Starting phenix.real_space_refine on Thu Mar 5 06:31:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekq_28210/03_2026/8ekq_28210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekq_28210/03_2026/8ekq_28210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ekq_28210/03_2026/8ekq_28210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekq_28210/03_2026/8ekq_28210.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekq_28210/03_2026/8ekq_28210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekq_28210/03_2026/8ekq_28210.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 108 5.16 5 C 13020 2.51 5 N 3264 2.21 5 O 3464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19864 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4896 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 586} Chain breaks: 6 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'PEX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 3.93, per 1000 atoms: 0.20 Number of scatterers: 19864 At special positions: 0 Unit cell: (136.51, 136.51, 108.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 8 15.00 O 3464 8.00 N 3264 7.00 C 13020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 777.2 milliseconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 65.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.768A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.528A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.540A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 220 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 Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.642A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (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 323 through 327 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 430 through 466 removed outlier: 7.223A pdb=" N LEU A 461 " --> pdb=" O TRP A 457 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE A 462 " --> pdb=" O ARG A 458 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 492 removed outlier: 3.796A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.944A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.632A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.842A pdb=" N ILE A 524 " --> pdb=" O GLN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 560 Processing helix chain 'A' and resid 592 through 605 Processing helix chain 'A' and resid 618 through 649 removed outlier: 4.017A pdb=" N GLU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 672 Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.578A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 719 " --> pdb=" O TRP A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.768A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.528A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.540A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 220 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 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.642A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (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 323 through 327 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 377 through 389 Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 430 through 466 removed outlier: 7.223A pdb=" N LEU B 461 " --> pdb=" O TRP B 457 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE B 462 " --> pdb=" O ARG B 458 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 492 removed outlier: 3.796A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.944A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.632A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 removed outlier: 3.842A pdb=" N ILE B 524 " --> pdb=" O GLN B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 560 Processing helix chain 'B' and resid 592 through 605 Processing helix chain 'B' and resid 618 through 649 removed outlier: 4.017A pdb=" N GLU B 647 " --> pdb=" O ALA B 643 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 672 Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.578A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 719 " --> pdb=" O TRP B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.768A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.528A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.540A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 220 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 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.642A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (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 323 through 327 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 430 through 466 removed outlier: 7.223A pdb=" N LEU C 461 " --> pdb=" O TRP C 457 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE C 462 " --> pdb=" O ARG C 458 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 492 removed outlier: 3.796A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.944A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.632A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 524 removed outlier: 3.842A pdb=" N ILE C 524 " --> pdb=" O GLN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 560 Processing helix chain 