Starting phenix.real_space_refine on Tue Jun 17 14:17:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekq_28210/06_2025/8ekq_28210.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekq_28210/06_2025/8ekq_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_28210/06_2025/8ekq_28210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekq_28210/06_2025/8ekq_28210.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekq_28210/06_2025/8ekq_28210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekq_28210/06_2025/8ekq_28210.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5, 'TRP:plan': 3} 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: C, B, D Time building chain proxies: 12.80, per 1000 atoms: 0.64 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: 4.98 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.09 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: 6.53 Time building geometry restraints manager: 5.91 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 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: 1.000 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 46.460 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.043 0.002 TRP B 660 HIS 0.010 0.001 HIS D 165 PHE 0.018 0.002 PHE B 311 TYR 0.023 0.002 TYR B 412 ARG 0.017 0.001 ARG B 459 Details of bonding type rmsd hydrogen bonds : bond 0.13409 ( 1092) hydrogen bonds : angle 5.13687 ( 3144) covalent geometry : bond 0.00411 (20328) covalent geometry : angle 0.84550 (27516) *********************** 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 : 2.078 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: 1.2940 time to fit residues: 550.6518 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 : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 294 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 165 HIS 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 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.146975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.118313 restraints weight = 21182.595| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.43 r_work: 0.3117 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20328 Z= 0.164 Angle : 0.535 7.973 27516 Z= 0.271 Chirality : 0.038 0.136 3104 Planarity : 0.004 0.034 3384 Dihedral : 9.868 79.940 2876 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.27 % Allowed : 5.92 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.17), residues: 2376 helix: 1.45 (0.13), residues: 1476 sheet: 1.54 (0.51), residues: 112 loop : -0.32 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 660 HIS 0.009 0.001 HIS C 165 PHE 0.012 0.001 PHE D 394 TYR 0.023 0.002 TYR D 471 ARG 0.005 0.001 ARG C 459 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 1092) hydrogen bonds : angle 3.84760 ( 3144) covalent geometry : bond 0.00382 (20328) covalent geometry : angle 0.53519 (27516) *********************** 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 359 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 2.123 Fit side-chains REVERT: A 163 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7756 (tt0) REVERT: A 286 GLN cc_start: 0.7564 (mt0) cc_final: 0.7357 (mm-40) REVERT: A 352 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7437 (tp30) REVERT: A 687 ARG cc_start: 0.7326 (mtm180) cc_final: 0.6945 (mtp180) REVERT: B 163 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: B 286 GLN cc_start: 0.7592 (mt0) cc_final: 0.7383 (mm-40) REVERT: B 687 ARG cc_start: 0.7327 (mtm180) cc_final: 0.6945 (mtp180) REVERT: C 286 GLN cc_start: 0.7588 (mt0) cc_final: 0.7385 (mm-40) REVERT: C 352 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7451 (tp30) REVERT: C 687 ARG cc_start: 0.7313 (mtm180) cc_final: 0.6928 (mtp180) REVERT: D 286 GLN cc_start: 0.7577 (mt0) cc_final: 0.7373 (mm-40) REVERT: D 352 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7456 (tp30) REVERT: D 687 ARG cc_start: 0.7318 (mtm180) cc_final: 0.6932 (mtp180) outliers start: 48 outliers final: 22 residues processed: 331 average time/residue: 1.2636 time to fit residues: 475.2441 Evaluate side-chains 309 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 285 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 68 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN A 673 ASN B 263 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN C 263 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.143404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.115103 restraints weight = 21281.317| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.39 