.16), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 454 HIS 0.004 0.001 HIS D 251 PHE 0.019 0.001 PHE B 540 TYR 0.013 0.001 TYR C 629 ARG 0.003 0.000 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 320 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6310 (mmtm) cc_final: 0.5967 (mtmt) REVERT: A 205 THR cc_start: 0.8976 (t) cc_final: 0.8698 (m) REVERT: A 383 GLN cc_start: 0.7802 (tp40) cc_final: 0.7459 (tt0) REVERT: A 591 ARG cc_start: 0.8122 (ptm160) cc_final: 0.7681 (mmm160) REVERT: A 595 ASP cc_start: 0.7323 (m-30) cc_final: 0.6960 (t0) REVERT: A 634 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: B 104 LYS cc_start: 0.6364 (mmtm) cc_final: 0.6021 (mtmt) REVERT: B 205 THR cc_start: 0.8984 (t) cc_final: 0.8710 (m) REVERT: B 383 GLN cc_start: 0.7754 (tp40) cc_final: 0.7423 (tt0) REVERT: B 591 ARG cc_start: 0.8128 (ptm160) cc_final: 0.7691 (mmm160) REVERT: B 595 ASP cc_start: 0.7333 (m-30) cc_final: 0.6945 (t0) REVERT: B 634 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: C 104 LYS cc_start: 0.6382 (mmtm) cc_final: 0.5977 (mtmt) REVERT: C 205 THR cc_start: 0.8983 (t) cc_final: 0.8709 (m) REVERT: C 383 GLN cc_start: 0.7754 (tp40) cc_final: 0.7422 (tt0) REVERT: C 591 ARG cc_start: 0.8126 (ptm160) cc_final: 0.7688 (mmm160) REVERT: C 595 ASP cc_start: 0.7332 (m-30) cc_final: 0.6952 (t0) REVERT: C 634 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: D 104 LYS cc_start: 0.6374 (mmtm) cc_final: 0.5971 (mtmt) REVERT: D 205 THR cc_start: 0.8982 (t) cc_final: 0.8708 (m) REVERT: D 383 GLN cc_start: 0.7732 (tp40) cc_final: 0.7413 (tt0) REVERT: D 469 ASP cc_start: 0.7282 (p0) cc_final: 0.6980 (p0) REVERT: D 591 ARG cc_start: 0.8117 (ptm160) cc_final: 0.7693 (mmm160) REVERT: D 595 ASP cc_start: 0.7329 (m-30) cc_final: 0.6937 (t0) REVERT: D 634 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7682 (m-80) outliers start: 39 outliers final: 12 residues processed: 336 average time/residue: 0.3309 time to fit residues: 167.7843 Evaluate side-chains 291 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 275 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 chunk 239 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN B 263 ASN C 263 ASN D 263 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20512 Z= 0.336 Angle : 0.609 6.197 27816 Z= 0.302 Chirality : 0.041 0.168 3116 Planarity : 0.005 0.070 3428 Dihedral : 7.911 51.545 2772 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.77 % Allowed : 13.05 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.95 (0.16), residues: 2412 helix: 0.44 (0.13), residues: 1444 sheet: -2.44 (0.45), residues: 124 loop : -2.22 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 677 HIS 0.005 0.001 HIS D 251 PHE 0.015 0.002 PHE B 540 TYR 0.015 0.002 TYR B 629 ARG 0.002 0.000 ARG C 560 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 293 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6304 (mmtm) cc_final: 0.5730 (mtmt) REVERT: A 111 TYR cc_start: 0.7776 (m-80) cc_final: 0.7315 (m-80) REVERT: A 163 GLN cc_start: 0.7212 (tt0) cc_final: 0.7008 (tp40) REVERT: A 205 THR cc_start: 0.9014 (t) cc_final: 0.8776 (m) REVERT: A 375 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8323 (pp) REVERT: A 591 ARG cc_start: 0.8148 (ptm160) cc_final: 0.7684 (mmt-90) REVERT: A 595 ASP cc_start: 0.7354 (m-30) cc_final: 0.6963 (t0) REVERT: A 634 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7599 (m-80) REVERT: B 104 LYS cc_start: 0.6266 (mmtm) cc_final: 0.5773 (mtmt) REVERT: B 111 TYR cc_start: 0.7740 (m-80) cc_final: 0.7334 (m-80) REVERT: B 163 GLN cc_start: 0.7210 (tt0) cc_final: 0.7007 (tp40) REVERT: B 205 THR cc_start: 0.9016 (t) cc_final: 0.8778 (m) REVERT: B 375 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8317 (pp) REVERT: B 383 GLN cc_start: 0.7871 (tp40) cc_final: 0.7326 (tm-30) REVERT: B 591 ARG cc_start: 0.8154 (ptm160) cc_final: 0.7696 (mmt-90) REVERT: B 595 ASP cc_start: 0.7366 (m-30) cc_final: 0.6981 (t0) REVERT: B 634 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: C 104 LYS cc_start: 0.6271 (mmtm) cc_final: 0.5777 (mtmt) REVERT: C 111 TYR cc_start: 0.7763 (m-80) cc_final: 0.7308 (m-80) REVERT: C 163 GLN cc_start: 0.7213 (tt0) cc_final: 0.7009 (tp40) REVERT: C 205 THR cc_start: 0.9015 (t) cc_final: 0.8777 (m) REVERT: C 375 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8317 (pp) REVERT: C 591 ARG cc_start: 0.8151 (ptm160) cc_final: 0.7694 (mmt-90) REVERT: C 595 ASP cc_start: 0.7366 (m-30) cc_final: 0.6980 (t0) REVERT: C 634 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: D 104 LYS cc_start: 0.6269 (mmtm) cc_final: 0.5776 (mtmt) REVERT: D 111 TYR cc_start: 0.7766 (m-80) cc_final: 0.7310 (m-80) REVERT: D 163 GLN cc_start: 0.7210 (tt0) cc_final: 0.7006 (tp40) REVERT: D 205 THR cc_start: 0.9016 (t) cc_final: 0.8779 (m) REVERT: D 375 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8275 (pp) REVERT: D 591 ARG cc_start: 0.8156 (ptm160) cc_final: 0.7725 (mmt-90) REVERT: D 595 ASP cc_start: 0.7371 (m-30) cc_final: 0.6985 (t0) REVERT: D 634 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7602 (m-80) outliers start: 60 outliers final: 43 residues processed: 333 average time/residue: 0.3022 time to fit residues: 156.4610 Evaluate side-chains 332 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 281 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 211 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20512 Z= 0.202 Angle : 0.529 5.550 27816 Z= 0.262 Chirality : 0.038 0.140 3116 Planarity : 0.004 0.063 3428 Dihedral : 7.351 51.294 2772 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.81 % Allowed : 14.53 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.21 (0.17), residues: 2412 helix: 1.05 (0.14), residues: 1440 sheet: -2.43 (0.45), residues: 116 loop : -1.90 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 454 HIS 0.004 0.001 HIS D 251 PHE 0.011 0.001 PHE B 540 TYR 0.011 0.001 TYR B 629 ARG 0.001 0.000 ARG C 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 301 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6389 (mmtm) cc_final: 0.5866 (mttt) REVERT: A 111 TYR cc_start: 0.7763 (m-80) cc_final: 0.7271 (m-80) REVERT: A 135 CYS cc_start: 0.7864 (t) cc_final: 0.7445 (p) REVERT: A 163 GLN cc_start: 0.7198 (tt0) cc_final: 0.6960 (tp40) REVERT: A 173 GLU cc_start: 0.8053 (tp30) cc_final: 0.7700 (tp30) REVERT: A 205 THR cc_start: 0.9002 (t) cc_final: 0.8769 (m) REVERT: A 375 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8305 (pp) REVERT: A 383 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7293 (tm-30) REVERT: A 591 ARG cc_start: 0.8114 (ptm160) cc_final: 0.7644 (mmm160) REVERT: A 634 TYR cc_start: 0.8157 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: A 640 MET cc_start: 0.7971 (tmm) cc_final: 0.7522 (ttp) REVERT: B 104 LYS cc_start: 0.6189 (mmtm) cc_final: 0.5748 (mtmt) REVERT: B 135 CYS cc_start: 0.7941 (t) cc_final: 0.7553 (p) REVERT: B 163 GLN cc_start: 0.7186 (tt0) cc_final: 0.6960 (tp40) REVERT: B 173 GLU cc_start: 0.8060 (tp30) cc_final: 0.7711 (tp30) REVERT: B 205 THR cc_start: 0.9001 (t) cc_final: 0.8764 (m) REVERT: B 375 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8293 (pp) REVERT: B 591 ARG cc_start: 0.8114 (ptm160) cc_final: 0.7645 (mmm160) REVERT: B 634 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: B 640 MET cc_start: 0.7981 (tmm) cc_final: 0.7522 (ttp) REVERT: C 104 LYS cc_start: 0.6201 (mmtm) cc_final: 0.5758 (mtmt) REVERT: C 111 TYR cc_start: 0.7792 (m-80) cc_final: 0.7271 (m-80) REVERT: C 135 CYS cc_start: 0.7944 (t) cc_final: 0.7554 (p) REVERT: C 163 GLN cc_start: 0.7198 (tt0) cc_final: 0.6959 (tp40) REVERT: C 173 GLU cc_start: 0.8060 (tp30) cc_final: 0.7709 (tp30) REVERT: C 205 THR cc_start: 0.9000 (t) cc_final: 0.8763 (m) REVERT: C 375 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8296 (pp) REVERT: C 383 GLN cc_start: 0.7871 (tp-100) cc_final: 0.7290 (tm-30) REVERT: C 591 ARG cc_start: 0.8114 (ptm160) cc_final: 0.7643 (mmm160) REVERT: C 634 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: C 640 MET cc_start: 0.7958 (tmm) cc_final: 0.7508 (ttp) REVERT: D 104 LYS cc_start: 0.6196 (mmtm) cc_final: 0.5757 (mtmt) REVERT: D 111 TYR cc_start: 0.7757 (m-80) cc_final: 0.7223 (m-80) REVERT: D 135 CYS cc_start: 0.7940 (t) cc_final: 0.7549 (p) REVERT: D 163 GLN cc_start: 0.7188 (tt0) cc_final: 0.6964 (tp40) REVERT: D 173 GLU cc_start: 0.8062 (tp30) cc_final: 0.7709 (tp30) REVERT: D 205 THR cc_start: 0.9001 (t) cc_final: 0.8765 (m) REVERT: D 375 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8263 (pp) REVERT: D 591 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7645 (mmm160) REVERT: D 634 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: D 640 MET cc_start: 0.7950 (tmm) cc_final: 0.7517 (ttp) outliers start: 61 outliers final: 47 residues processed: 349 average time/residue: 0.3090 time to fit residues: 166.5383 Evaluate side-chains 344 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 289 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 chunk 211 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20512 Z= 0.293 Angle : 0.575 6.033 27816 Z= 0.283 Chirality : 0.040 0.127 3116 Planarity : 0.004 0.064 3428 Dihedral : 7.149 49.672 2772 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.68 % Allowed : 16.28 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.11 (0.17), residues: 2412 helix: 1.22 (0.14), residues: 1444 sheet: -2.14 (0.47), residues: 124 loop : -1.60 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 454 HIS 0.005 0.001 HIS B 251 PHE 0.011 0.001 PHE C 405 TYR 0.013 0.001 TYR B 629 ARG 0.002 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 279 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6409 (mmtm) cc_final: 0.5914 (mttt) REVERT: A 111 TYR cc_start: 0.7774 (m-80) cc_final: 0.7317 (m-80) REVERT: A 205 THR cc_start: 0.9021 (t) cc_final: 0.8774 (m) REVERT: A 375 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8356 (pp) REVERT: A 383 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7373 (tm-30) REVERT: A 591 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7704 (mmt-90) REVERT: A 634 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: B 104 LYS cc_start: 0.6251 (mmtm) cc_final: 0.5700 (mttt) REVERT: B 111 TYR cc_start: 0.7741 (m-80) cc_final: 0.7274 (m-80) REVERT: B 135 CYS cc_start: 0.7800 (t) cc_final: 0.7362 (p) REVERT: B 205 THR cc_start: 0.9029 (t) cc_final: 0.8781 (m) REVERT: B 375 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8351 (pp) REVERT: B 383 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7243 (tm-30) REVERT: B 591 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7705 (mmt-90) REVERT: B 634 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: C 104 LYS cc_start: 0.6264 (mmtm) cc_final: 0.5710 (mttt) REVERT: C 111 TYR cc_start: 0.7793 (m-80) cc_final: 0.7287 (m-80) REVERT: C 135 CYS cc_start: 0.7804 (t) cc_final: 0.7344 (p) REVERT: C 205 THR cc_start: 0.9029 (t) cc_final: 0.8782 (m) REVERT: C 375 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8348 (pp) REVERT: C 383 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7338 (tm-30) REVERT: C 591 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7705 (mmt-90) REVERT: C 634 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7502 (m-80) REVERT: D 104 LYS cc_start: 0.6295 (mmtm) cc_final: 0.5719 (mttt) REVERT: D 111 TYR cc_start: 0.7802 (m-80) cc_final: 0.7287 (m-80) REVERT: D 135 CYS cc_start: 0.7806 (t) cc_final: 0.7353 (p) REVERT: D 205 THR cc_start: 0.9025 (t) cc_final: 0.8777 (m) REVERT: D 255 MET cc_start: 0.7968 (mmt) cc_final: 0.7437 (mmt) REVERT: D 375 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8333 (pp) REVERT: D 383 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7197 (tm-30) REVERT: D 591 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7687 (mmt-90) REVERT: D 634 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7492 (m-80) outliers start: 58 outliers final: 49 residues processed: 323 average time/residue: 0.2906 time to fit residues: 146.9679 Evaluate side-chains 325 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 268 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 1.9990 chunk 212 optimal weight: 0.0470 chunk 46 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 195 optimal weight: 0.0770 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20512 Z= 0.136 Angle : 0.499 6.131 27816 Z= 0.247 Chirality : 0.036 0.119 3116 Planarity : 0.004 0.056 3428 Dihedral : 6.800 50.919 2772 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.95 % Allowed : 16.28 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.61 (0.17), residues: 2412 helix: 1.67 (0.14), residues: 1436 sheet: -2.15 (0.46), residues: 116 loop : -1.45 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 454 HIS 0.003 0.001 HIS D 313 PHE 0.009 0.001 PHE D 540 TYR 0.009 0.001 TYR C 98 ARG 0.001 0.000 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 314 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6285 (mmtm) cc_final: 0.5933 (mtmt) REVERT: A 111 TYR cc_start: 0.7784 (m-80) cc_final: 0.7346 (m-80) REVERT: A 135 CYS cc_start: 0.7795 (t) cc_final: 0.7388 (p) REVERT: A 205 THR cc_start: 0.8957 (t) cc_final: 0.8713 (m) REVERT: A 375 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8301 (pp) REVERT: A 383 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7261 (tm-30) REVERT: A 591 ARG cc_start: 0.8095 (ptm160) cc_final: 0.7610 (mmm160) REVERT: A 634 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: B 104 LYS cc_start: 0.6168 (mmtm) cc_final: 0.5702 (mtmt) REVERT: B 111 TYR cc_start: 0.7781 (m-80) cc_final: 0.7338 (m-80) REVERT: B 135 CYS cc_start: 0.7873 (t) cc_final: 0.7608 (p) REVERT: B 173 GLU cc_start: 0.7833 (tp30) cc_final: 0.7486 (tp30) REVERT: B 205 THR cc_start: 0.8964 (t) cc_final: 0.8719 (m) REVERT: B 375 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8298 (pp) REVERT: B 383 GLN cc_start: 0.7814 (tp-100) cc_final: 0.7265 (tm-30) REVERT: B 591 ARG cc_start: 0.8096 (ptm160) cc_final: 0.7613 (mmm160) REVERT: B 634 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7496 (m-80) REVERT: C 104 LYS cc_start: 0.6175 (mmtm) cc_final: 0.5699 (mtmt) REVERT: C 111 TYR cc_start: 0.7765 (m-80) cc_final: 0.7329 (m-80) REVERT: C 135 CYS cc_start: 0.7879 (t) cc_final: 0.7593 (p) REVERT: C 173 GLU cc_start: 0.7844 (tp30) cc_final: 0.7507 (tp30) REVERT: C 205 THR cc_start: 0.8961 (t) cc_final: 0.8721 (m) REVERT: C 375 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8287 (pp) REVERT: C 591 ARG cc_start: 0.8093 (ptm160) cc_final: 0.7610 (mmm160) REVERT: C 634 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: C 640 MET cc_start: 0.7834 (tmm) cc_final: 0.7575 (ttp) REVERT: D 104 LYS cc_start: 0.6143 (mmtm) cc_final: 0.5698 (mtmt) REVERT: D 111 TYR cc_start: 0.7762 (m-80) cc_final: 0.7324 (m-80) REVERT: D 135 CYS cc_start: 0.7872 (t) cc_final: 0.7599 (p) REVERT: D 205 THR cc_start: 0.8959 (t) cc_final: 0.8718 (m) REVERT: D 375 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8261 (pp) REVERT: D 383 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7214 (tm-30) REVERT: D 591 ARG cc_start: 0.8092 (ptm160) cc_final: 0.7610 (mmm160) REVERT: D 634 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7509 (m-80) outliers start: 64 outliers final: 42 residues processed: 361 average time/residue: 0.2963 time to fit residues: 167.4165 Evaluate side-chains 339 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 289 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 609 GLU Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 632 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 235 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20512 Z= 0.241 Angle : 0.559 7.855 27816 Z= 0.273 Chirality : 0.039 0.129 3116 Planarity : 0.004 0.057 3428 Dihedral : 7.095 57.150 2772 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.81 % Allowed : 17.67 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.62 (0.17), residues: 2412 helix: 1.63 (0.14), residues: 1440 sheet: -2.09 (0.47), residues: 116 loop : -1.36 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 454 HIS 0.004 0.001 HIS B 251 PHE 0.010 0.001 PHE D 540 TYR 0.020 0.001 TYR C 447 ARG 0.002 0.000 ARG D 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 286 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6265 (mmtm) cc_final: 0.5872 (mtmt) REVERT: A 111 TYR cc_start: 0.7782 (m-80) cc_final: 0.7341 (m-80) REVERT: A 205 THR cc_start: 0.8978 (t) cc_final: 0.8738 (m) REVERT: A 375 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8333 (pp) REVERT: A 383 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7350 (tm-30) REVERT: A 591 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7670 (mmt-90) REVERT: A 634 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: B 104 LYS cc_start: 0.6265 (mmtm) cc_final: 0.5784 (mttt) REVERT: B 111 TYR cc_start: 0.7747 (m-80) cc_final: 0.7363 (m-80) REVERT: B 173 GLU cc_start: 0.7944 (tp30) cc_final: 0.7617 (tp30) REVERT: B 205 THR cc_start: 0.8986 (t) cc_final: 0.8740 (m) REVERT: B 375 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8331 (pp) REVERT: B 383 GLN cc_start: 0.7903 (tp-100) cc_final: 0.7356 (tm-30) REVERT: B 591 ARG cc_start: 0.8145 (ptm160) cc_final: 0.7675 (mmt-90) REVERT: B 634 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7514 (m-80) REVERT: C 104 LYS cc_start: 0.6223 (mmtm) cc_final: 0.5778 (mttt) REVERT: C 111 TYR cc_start: 0.7801 (m-80) cc_final: 0.7377 (m-80) REVERT: C 173 GLU cc_start: 0.7946 (tp30) cc_final: 0.7620 (tp30) REVERT: C 205 THR cc_start: 0.8979 (t) cc_final: 0.8732 (m) REVERT: C 375 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8330 (pp) REVERT: C 383 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7325 (tm-30) REVERT: C 591 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7674 (mmt-90) REVERT: C 634 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: D 104 LYS cc_start: 0.6231 (mmtm) cc_final: 0.5705 (mttt) REVERT: D 111 TYR cc_start: 0.7799 (m-80) cc_final: 0.7374 (m-80) REVERT: D 173 GLU cc_start: 0.8060 (tp30) cc_final: 0.7839 (tp30) REVERT: D 205 THR cc_start: 0.8980 (t) cc_final: 0.8737 (m) REVERT: D 375 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8291 (pp) REVERT: D 383 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7324 (tm-30) REVERT: D 591 ARG cc_start: 0.8132 (ptm160) cc_final: 0.7676 (mmt-90) REVERT: D 634 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7502 (m-80) outliers start: 61 outliers final: 50 residues processed: 333 average time/residue: 0.2799 time to fit residues: 147.2896 Evaluate side-chains 331 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 273 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 609 GLU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20512 Z= 0.148 Angle : 0.518 6.419 27816 Z= 0.256 Chirality : 0.037 0.156 3116 Planarity : 0.004 0.055 3428 Dihedral : 7.017 59.625 2772 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.72 % Allowed : 17.76 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.17), residues: 2412 helix: 1.84 (0.14), residues: 1436 sheet: -1.95 (0.47), residues: 116 loop : -1.27 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 464 HIS 0.003 0.001 HIS D 313 PHE 0.009 0.001 PHE B 547 TYR 0.019 0.001 TYR C 447 ARG 0.001 0.000 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 308 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6207 (mmtm) cc_final: 0.5903 (mtmt) REVERT: A 111 TYR cc_start: 0.7750 (m-80) cc_final: 0.7395 (m-80) REVERT: A 135 CYS cc_start: 0.7819 (t) cc_final: 0.7396 (p) REVERT: A 345 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8249 (mt) REVERT: A 375 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8318 (pp) REVERT: A 383 GLN cc_start: 0.7837 (tp-100) cc_final: 0.7269 (tm-30) REVERT: A 591 ARG cc_start: 0.8114 (ptm160) cc_final: 0.7622 (mmm160) REVERT: A 634 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: B 104 LYS cc_start: 0.6231 (mmtm) cc_final: 0.5777 (mtmt) REVERT: B 111 TYR cc_start: 0.7757 (m-80) cc_final: 0.7451 (m-80) REVERT: B 173 GLU cc_start: 0.7927 (tp30) cc_final: 0.7617 (tp30) REVERT: B 345 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8263 (mt) REVERT: B 375 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8314 (pp) REVERT: B 383 GLN cc_start: 0.7835 (tp-100) cc_final: 0.7275 (tm-30) REVERT: B 591 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7641 (mmm160) REVERT: B 634 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: B 640 MET cc_start: 0.7873 (tmm) cc_final: 0.7391 (ttp) REVERT: C 104 LYS cc_start: 0.6206 (mmtm) cc_final: 0.5751 (mtmt) REVERT: C 111 TYR cc_start: 0.7755 (m-80) cc_final: 0.7418 (m-80) REVERT: C 173 GLU cc_start: 0.7931 (tp30) cc_final: 0.7623 (tp30) REVERT: C 345 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8251 (mt) REVERT: C 375 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8308 (pp) REVERT: C 383 GLN cc_start: 0.7845 (tp-100) cc_final: 0.7238 (tm-30) REVERT: C 591 ARG cc_start: 0.8085 (ptm160) cc_final: 0.7638 (mmm160) REVERT: C 634 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7509 (m-80) REVERT: D 104 LYS cc_start: 0.6196 (mmtm) cc_final: 0.5768 (mtmt) REVERT: D 111 TYR cc_start: 0.7757 (m-80) cc_final: 0.7416 (m-80) REVERT: D 135 CYS cc_start: 0.7856 (t) cc_final: 0.7414 (p) REVERT: D 173 GLU cc_start: 0.7936 (tp30) cc_final: 0.7677 (tp30) REVERT: D 345 LEU cc_start: 0.8517 (pp) cc_final: 0.8243 (mt) REVERT: D 375 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8253 (pp) REVERT: D 383 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7231 (tm-30) REVERT: D 591 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7615 (mmm160) REVERT: D 634 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7445 (m-80) outliers start: 59 outliers final: 38 residues processed: 354 average time/residue: 0.3009 time to fit residues: 166.5448 Evaluate side-chains 339 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 290 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 609 GLU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 218 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 148 ASN ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20512 Z= 0.155 Angle : 0.526 8.419 27816 Z= 0.261 Chirality : 0.038 0.203 3116 Planarity : 0.004 0.055 3428 Dihedral : 6.990 59.633 2772 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.40 % Allowed : 18.40 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.17), residues: 2412 helix: 1.98 (0.13), residues: 1432 sheet: -1.87 (0.47), residues: 116 loop : -1.25 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 454 HIS 0.003 0.001 HIS D 313 PHE 0.009 0.001 PHE B 547 TYR 0.019 0.001 TYR C 447 ARG 0.001 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 300 