'C' and resid 592 through 605 Processing helix chain 'C' and resid 618 through 649 removed outlier: 4.017A pdb=" N GLU C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 648 " --> pdb=" O LEU C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 672 Processing helix chain 'C' and resid 711 through 719 removed outlier: 3.578A pdb=" N LYS C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 719 " --> pdb=" O TRP C 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.768A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.528A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.540A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 220 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 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.642A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (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 323 through 327 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 430 through 466 removed outlier: 7.223A pdb=" N LEU D 461 " --> pdb=" O TRP D 457 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 492 removed outlier: 3.796A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.944A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.632A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 524 removed outlier: 3.842A pdb=" N ILE D 524 " --> pdb=" O GLN D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 560 Processing helix chain 'D' and resid 592 through 605 Processing helix chain 'D' and resid 618 through 649 removed outlier: 4.017A pdb=" N GLU D 647 " --> pdb=" O ALA D 643 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 672 Processing helix chain 'D' and resid 711 through 719 removed outlier: 3.578A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 719 " --> pdb=" O TRP D 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.818A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.867A 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: 6.819A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.867A 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: 6.818A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.867A 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: 6.818A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3072 1.31 - 1.43: 5656 1.43 - 1.56: 11420 1.56 - 1.69: 16 1.69 - 1.81: 164 Bond restraints: 20328 Sorted by residual: bond pdb=" C4 PEX A 802 " pdb=" O4 PEX A 802 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C4 PEX B 802 " pdb=" O4 PEX B 802 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C4 PEX D 802 " pdb=" O4 PEX D 802 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C4 PEX C 802 " pdb=" O4 PEX C 802 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C4 PEX C 801 " pdb=" O4 PEX C 801 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 20323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 27160 3.21 - 6.41: 300 6.41 - 9.62: 48 9.62 - 12.82: 0 12.82 - 16.03: 8 Bond angle restraints: 27516 Sorted by residual: angle pdb=" O3 PEX D 802 " pdb=" P1 PEX D 802 " pdb=" O8 PEX D 802 " ideal model delta sigma weight residual 93.74 109.77 -16.03 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O3 PEX A 802 " pdb=" P1 PEX A 802 " pdb=" O8 PEX A 802 " ideal model delta sigma weight residual 93.74 109.77 -16.03 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O3 PEX C 802 " pdb=" P1 PEX C 802 " pdb=" O8 PEX C 802 " ideal model delta sigma weight residual 93.74 109.77 -16.03 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O3 PEX B 802 " pdb=" P1 PEX B 802 " pdb=" O8 PEX B 802 " ideal model delta sigma weight residual 93.74 109.77 -16.03 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O3 PEX B 801 " pdb=" P1 PEX B 801 " pdb=" O8 PEX B 801 " ideal model delta sigma weight residual 93.74 109.04 -15.30 3.00e+00 1.11e-01 2.60e+01 ... (remaining 27511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 11196 20.59 - 41.17: 692 41.17 - 61.76: 88 61.76 - 82.34: 36 82.34 - 102.93: 16 Dihedral angle restraints: 12028 sinusoidal: 4924 harmonic: 7104 Sorted by residual: dihedral pdb=" CA TRP B 351 " pdb=" C TRP B 351 " pdb=" N GLU B 352 " pdb=" CA GLU B 352 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA TRP A 351 " pdb=" C TRP A 351 " pdb=" N GLU A 352 " pdb=" CA GLU A 352 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA TRP C 351 " pdb=" C TRP C 351 " pdb=" N GLU C 352 " pdb=" CA GLU C 352 " ideal model delta harmonic sigma weight residual 180.00 159.40 20.60 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 12025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2179 0.040 - 0.080: 724 0.080 - 0.121: 161 0.121 - 0.161: 24 0.161 - 0.201: 16 Chirality restraints: 3104 Sorted by residual: chirality pdb=" CA GLN A 414 " pdb=" N GLN A 414 " pdb=" C GLN A 414 " pdb=" CB GLN A 414 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLN B 414 " pdb=" N GLN B 414 " pdb=" C GLN B 414 " pdb=" CB GLN B 414 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA GLN C 414 " pdb=" N GLN C 414 " pdb=" C GLN C 414 " pdb=" CB GLN C 414 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 3101 not shown) Planarity restraints: 3384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 660 " -0.022 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP B 660 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 660 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 660 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 660 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 660 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 660 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 660 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 660 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 660 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 660 " -0.022 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP A 660 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP A 660 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 660 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 660 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 660 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 660 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 660 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 660 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 660 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 660 " 0.022 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP D 660 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 660 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 660 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 660 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 660 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 660 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 660 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 660 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 660 " 0.009 2.00e-02 2.50e+03 ... (remaining 3381 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3935 2.78 - 3.31: 18105 3.31 - 3.84: 33856 3.84 - 4.37: 40079 4.37 - 4.90: 67606 Nonbonded interactions: 163581 Sorted by model distance: nonbonded pdb=" N GLU C 495 " pdb=" OE1 GLU C 495 " model vdw 2.245 3.120 nonbonded pdb=" N GLU D 495 " pdb=" OE1 GLU D 495 " model vdw 2.245 3.120 nonbonded pdb=" N GLU A 495 " pdb=" OE1 GLU A 495 " model vdw 2.245 3.120 nonbonded pdb=" N GLU B 495 " pdb=" OE1 GLU B 495 " model vdw 2.245 3.120 nonbonded pdb=" NH2 ARG A 369 " pdb=" OD2 ASP A 469 " model vdw 2.307 3.120 ... (remaining 163576 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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: 7.240 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.010 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.004 0.071 20328 Z= 0.199 Angle : 0.845 16.027 27516 Z= 0.404 Chirality : 0.043 0.201 3104 Planarity : 0.006 0.077 3384 Dihedral : 14.355 102.928 7428 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2376 helix: 0.15 (0.12), residues: 1472 sheet: 1.19 (0.50), residues: 112 loop : -0.59 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 459 TYR 0.023 0.002 TYR B 412 PHE 0.018 0.002 PHE B 311 TRP 0.043 0.002 TRP B 660 HIS 0.010 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00411 (20328) covalent geometry : angle 0.84550 (27516) hydrogen bonds : bond 0.13409 ( 1092) hydrogen bonds : angle 5.13687 ( 3144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.740 Fit side-chains REVERT: A 286 GLN cc_start: 0.7548 (mt0) cc_final: 0.7268 (mm-40) REVERT: A 370 HIS cc_start: 0.8370 (p90) cc_final: 0.8154 (p-80) REVERT: A 671 MET cc_start: 0.8907 (mtm) cc_final: 0.8698 (mtm) REVERT: A 687 ARG cc_start: 0.7138 (mtm180) cc_final: 0.6894 (mtp180) REVERT: B 286 GLN cc_start: 0.7568 (mt0) cc_final: 0.7288 (mm-40) REVERT: B 370 HIS cc_start: 0.8374 (p90) cc_final: 0.8158 (p-80) REVERT: B 671 MET cc_start: 0.8906 (mtm) cc_final: 0.8700 (mtm) REVERT: B 687 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6892 (mtp180) REVERT: C 286 GLN cc_start: 0.7563 (mt0) cc_final: 0.7287 (mm-40) REVERT: C 370 HIS cc_start: 0.8373 (p90) cc_final: 0.8154 (p-80) REVERT: C 671 MET cc_start: 0.8908 (mtm) cc_final: 0.8701 (mtm) REVERT: C 687 ARG cc_start: 0.7133 (mtm180) cc_final: 0.6887 (mtp180) REVERT: D 286 GLN cc_start: 0.7545 (mt0) cc_final: 0.7268 (mm-40) REVERT: D 370 HIS cc_start: 0.8373 (p90) cc_final: 0.8155 (p-80) REVERT: D 671 MET cc_start: 0.8907 (mtm) cc_final: 0.8700 (mtm) REVERT: D 687 ARG cc_start: 0.7136 (mtm180) cc_final: 0.6887 (mtp180) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.6011 time to fit residues: 255.1611 Evaluate side-chains 302 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 165 HIS A 186 ASN A 294 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 186 ASN B 294 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 186 ASN C 294 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN D 165 HIS D 186 ASN D 294 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.145370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116805 restraints weight = 21104.068| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.42 r_work: 0.3096 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20328 Z= 0.220 Angle : 0.587 8.308 27516 Z= 0.298 Chirality : 0.041 0.150 3104 Planarity : 0.005 0.040 3384 Dihedral : 10.169 77.483 2876 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.41 % Allowed : 6.16 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2376 helix: 1.27 (0.13), residues: 1476 sheet: 1.55 (0.51), residues: 112 loop : -0.41 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 459 TYR 0.029 0.003 TYR B 471 PHE 0.016 0.002 PHE D 394 TRP 0.026 0.002 TRP B 660 HIS 0.011 0.001 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00520 (20328) covalent geometry : angle 0.58745 (27516) hydrogen bonds : bond 0.04507 ( 1092) hydrogen bonds : angle 3.98243 ( 3144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 0.843 Fit side-chains REVERT: A 137 MET cc_start: 0.6931 (tpt) cc_final: 0.6637 (tpp) REVERT: A 163 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: A 286 GLN cc_start: 0.7581 (mt0) cc_final: 0.7365 (mm-40) REVERT: A 687 ARG cc_start: 0.7343 (mtm180) cc_final: 0.6968 (mtp180) REVERT: B 108 ASP cc_start: 0.7070 (m-30) cc_final: 0.6793 (m-30) REVERT: B 137 MET cc_start: 0.6928 (tpt) cc_final: 0.6635 (tpp) REVERT: B 163 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7605 (tt0) REVERT: B 286 GLN cc_start: 0.7599 (mt0) cc_final: 0.7384 (mm-40) REVERT: B 687 ARG cc_start: 0.7346 (mtm180) cc_final: 0.6970 (mtp180) REVERT: C 137 MET cc_start: 0.6946 (tpt) cc_final: 0.6648 (tpp) REVERT: C 286 GLN cc_start: 0.7592 (mt0) cc_final: 0.7382 (mm-40) REVERT: C 687 ARG cc_start: 0.7332 (mtm180) cc_final: 0.6953 (mtp180) REVERT: D 137 MET cc_start: 0.6962 (tpt) cc_final: 0.6667 (tpp) REVERT: D 286 GLN cc_start: 0.7578 (mt0) cc_final: 0.7366 (mm-40) REVERT: D 687 ARG cc_start: 0.7303 (mtm180) cc_final: 0.6933 (mtp180) outliers start: 51 outliers final: 26 residues processed: 339 average time/residue: 0.5879 time to fit residues: 225.0719 Evaluate side-chains 326 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 298 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN B 186 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN C 186 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN D 294 GLN ** D 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.144224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115926 restraints weight = 21363.377| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.39 r_work: 0.3099 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20328 Z= 0.203 Angle : 0.557 9.102 27516 Z= 0.282 Chirality : 0.040 0.148 3104 Planarity : 0.005 0.040 3384 Dihedral : 9.980 71.964 2876 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.94 % Allowed : 6.82 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.17), residues: 2376 helix: 1.55 (0.14), residues: 1472 sheet: 1.61 (0.51), residues: 112 loop : -0.40 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 459 TYR 0.024 0.002 TYR B 471 PHE 0.018 0.002 PHE C 394 TRP 0.023 0.002 TRP A 660 HIS 0.006 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00482 (20328) covalent geometry : angle 0.55693 (27516) hydrogen bonds : bond 0.04204 ( 1092) hydrogen bonds : angle 3.95716 ( 3144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 309 time to evaluate : 0.770 Fit side-chains REVERT: A 163 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7599 (tt0) REVERT: A 286 GLN cc_start: 0.7593 (mt0) cc_final: 0.7390 (mm-40) REVERT: A 473 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8113 (mm-30) REVERT: A 640 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6625 (ttp) REVERT: A 687 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6873 (mtp180) REVERT: B 108 ASP cc_start: 0.7230 (m-30) cc_final: 0.7000 (m-30) REVERT: B 137 MET cc_start: 0.7076 (tpt) cc_final: 0.6804 (tpp) REVERT: B 163 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: B 473 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8122 (mm-30) REVERT: B 687 ARG cc_start: 0.7245 (mtm180) cc_final: 0.6891 (mtp180) REVERT: C 286 GLN cc_start: 0.7607 (mt0) cc_final: 0.7406 (mm-40) REVERT: C 473 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8131 (mm-30) REVERT: C 640 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6642 (ttp) REVERT: C 687 ARG cc_start: 0.7226 (mtm180) cc_final: 0.6879 (mtp180) REVERT: D 473 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8118 (mm-30) REVERT: D 687 ARG cc_start: 0.7201 (mtm180) cc_final: 0.6873 (mtp180) outliers start: 62 outliers final: 39 residues processed: 334 average time/residue: 0.5885 time to fit residues: 222.5786 Evaluate side-chains 333 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 137 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 178 optimal weight: 0.1980 chunk 152 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 487 GLN A 639 ASN B 414 GLN B 487 GLN C 414 GLN C 487 GLN C 639 ASN D 294 GLN D 414 GLN D 487 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.145413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.116949 restraints weight = 21521.642| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.42 r_work: 0.3120 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20328 Z= 0.128 Angle : 0.488 9.257 27516 Z= 0.247 Chirality : 0.037 0.126 3104 Planarity : 0.004 0.035 3384 Dihedral : 9.372 71.557 2876 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.13 % Allowed : 9.04 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.18), residues: 2376 helix: 1.89 (0.14), residues: 1472 sheet: 1.60 (0.52), residues: 112 loop : -0.26 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.015 0.002 TYR B 471 PHE 0.011 0.001 PHE C 394 TRP 0.026 0.001 TRP D 660 HIS 0.004 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00297 (20328) covalent geometry : angle 0.48799 (27516) hydrogen bonds : bond 0.03569 ( 1092) hydrogen bonds : angle 3.75826 ( 3144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 299 time to evaluate : 0.762 Fit side-chains REVERT: A 163 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: A 286 GLN cc_start: 0.7522 (mt0) cc_final: 0.7319 (mm-40) REVERT: A 473 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8049 (mm-30) REVERT: A 531 LYS cc_start: 0.6841 (ttmt) cc_final: 0.5404 (tptm) REVERT: A 660 TRP cc_start: 0.8752 (t60) cc_final: 0.8544 (t60) REVERT: A 663 GLN cc_start: 0.8963 (mt0) cc_final: 0.8744 (mt0) REVERT: A 687 ARG cc_start: 0.7206 (mtm180) cc_final: 0.6826 (mtp-110) REVERT: B 137 MET cc_start: 0.7050 (tpt) cc_final: 0.6800 (tpp) REVERT: B 163 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: B 473 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 531 LYS cc_start: 0.6802 (ttmt) cc_final: 0.5391 (tptm) REVERT: B 640 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6663 (ttp) REVERT: B 663 GLN cc_start: 0.8969 (mt0) cc_final: 0.8751 (mt0) REVERT: B 687 ARG cc_start: 0.7221 (mtm180) cc_final: 0.6830 (mtp-110) REVERT: C 286 GLN cc_start: 0.7541 (mt0) cc_final: 0.7337 (mm-40) REVERT: C 473 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8052 (mm-30) REVERT: C 531 LYS cc_start: 0.6889 (ttmt) cc_final: 0.5451 (tptm) REVERT: C 640 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6632 (ttp) REVERT: C 687 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6817 (mtp-110) REVERT: D 473 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8041 (mm-30) REVERT: D 531 LYS cc_start: 0.6830 (ttmt) cc_final: 0.5408 (tptm) REVERT: D 640 MET cc_start: 0.7036 (ttp) cc_final: 0.6808 (tmm) REVERT: D 687 ARG cc_start: 0.7191 (mtm180) cc_final: 0.6814 (mtp-110) outliers start: 45 outliers final: 27 residues processed: 326 average time/residue: 0.6388 time to fit residues: 233.4299 Evaluate side-chains 318 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 13 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 414 GLN B 639 ASN C 479 GLN D 294 GLN D 479 GLN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.142999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.114449 restraints weight = 21438.340| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.42 r_work: 0.3090 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20328 Z= 0.207 Angle : 0.552 9.667 27516 Z= 0.279 Chirality : 0.041 0.144 3104 Planarity : 0.004 0.040 3384 Dihedral : 9.860 71.075 2876 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.18 % Allowed : 9.99 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.17), residues: 2376 helix: 1.73 (0.14), residues: 1472 sheet: 1.58 (0.52), residues: 112 loop : -0.28 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 197 TYR 0.024 0.002 TYR B 471 PHE 0.018 0.002 PHE A 394 TRP 0.029 0.002 TRP D 660 HIS 0.005 0.001 HIS A 165 Details of bonding type rmsd covalent geometry : bond 0.00492 (20328) covalent geometry : angle 0.55197 (27516) hydrogen bonds : bond 0.04130 ( 1092) hydrogen bonds : angle 3.90976 ( 3144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 308 time to evaluate : 0.727 Fit side-chains REVERT: A 163 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: A 286 GLN cc_start: 0.7557 (mt0) cc_final: 0.7350 (mm-40) REVERT: A 407 PHE cc_start: 0.8591 (t80) cc_final: 0.8344 (t80) REVERT: A 473 GLU cc_start: 0.8359 (mm-30) cc_final: 0.8120 (mm-30) REVERT: A 640 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6686 (ttp) REVERT: A 687 ARG cc_start: 0.7174 (mtm180) cc_final: 0.6821 (mtp180) REVERT: B 137 MET cc_start: 0.7028 (tpt) cc_final: 0.6782 (tpp) REVERT: B 163 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: B 352 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 407 PHE cc_start: 0.8595 (t80) cc_final: 0.8335 (t80) REVERT: B 473 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8121 (mm-30) REVERT: B 640 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6642 (ttp) REVERT: B 687 ARG cc_start: 0.7197 (mtm180) cc_final: 0.6830 (mtp180) REVERT: C 286 GLN cc_start: 0.7540 (mt0) cc_final: 0.7340 (mm-40) REVERT: C 407 PHE cc_start: 0.8586 (t80) cc_final: 0.8337 (t80) REVERT: C 473 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8131 (mm-30) REVERT: C 640 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6636 (ttp) REVERT: C 687 ARG cc_start: 0.7192 (mtm180) cc_final: 0.6832 (mtp180) REVERT: D 352 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7600 (mm-30) REVERT: D 407 PHE cc_start: 0.8598 (t80) cc_final: 0.8344 (t80) REVERT: D 473 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8114 (mm-30) REVERT: D 687 ARG cc_start: 0.7155 (mtm180) cc_final: 0.6799 (mtp180) outliers start: 46 outliers final: 38 residues processed: 334 average time/residue: 0.6354 time to fit residues: 238.0239 Evaluate side-chains 341 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 298 