r_work: 0.3096 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20328 Z= 0.238 Angle : 0.590 9.118 27516 Z= 0.298 Chirality : 0.042 0.154 3104 Planarity : 0.005 0.044 3384 Dihedral : 10.181 72.759 2876 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.51 % Allowed : 6.87 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2376 helix: 1.49 (0.13), residues: 1476 sheet: 1.56 (0.51), residues: 112 loop : -0.39 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 660 HIS 0.006 0.001 HIS D 165 PHE 0.019 0.002 PHE A 394 TYR 0.029 0.003 TYR B 471 ARG 0.004 0.001 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 1092) hydrogen bonds : angle 4.01181 ( 3144) covalent geometry : bond 0.00567 (20328) covalent geometry : angle 0.58960 (27516) *********************** 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 365 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 2.222 Fit side-chains REVERT: A 108 ASP cc_start: 0.7234 (m-30) cc_final: 0.7019 (m-30) REVERT: A 137 MET cc_start: 0.7248 (tpt) cc_final: 0.6822 (tpp) REVERT: A 163 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: A 473 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8140 (mm-30) REVERT: A 640 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6652 (ttp) REVERT: A 687 ARG cc_start: 0.7197 (mtm180) cc_final: 0.6859 (mtp180) REVERT: B 108 ASP cc_start: 0.7237 (m-30) cc_final: 0.7019 (m-30) REVERT: B 163 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: B 473 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8140 (mm-30) REVERT: B 640 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6632 (ttp) REVERT: B 687 ARG cc_start: 0.7221 (mtm180) cc_final: 0.6865 (mtp180) REVERT: C 108 ASP cc_start: 0.7234 (m-30) cc_final: 0.7017 (m-30) REVERT: C 137 MET cc_start: 0.7279 (tpt) cc_final: 0.6861 (tpp) REVERT: C 473 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8150 (mm-30) REVERT: C 640 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6639 (ttp) REVERT: C 687 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6873 (mtp180) REVERT: D 108 ASP cc_start: 0.7239 (m-30) cc_final: 0.7023 (m-30) REVERT: D 473 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8135 (mm-30) REVERT: D 640 MET cc_start: 0.7132 (OUTLIER) cc_final: 0.6649 (ttp) REVERT: D 687 ARG cc_start: 0.7186 (mtm180) cc_final: 0.6855 (mtp180) outliers start: 53 outliers final: 30 residues processed: 337 average time/residue: 1.3888 time to fit residues: 531.1985 Evaluate side-chains 339 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 303 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLN 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 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 B residue 640 MET 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 260 SER Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 640 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 176 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN D 294 GLN D 414 GLN D 487 GLN D 639 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.143844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115294 restraints weight = 21562.863| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.43 r_work: 0.3099 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20328 Z= 0.171 Angle : 0.523 8.688 27516 Z= 0.266 Chirality : 0.039 0.134 3104 Planarity : 0.004 0.038 3384 Dihedral : 9.777 71.561 2876 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.23 % Allowed : 8.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.17), residues: 2376 helix: 1.72 (0.14), residues: 1472 sheet: 1.59 (0.52), residues: 112 loop : -0.32 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 660 HIS 0.004 0.001 HIS D 165 PHE 0.015 0.001 PHE C 394 TYR 0.020 0.002 TYR D 471 ARG 0.003 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03911 ( 1092) hydrogen bonds : angle 3.88140 ( 3144) covalent geometry : bond 0.00404 (20328) covalent geometry : angle 0.52311 (27516) *********************** 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 353 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 2.463 Fit side-chains REVERT: A 108 ASP cc_start: 0.7214 (m-30) cc_final: 0.7012 (m-30) REVERT: A 137 MET cc_start: 0.7271 (tpt) cc_final: 0.6871 (tpp) REVERT: A 163 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: A 473 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 640 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6637 (ttp) REVERT: A 687 ARG cc_start: 0.7222 (mtm180) cc_final: 0.6830 (mtp-110) REVERT: B 108 ASP