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6067 (mmtm) cc_final: 0.5731 (mtmt) REVERT: A 111 TYR cc_start: 0.7760 (m-80) cc_final: 0.7424 (m-80) REVERT: A 205 THR cc_start: 0.8961 (t) cc_final: 0.8653 (m) REVERT: A 345 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8302 (mt) REVERT: A 375 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8293 (pp) REVERT: A 383 GLN cc_start: 0.7835 (tp-100) cc_final: 0.7276 (tm-30) REVERT: A 591 ARG cc_start: 0.8089 (ptm160) cc_final: 0.7645 (mmm160) REVERT: A 634 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: A 655 ASN cc_start: 0.8042 (m-40) cc_final: 0.7804 (t0) REVERT: B 104 LYS cc_start: 0.6235 (mmtm) cc_final: 0.5748 (mtmt) REVERT: B 111 TYR cc_start: 0.7791 (m-80) cc_final: 0.7493 (m-80) REVERT: B 148 ASN cc_start: 0.6578 (t0) cc_final: 0.6308 (t0) REVERT: B 173 GLU cc_start: 0.7920 (tp30) cc_final: 0.7631 (tp30) REVERT: B 205 THR cc_start: 0.8902 (t) cc_final: 0.8598 (m) REVERT: B 277 MET cc_start: 0.8338 (tpp) cc_final: 0.7802 (mmt) REVERT: B 375 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8292 (pp) REVERT: B 383 GLN cc_start: 0.7843 (tp-100) cc_final: 0.7296 (tm-30) REVERT: B 591 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7649 (mmm160) REVERT: B 634 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: B 655 ASN cc_start: 0.8045 (m-40) cc_final: 0.7818 (t0) REVERT: C 104 LYS cc_start: 0.6227 (mmtm) cc_final: 0.5748 (mtmt) REVERT: C 111 TYR cc_start: 0.7771 (m-80) cc_final: 0.7441 (m-80) REVERT: C 173 GLU cc_start: 0.7926 (tp30) cc_final: 0.7638 (tp30) REVERT: C 205 THR cc_start: 0.8901 (t) cc_final: 0.8598 (m) REVERT: C 345 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8302 (mt) REVERT: C 375 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8289 (pp) REVERT: C 383 GLN cc_start: 0.7835 (tp-100) cc_final: 0.7271 (tm-30) REVERT: C 591 ARG cc_start: 0.8089 (ptm160) cc_final: 0.7646 (mmm160) REVERT: C 634 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: C 655 ASN cc_start: 0.8048 (m-40) cc_final: 0.7811 (t0) REVERT: D 104 LYS cc_start: 0.6185 (mmtm) cc_final: 0.5737 (mtmt) REVERT: D 111 TYR cc_start: 0.7785 (m-80) cc_final: 0.7457 (m-80) REVERT: D 173 GLU cc_start: 0.7851 (tp30) cc_final: 0.7509 (tp30) REVERT: D 205 THR cc_start: 0.8945 (t) cc_final: 0.8630 (m) REVERT: D 345 LEU cc_start: 0.8554 (pp) cc_final: 0.8328 (mt) REVERT: D 375 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8255 (pp) REVERT: D 383 GLN cc_start: 0.7843 (tp-100) cc_final: 0.7272 (tm-30) REVERT: D 591 ARG cc_start: 0.8081 (ptm160) cc_final: 0.7685 (mmt-90) REVERT: D 634 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: D 655 ASN cc_start: 0.8049 (m-40) cc_final: 0.7823 (t0) outliers start: 52 outliers final: 39 residues processed: 341 average time/residue: 0.3146 time to fit residues: 165.9352 Evaluate side-chains 344 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 295 time to evaluate : 2.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 10.0000 chunk 231 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 243 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20512 Z= 0.242 Angle : 0.579 10.281 27816 Z= 0.285 Chirality : 0.040 0.189 3116 Planarity : 0.004 0.055 3428 Dihedral : 7.208 58.642 2772 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.58 % Allowed : 17.76 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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 (0.17), residues: 2412 helix: 1.81 (0.13), residues: 1436 sheet: -1.89 (0.48), residues: 116 loop : -1.23 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 677 HIS 0.004 0.001 HIS B 251 PHE 0.012 0.001 PHE D 394 TYR 0.018 0.001 TYR C 447 ARG 0.002 0.000 ARG C 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 269 time to evaluate : 2.