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 595 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 131 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 639 ASN B 487 GLN C 479 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN D 294 GLN D 479 GLN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.143225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.114690 restraints weight = 21376.096| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.41 r_work: 0.3093 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20328 Z= 0.200 Angle : 0.549 9.598 27516 Z= 0.277 Chirality : 0.040 0.142 3104 Planarity : 0.004 0.040 3384 Dihedral : 9.675 70.005 2876 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.60 % Allowed : 10.04 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.18), residues: 2376 helix: 1.71 (0.14), residues: 1472 sheet: 1.59 (0.52), residues: 112 loop : -0.25 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 687 TYR 0.021 0.002 TYR D 471 PHE 0.018 0.002 PHE C 394 TRP 0.035 0.002 TRP D 660 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00475 (20328) covalent geometry : angle 0.54862 (27516) hydrogen bonds : bond 0.04076 ( 1092) hydrogen bonds : angle 3.91051 ( 3144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 310 time to evaluate : 0.678 Fit side-chains REVERT: A 163 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: A 407 PHE cc_start: 0.8604 (t80) cc_final: 0.8360 (t80) REVERT: A 473 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8126 (mm-30) REVERT: A 560 ARG cc_start: 0.7048 (mtt90) cc_final: 0.6724 (mtt-85) REVERT: A 640 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6674 (ttp) REVERT: A 660 TRP cc_start: 0.8791 (t60) cc_final: 0.8482 (t60) REVERT: A 687 ARG cc_start: 0.7215 (mtm180) cc_final: 0.6874 (mtp180) REVERT: B 163 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: B 407 PHE cc_start: 0.8603 (t80) cc_final: 0.8348 (t80) REVERT: B 473 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8118 (mm-30) REVERT: B 560 ARG cc_start: 0.7024 (mtt90) cc_final: 0.6705 (mtt-85) REVERT: B 640 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6645 (ttp) REVERT: B 660 TRP cc_start: 0.8807 (t60) cc_final: 0.8572 (t60) REVERT: B 687 ARG cc_start: 0.7218 (mtm180) cc_final: 0.6877 (mtp180) REVERT: C 137 MET cc_start: 0.7320 (tpt) cc_final: 0.6936 (tpp) REVERT: C 407 PHE cc_start: 0.8600 (t80) cc_final: 0.8355 (t80) REVERT: C 473 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8124 (mm-30) REVERT: C 560 ARG cc_start: 0.7022 (mtt90) cc_final: 0.6705 (mtt-85) REVERT: C 640 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6619 (ttp) REVERT: C 660 TRP cc_start: 0.8815 (t60) cc_final: 0.8596 (t60) REVERT: C 687 ARG cc_start: 0.7225 (mtm180) cc_final: 0.6885 (mtp180) REVERT: D 407 PHE cc_start: 0.8612 (t80) cc_final: 0.8368 (t80) REVERT: D 473 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8109 (mm-30) REVERT: D 560 ARG cc_start: 0.7041 (mtt90) cc_final: 0.6724 (mtt-85) REVERT: D 640 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6669 (ttp) REVERT: D 660 TRP cc_start: 0.8805 (t60) cc_final: 0.8570 (t60) REVERT: D 687 ARG cc_start: 0.7204 (mtm180) cc_final: 0.6863 (mtp180) outliers start: 55 outliers final: 41 residues processed: 344 average time/residue: 0.6198 time to fit residues: 239.5116 Evaluate side-chains 344 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 297 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 640 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 76 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 210 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 209 optimal weight: 1.9990 chunk 134 optimal weight: 0.0770 chunk 150 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 overall best weight: 1.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN D 294 GLN D 639 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.151033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124633 restraints weight = 21715.720| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.32 r_work: 0.3166 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20328 Z= 0.142 Angle : 0.512 9.638 27516 Z= 0.256 Chirality : 0.038 0.129 3104 Planarity : 0.004 0.038 3384 Dihedral : 9.308 69.440 2876 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.89 % Allowed : 11.03 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.18), residues: 2376 helix: 1.88 (0.14), residues: 1472 sheet: 1.56 (0.52), residues: 112 loop : -0.21 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 197 TYR 0.016 0.002 TYR D 471 PHE 0.014 0.001 PHE A 394 TRP 0.027 0.001 TRP D 660 HIS 0.003 0.001 HIS C 293 Details of bonding type rmsd covalent geometry : bond 0.00332 (20328) covalent geometry : angle 0.51169 (27516) hydrogen bonds : bond 0.03685 ( 1092) hydrogen bonds : angle 3.80596 ( 3144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 306 time to evaluate : 0.692 Fit side-chains REVERT: A 163 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: A 407 PHE cc_start: 0.8577 (t80) cc_final: 0.8330 (t80) REVERT: A 473 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 490 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.6785 (ttp-110) REVERT: A 560 