cc_start: 0.7209 (m-30) cc_final: 0.7005 (m-30) REVERT: B 163 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7622 (tt0) REVERT: B 473 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8118 (mm-30) REVERT: B 640 MET cc_start: 0.7149 (OUTLIER) cc_final: 0.6631 (ttp) REVERT: B 687 ARG cc_start: 0.7237 (mtm180) cc_final: 0.6884 (mtp180) REVERT: C 108 ASP cc_start: 0.7205 (m-30) cc_final: 0.7001 (m-30) REVERT: C 137 MET cc_start: 0.7268 (tpt) cc_final: 0.6873 (tpp) REVERT: C 473 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8121 (mm-30) REVERT: C 640 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6597 (ttp) REVERT: C 687 ARG cc_start: 0.7229 (mtm180) cc_final: 0.6881 (mtp180) REVERT: D 108 ASP cc_start: 0.7199 (m-30) cc_final: 0.6996 (m-30) REVERT: D 407 PHE cc_start: 0.8609 (t80) cc_final: 0.8355 (t80) REVERT: D 473 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8113 (mm-30) REVERT: D 640 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6631 (ttp) REVERT: D 687 ARG cc_start: 0.7194 (mtm180) cc_final: 0.6803 (mtp-110) outliers start: 47 outliers final: 27 residues processed: 329 average time/residue: 1.2871 time to fit residues: 480.4056 Evaluate side-chains 322 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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 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 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 640 MET Chi-restraints excluded: chain C residue 136 ILE 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 594 LEU 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 436 LEU Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 640 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 125 optimal weight: 0.0030 chunk 84 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.142624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.114031 restraints weight = 21498.787| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.42 r_work: 0.3086 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20328 Z= 0.222 Angle : 0.571 9.502 27516 Z= 0.289 Chirality : 0.041 0.145 3104 Planarity : 0.005 0.045 3384 Dihedral : 10.082 70.691 2876 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.60 % Allowed : 10.13 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.17), residues: 2376 helix: 1.58 (0.14), residues: 1472 sheet: 1.50 (0.52), residues: 112 loop : -0.32 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 660 HIS 0.005 0.001 HIS B 165 PHE 0.019 0.002 PHE D 394 TYR 0.025 0.002 TYR B 471 ARG 0.003 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 1092) hydrogen bonds : angle 3.99419 ( 3144) covalent geometry : bond 0.00528 (20328) covalent geometry : angle 0.57126 (27516) *********************** 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 363 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 308 time to evaluate : 2.141 Fit side-chains REVERT: A 108 ASP cc_start: 0.7319 (m-30) cc_final: 0.7102 (m-30) REVERT: A 163 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: A 407 PHE cc_start: 0.8597 (t80) cc_final: 0.8349 (t80) REVERT: A 473 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8126 (mm-30) REVERT: A 640 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6638 (ttp) REVERT: A 660 TRP cc_start: 0.8828 (t60) cc_final: 0.8619 (t60) REVERT: A 687 ARG cc_start: 0.7172 (mtm180) cc_final: 0.6832 (mtp180) REVERT: B 108 ASP cc_start: 0.7311 (m-30) cc_final: 0.7093 (m-30) REVERT: B 163 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: B 407 PHE cc_start: 0.8608 (t80) cc_final: 0.8344 (t80) REVERT: B 473 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 640 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6665 (ttp) REVERT: B 687 ARG cc_start: 0.7191 (mtm180) cc_final: 0.6836 (mtp180) REVERT: C 108 ASP cc_start: 0.7322 (m-30) cc_final: 0.7105 (m-30) REVERT: C 407 PHE cc_start: 0.8595 (t80) cc_final: 0.8348 (t80) REVERT: C 473 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8118 (mm-30) REVERT: C 640 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6654 (ttp) REVERT: C 687 ARG cc_start: 0.7209 (mtm180) cc_final: 0.6839 (mtp180) REVERT: D 108 ASP cc_start: 0.7318 (m-30) cc_final: 0.7102 (m-30) REVERT: D 407 PHE cc_start: 0.8619 (t80) cc_final: 0.8380 (t80) REVERT: D 473 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8117 (mm-30) REVERT: D 640 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6655 (ttp) REVERT: D 660 TRP cc_start: 0.8817 (t60) cc_final: 0.8588 (t60) REVERT: D 687 ARG cc_start: 0.7186 (mtm180) cc_final: 0.6827 (mtp180) outliers start: 55 outliers final: 43 residues processed: 342 average time/residue: 1.2847 time to fit residues: 496.5945 Evaluate side-chains 353 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 136 ILE Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 260 SER 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 594 LEU Chi-restraints excluded: chain A residue 595 ASP 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 260 SER 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 136 ILE 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 594 LEU 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 136 ILE 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 436 LEU 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 640 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 44 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 214 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN C 639 ASN D 294 GLN D 414 GLN D 487 GLN D 639 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.145790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.117347 restraints weight = 21596.538| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.43 r_work: 0.3130 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20328 Z= 0.104 Angle : 0.468 9.127 27516 Z= 0.237 Chirality : 0.036 0.117 3104 Planarity : 0.004 0.035 3384 Dihedral : 8.994 70.259 2876 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.80 % Allowed : 11.08 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2376 helix: 2.01 (0.14), residues: 1472 sheet: 1.58 (0.53), residues: 112 loop : -0.19 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 660 HIS 0.003 0.001 HIS C 165 PHE 0.013 0.001 PHE C 540 TYR 0.012 0.001 TYR D 403 ARG 0.003 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 1092) hydrogen bonds : angle 3.70207 ( 3144) covalent geometry : bond 0.00231 (20328) covalent geometry : angle 0.46818 (27516) *********************** 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 361 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 323 time to evaluate : 4.872 Fit side-chains REVERT: A 163 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7579 (tt0) REVERT: A 473 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8007 (mm-30) REVERT: A 660 TRP cc_start: 0.8724 (t60) cc_final: 0.8522 (t60) REVERT: A 687 ARG cc_start: 0.7239 (mtm180) cc_final: 0.6835 (mtp180) REVERT: B 137 MET cc_start: 0.7228 (tpt) cc_final: 0.6843 (tpp) REVERT: B 163 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: B 473 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8030 (mm-30) REVERT: B 531 LYS cc_start: 0.6823 (ttmt) cc_final: 0.5420 (tptm) REVERT: B 687 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6841 (mtp180) REVERT: C 473 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8009 (mm-30) REVERT: C 687 ARG cc_start: 0.7242 (mtm180) cc_final: 0.6831 (mtp180) REVERT: D 407 PHE cc_start: 0.8593 (t80) cc_final: 0.8319 (t80) REVERT: D 473 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8000 (mm-30) REVERT: D 487 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8057 (mm110) REVERT: D 531 LYS cc_start: 0.6808 (ttmt) cc_final: 0.5410 (tptm) REVERT: D 687 ARG cc_start: 0.7229 (mtm180) cc_final: 0.6825 (mtp180) outliers start: 38 outliers final: 23 residues processed: 353 average time/residue: 1.7431 time to fit residues: 701.0114 Evaluate side-chains 326 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 300 time to evaluate : 2.188 ------------------------------------------------------------------------------- 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 433 MET Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 522 THR 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 433 MET Chi-restraints excluded: chain B residue 436 LEU 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 433 MET Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 487 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 179 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 180 optimal weight: 0.0370 chunk 230 optimal weight: 5.9990 chunk 74 optimal weight: 0.0870 chunk 19 optimal weight: 0.3980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 639 ASN B 479 GLN C 479 GLN D 294 GLN D 479 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.148359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.120338 restraints weight = 21390.486| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.40 r_work: 0.3163 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20328 Z= 0.088 