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6007 (mmtm) cc_final: 0.5686 (mtmt) REVERT: A 111 TYR cc_start: 0.7806 (m-80) cc_final: 0.7456 (m-80) REVERT: A 205 THR cc_start: 0.8943 (t) cc_final: 0.8624 (m) REVERT: A 277 MET cc_start: 0.8284 (tpp) cc_final: 0.7771 (mmt) REVERT: A 375 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8332 (pp) REVERT: A 383 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7327 (tm-30) REVERT: A 591 ARG cc_start: 0.8105 (ptm160) cc_final: 0.7704 (mmt-90) REVERT: A 634 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: B 104 LYS cc_start: 0.6210 (mmtm) cc_final: 0.5790 (mtmt) REVERT: B 111 TYR cc_start: 0.7791 (m-80) cc_final: 0.7477 (m-80) REVERT: B 148 ASN cc_start: 0.6626 (t0) cc_final: 0.6354 (t0) REVERT: B 173 GLU cc_start: 0.8012 (tp30) cc_final: 0.7765 (tp30) REVERT: B 205 THR cc_start: 0.8945 (t) cc_final: 0.8624 (m) REVERT: B 375 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8331 (pp) REVERT: B 383 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7314 (tm-30) REVERT: B 591 ARG cc_start: 0.8106 (ptm160) cc_final: 0.7705 (mmt-90) REVERT: B 634 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: C 104 LYS cc_start: 0.6257 (mmtm) cc_final: 0.5767 (mtmt) REVERT: C 111 TYR cc_start: 0.7806 (m-80) cc_final: 0.7459 (m-80) REVERT: C 173 GLU cc_start: 0.8019 (tp30) cc_final: 0.7767 (tp30) REVERT: C 205 THR cc_start: 0.8945 (t) cc_final: 0.8627 (m) REVERT: C 277 MET cc_start: 0.8276 (tpp) cc_final: 0.7762 (mmt) REVERT: C 375 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8323 (pp) REVERT: C 383 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7336 (tm-30) REVERT: C 591 ARG cc_start: 0.8105 (ptm160) cc_final: 0.7705 (mmt-90) REVERT: C 634 TYR cc_start: 0.8173 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: D 104 LYS cc_start: 0.6197 (mmtm) cc_final: 0.5733 (mtmt) REVERT: D 111 TYR cc_start: 0.7807 (m-80) cc_final: 0.7462 (m-80) REVERT: D 205 THR cc_start: 0.8942 (t) cc_final: 0.8623 (m) REVERT: D 277 MET cc_start: 0.8282 (tpp) cc_final: 0.7772 (mmt) REVERT: D 345 LEU cc_start: 0.8706 (pp) cc_final: 0.8451 (mt) REVERT: D 375 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8301 (pp) REVERT: D 383 GLN cc_start: 0.7901 (tp-100) cc_final: 0.7320 (tm-30) REVERT: D 591 ARG cc_start: 0.8104 (ptm160) cc_final: 0.7678 (mmm160) REVERT: D 634 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7508 (m-80) outliers start: 56 outliers final: 45 residues processed: 315 average time/residue: 0.2942 time to fit residues: 147.2582 Evaluate side-chains 320 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 267 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 178 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.0040 chunk 193 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 199 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN B 263 ASN C 263 ASN D 129 GLN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.142328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115243 restraints weight = 26306.497| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.10 r_work: 0.3174 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20512 Z= 0.138 Angle : 0.518 9.833 27816 Z= 0.258 Chirality : 0.037 0.182 3116 Planarity : 0.004 0.054 3428 Dihedral : 6.850 55.390 2772 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.63 % Allowed : 18.27 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.17), residues: 2412 helix: 2.10 (0.13), residues: 1436 sheet: -1.70 (0.48), residues: 116 loop : -1.15 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 464 HIS 0.003 0.001 HIS D 313 PHE 0.010 0.001 PHE C 705 TYR 0.017 0.001 TYR C 447 ARG 0.002 0.000 ARG C 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4214.18 seconds wall clock time: 75 minutes 56.72 seconds (4556.72 seconds total)