ARG cc_start: 0.7059 (mtt90) cc_final: 0.6742 (mtt-85) REVERT: A 640 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6751 (ttp) REVERT: A 660 TRP cc_start: 0.8769 (t60) cc_final: 0.8526 (t60) REVERT: A 687 ARG cc_start: 0.7245 (mtm180) cc_final: 0.6949 (mtp180) REVERT: B 137 MET cc_start: 0.7384 (tpt) cc_final: 0.7021 (tpp) REVERT: B 163 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: B 407 PHE cc_start: 0.8557 (t80) cc_final: 0.8311 (t80) REVERT: B 473 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8062 (mm-30) REVERT: B 490 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.6798 (ttp-110) REVERT: B 687 ARG cc_start: 0.7287 (mtm180) cc_final: 0.6963 (mtp180) REVERT: C 473 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8069 (mm-30) REVERT: C 560 ARG cc_start: 0.7023 (mtt90) cc_final: 0.6696 (mtt-85) REVERT: C 640 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6719 (ttp) REVERT: C 687 ARG cc_start: 0.7286 (mtm180) cc_final: 0.6959 (mtp180) REVERT: D 407 PHE cc_start: 0.8569 (t80) cc_final: 0.8321 (t80) REVERT: D 473 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8074 (mm-30) REVERT: D 560 ARG cc_start: 0.7036 (mtt90) cc_final: 0.6715 (mtt-85) REVERT: D 687 ARG cc_start: 0.7248 (mtm180) cc_final: 0.6946 (mtp180) outliers start: 40 outliers final: 32 residues processed: 331 average time/residue: 0.6340 time to fit residues: 235.8061 Evaluate side-chains 336 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 298 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 594 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 28 optimal weight: 4.9990 chunk 221 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 4 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN A 639 ASN B 487 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN D 294 GLN ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.149523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.123113 restraints weight = 21741.696| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.32 r_work: 0.3092 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20328 Z= 0.215 Angle : 0.570 10.113 27516 Z= 0.286 Chirality : 0.041 0.144 3104 Planarity : 0.004 0.045 3384 Dihedral : 9.719 69.222 2876 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.51 % Allowed : 10.75 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.18), residues: 2376 helix: 1.68 (0.14), residues: 1472 sheet: 1.60 (0.52), residues: 112 loop : -0.26 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 312 TYR 0.023 0.002 TYR B 471 PHE 0.019 0.002 PHE D 394 TRP 0.040 0.002 TRP D 660 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00512 (20328) covalent geometry : angle 0.57041 (27516) hydrogen bonds : bond 0.04185 ( 1092) hydrogen bonds : angle 3.94029 ( 3144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 296 time to evaluate : 0.738 Fit side-chains REVERT: A 163 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: A 490 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6823 (ttp-110) REVERT: A 640 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6718 (ttp) REVERT: A 687 ARG cc_start: 0.7289 (mtm180) cc_final: 0.6950 (mtp180) REVERT: B 137 MET cc_start: 0.7363 (tpt) cc_final: 0.6997 (tpp) REVERT: B 163 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: B 490 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6817 (ttp-110) REVERT: B 640 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6697 (ttp) REVERT: B 687 ARG cc_start: 0.7309 (mtm180) cc_final: 0.6958 (mtp180) REVERT: C 490 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6844 (ttp-110) REVERT: C 640 MET cc_start: 0.7159 (OUTLIER) cc_final: 0.6629 (ttp) REVERT: C 687 ARG cc_start: 0.7304 (mtm180) cc_final: 0.6950 (mtp180) REVERT: D 490 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6820 (ttp-110) REVERT: D 640 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6690 (ttp) REVERT: D 687 ARG cc_start: 0.7291 (mtm180) cc_final: 0.6944 (mtp180) outliers start: 53 outliers final: 36 residues processed: 326 average time/residue: 0.6204 time to fit residues: 226.8380 Evaluate side-chains 331 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 285 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 487 GLN Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 487 GLN Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 384 GLU Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 640 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 112 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 134 optimal weight: 0.0570 chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.151753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125407 restraints weight = 21741.260| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.32 r_work: 0.3134 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20328 Z= 0.122 Angle : 0.498 9.927 27516 Z= 0.248 Chirality : 0.037 0.124 3104 Planarity : 0.004 0.037 3384 Dihedral : 9.143 68.681 2876 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.75 % Allowed : 11.51 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.18), residues: 2376 helix: 1.95 (0.14), residues: 1468 sheet: 1.61 (0.53), residues: 112 loop : -0.23 