Angle : 0.452 10.030 27516 Z= 0.225 Chirality : 0.035 0.207 3104 Planarity : 0.003 0.035 3384 Dihedral : 8.386 68.783 2876 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.23 % Allowed : 12.22 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.18), residues: 2376 helix: 2.27 (0.14), residues: 1468 sheet: 1.62 (0.53), residues: 112 loop : -0.08 (0.23), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 660 HIS 0.003 0.001 HIS C 165 PHE 0.012 0.001 PHE B 540 TYR 0.010 0.001 TYR C 403 ARG 0.003 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 1092) hydrogen bonds : angle 3.50960 ( 3144) covalent geometry : bond 0.00189 (20328) covalent geometry : angle 0.45228 (27516) *********************** 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 330 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 3.145 Fit side-chains REVERT: A 163 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7557 (tt0) REVERT: A 352 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7360 (tp30) REVERT: A 473 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7927 (mm-30) REVERT: A 531 LYS cc_start: 0.6654 (ttmt) cc_final: 0.5297 (tptm) REVERT: A 640 MET cc_start: 0.7219 (ttp) cc_final: 0.6962 (tmm) REVERT: A 660 TRP cc_start: 0.8698 (t60) cc_final: 0.8456 (t60) REVERT: A 671 MET cc_start: 0.8876 (mtm) cc_final: 0.8613 (mtm) REVERT: A 687 ARG cc_start: 0.7261 (mtm180) cc_final: 0.6848 (mtp180) REVERT: B 137 MET cc_start: 0.7200 (tpt) cc_final: 0.6841 (tpp) REVERT: B 163 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7574 (tt0) REVERT: B 473 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7909 (mm-30) REVERT: B 531 LYS cc_start: 0.6660 (ttmt) cc_final: 0.5313 (tptm) REVERT: B 640 MET cc_start: 0.7185 (ttp) cc_final: 0.6931 (tmm) REVERT: B 671 MET cc_start: 0.8868 (mtm) cc_final: 0.8618 (mtm) REVERT: B 687 ARG cc_start: 0.7280 (mtm180) cc_final: 0.6852 (mtp180) REVERT: C 182 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8066 (mp) REVERT: C 352 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7397 (tp30) REVERT: C 473 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7921 (mm-30) REVERT: C 531 LYS cc_start: 0.6699 (ttmt) cc_final: 0.5346 (tptm) REVERT: C 640 MET cc_start: 0.7184 (ttp) cc_final: 0.6926 (tmm) REVERT: C 671 MET cc_start: 0.8861 (mtm) cc_final: 0.8609 (mtm) REVERT: C 687 ARG cc_start: 0.7278 (mtm180) cc_final: 0.6849 (mtp180) REVERT: D 182 LEU cc_start: 0.8341 (tt) cc_final: 0.8035 (mp) REVERT: D 473 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7896 (mm-30) REVERT: D 531 LYS cc_start: 0.6685 (ttmt) cc_final: 0.5335 (tptm) REVERT: D 640 MET cc_start: 0.7224 (ttp) cc_final: 0.6975 (tmm) REVERT: D 671 MET cc_start: 0.8859 (mtm) cc_final: 0.8607 (mtm) REVERT: D 687 ARG cc_start: 0.7268 (mtm180) cc_final: 0.6851 (mtp180) outliers start: 26 outliers final: 17 residues processed: 320 average time/residue: 2.0111 time to fit residues: 724.0575 Evaluate side-chains 307 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 287 time to evaluate : 2.673 ------------------------------------------------------------------------------- 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 433 MET Chi-restraints excluded: chain A residue 488 VAL 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 433 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain D residue 88 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 144 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 230 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 175 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 chunk 77 optimal weight: 0.0270 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 GLN C 639 ASN D 479 GLN D 487 GLN D 639 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.146293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118019 restraints weight = 21571.020| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.40 r_work: 0.3133 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2065 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= 0.121 Angle : 0.493 10.404 27516 Z= 0.243 Chirality : 0.037 0.120 3104 Planarity : 0.004 0.035 3384 Dihedral : 8.504 68.002 2876 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.33 % Allowed : 12.74 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.18), residues: 2376 helix: 2.19 (0.14), residues: 1472 sheet: 1.59 (0.52), residues: 112 loop : -0.06 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 660 HIS 0.003 0.001 HIS A 251 PHE 0.012 0.001 PHE C 394 TYR 0.015 0.001 TYR D 471 ARG 0.004 