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 560 TYR 0.014 0.001 TYR D 403 PHE 0.012 0.001 PHE A 394 TRP 0.050 0.002 TRP D 660 HIS 0.004 0.001 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00279 (20328) covalent geometry : angle 0.49786 (27516) hydrogen bonds : bond 0.03536 ( 1092) hydrogen bonds : angle 3.78029 ( 3144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 299 time to evaluate : 0.796 Fit side-chains REVERT: A 137 MET cc_start: 0.7171 (tpt) cc_final: 0.6788 (tpp) REVERT: A 163 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 490 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6790 (ttp-110) REVERT: A 687 ARG cc_start: 0.7278 (mtm180) cc_final: 0.6952 (mtp180) REVERT: B 137 MET cc_start: 0.7318 (tpt) cc_final: 0.6966 (tpp) REVERT: B 163 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: B 490 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6800 (ttp-110) REVERT: B 687 ARG cc_start: 0.7303 (mtm180) cc_final: 0.6965 (mtp180) REVERT: C 182 LEU cc_start: 0.8401 (tt) cc_final: 0.8173 (tp) REVERT: C 490 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6813 (ttp-110) REVERT: C 687 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6964 (mtp180) REVERT: D 137 MET cc_start: 0.7186 (tpt) cc_final: 0.6806 (tpp) REVERT: D 490 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6800 (ttp-110) REVERT: D 687 ARG cc_start: 0.7277 (mtm180) cc_final: 0.6948 (mtp180) outliers start: 37 outliers final: 31 residues processed: 323 average time/residue: 0.6312 time to fit residues: 229.2128 Evaluate side-chains 327 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 670 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 177 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 223 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 120 optimal weight: 0.1980 chunk 222 optimal weight: 0.0060 chunk 195 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN B 479 GLN D 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126566 restraints weight = 22060.320| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.33 r_work: 0.3160 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20328 Z= 0.094 Angle : 0.468 10.518 27516 Z= 0.232 Chirality : 0.035 0.112 3104 Planarity : 0.004 0.036 3384 Dihedral : 8.402 68.404 2876 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.56 % Allowed : 11.93 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.18), residues: 2376 helix: 2.19 (0.14), residues: 1468 sheet: 1.63 (0.53), residues: 112 loop : -0.12 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 560 TYR 0.011 0.001 TYR A 403 PHE 0.011 0.001 PHE D 311 TRP 0.054 0.001 TRP D 660 HIS 0.003 0.001 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00206 (20328) covalent geometry : angle 0.46848 (27516) hydrogen bonds : bond 0.03120 ( 1092) hydrogen bonds : angle 3.56482 ( 3144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 294 time to evaluate : 0.773 Fit side-chains REVERT: A 163 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: A 640 MET cc_start: 0.7231 (ttp) cc_final: 0.6975 (tmm) REVERT: A 687 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6962 (mtp180) REVERT: B 163 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: B 640 MET cc_start: 0.7205 (ttp) cc_final: 0.6949 (tmm) REVERT: B 687 ARG cc_start: 0.7321 (mtm180) cc_final: 0.6971 (mtp180) REVERT: C 352 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7427 (tp30) REVERT: C 640 MET cc_start: 0.7213 (ttp) cc_final: 0.6953 (tmm) REVERT: C 687 ARG cc_start: 0.7312 (mtm180) cc_final: 0.6965 (mtp180) REVERT: D 490 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.6834 (ttp-110) REVERT: D 640 MET cc_start: 0.7228 (ttp) cc_final: 0.6973 (tmm) REVERT: D 687 ARG cc_start: 0.7297 (mtm180) cc_final: 0.6960 (mtp180) outliers start: 33 outliers final: 21 residues processed: 318 average time/residue: 0.6297 time to fit residues: 224.8012 Evaluate side-chains 305 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 670 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 0.4980 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 136 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 GLN D 479 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125510 restraints weight = 21857.056| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.33 r_work: 0.3126 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20328 Z= 0.134 Angle : 0.499 11.185 27516 Z= 0.250 Chirality : 0.037 0.124 3104 Planarity : 0.004 0.037 3384 Dihedral : 8.618 67.749 2876 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.33 % Allowed : 12.88 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.18), residues: 2376 helix: 2.09 (0.14), residues: 1468 sheet: 1.60 (0.52), residues: 112 loop : -0.14 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 197 TYR 0.016 0.002 TYR B 471 PHE 0.013 0.001 PHE B 394 TRP 0.066 0.002 TRP B 660 HIS 0.004 0.001 HIS D 293 Details of bonding type rmsd covalent geometry : bond 0.00311 (20328) covalent geometry : angle 0.49879 (27516) hydrogen bonds : bond 0.03562 ( 1092) hydrogen bonds : angle 3.67393 ( 3144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7273.10 seconds wall clock time: 124 minutes 13.98 seconds (7453.98 seconds total)