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 1092) hydrogen bonds : angle 3.60376 ( 3144) covalent geometry : bond 0.00279 (20328) covalent geometry : angle 0.49251 (27516) *********************** 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 315 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 287 time to evaluate : 4.616 Fit side-chains REVERT: A 163 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: A 266 LEU cc_start: 0.8267 (tt) cc_final: 0.8044 (tp) REVERT: A 473 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8038 (mm-30) REVERT: A 490 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6717 (ttp-110) REVERT: A 531 LYS cc_start: 0.6727 (ttmt) cc_final: 0.5359 (tptm) REVERT: A 640 MET cc_start: 0.7222 (ttp) cc_final: 0.6962 (tmm) REVERT: A 660 TRP cc_start: 0.8730 (t60) cc_final: 0.8516 (t60) REVERT: A 687 ARG cc_start: 0.7180 (mtm180) cc_final: 0.6827 (mtp180) REVERT: B 163 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: B 266 LEU cc_start: 0.8267 (tt) cc_final: 0.8042 (tp) REVERT: B 473 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8026 (mm-30) REVERT: B 490 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6727 (ttp-110) REVERT: B 531 LYS cc_start: 0.6749 (ttmt) cc_final: 0.5389 (tptm) REVERT: B 640 MET cc_start: 0.7191 (ttp) cc_final: 0.6930 (tmm) REVERT: B 687 ARG cc_start: 0.7226 (mtm180) cc_final: 0.6853 (mtp180) REVERT: C 266 LEU cc_start: 0.8269 (tt) cc_final: 0.8041 (tp) REVERT: C 473 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 531 LYS cc_start: 0.6760 (ttmt) cc_final: 0.5396 (tptm) REVERT: C 640 MET cc_start: 0.7169 (ttp) cc_final: 0.6907 (tmm) REVERT: C 687 ARG cc_start: 0.7205 (mtm180) cc_final: 0.6838 (mtp180) REVERT: D 266 LEU cc_start: 0.8260 (tt) cc_final: 0.8033 (tp) REVERT: D 473 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8031 (mm-30) REVERT: D 487 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.8001 (mm110) REVERT: D 531 LYS cc_start: 0.6743 (ttmt) cc_final: 0.5380 (tptm) REVERT: D 640 MET cc_start: 0.7207 (ttp) cc_final: 0.6950 (tmm) REVERT: D 687 ARG cc_start: 0.7193 (mtm180) cc_final: 0.6832 (mtp180) outliers start: 28 outliers final: 23 residues processed: 303 average time/residue: 1.9551 time to fit residues: 670.4191 Evaluate side-chains 302 residues out of total 2172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 2.391 ------------------------------------------------------------------------------- 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 433 MET 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 594 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 670 GLU Chi-restraints excluded: chain C residue 88 VAL 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 C residue 594 LEU Chi-restraints excluded: chain C residue 670 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain D residue 487 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.472 > 50: distance: 17 - 40: 9.691 distance: 21 - 52: 24.665 distance: 29 - 60: 22.595 distance: 35 - 40: 10.295 distance: 36 - 71: 25.311 distance: 40 - 41: 5.818 distance: 41 - 42: 12.056 distance: 41 - 44: 7.272 distance: 42 - 43: 34.159 distance: 42 - 52: 28.439 distance: 43 - 76: 21.106 distance: 44 - 45: 8.388 distance: 45 - 46: 8.400 distance: 45 - 47: 6.547 distance: 46 - 48: 8.236 distance: 47 - 49: 6.142 distance: 48 - 50: 5.088 distance: 49 - 50: 4.473 distance: 50 - 51: 4.971 distance: 52 - 53: 14.353 distance: 53 - 54: 39.768 distance: 53 - 56: 23.753 distance: 54 - 55: 42.578 distance: 54 - 60: 32.231 distance: 55 - 84: 8.406 distance: 56 - 57: 4.128 distance: 57 - 58: 12.251 distance: 57 - 59: 7.125 distance: 60 - 61: 21.089 distance: 61 - 62: 42.693 distance: 61 - 64: 26.483 distance: 62 - 63: 15.973 distance: 62 - 71: 40.172 distance: 64 - 65: 32.623 distance: 65 - 66: 14.623 distance: 66 - 67: 12.824 distance: 67 - 68: 4.120 distance: 68 - 69: 8.733 distance: 68 - 70: 9.898 distance: 71 - 72: 37.668 distance: 72 - 73: 37.694 distance: 72 - 75: 10.803 distance: 73 - 74: 21.743 distance: 73 - 76: 47.482 distance: 76 - 77: 33.757 distance: 77 - 78: 5.010 distance: 77 - 80: 15.627 distance: 78 - 79: 11.630 distance: 78 - 84: 45.711 distance: 80 - 81: 27.903 distance: 81 - 82: 34.320 distance: 81 - 83: 25.670 distance: 84 - 85: 10.121 distance: 85 - 86: 30.010 distance: 85 - 88: 21.282 distance: 86 - 87: 14.800 distance: 86 - 90: 38.829 distance: 88 - 89: 36.844 distance: 90 - 91: 34.107 distance: 91 - 92: 29.463 distance: 91 - 94: 20.567 distance: 92 - 93: 29.907 distance: 92 - 99: 30.257 distance: 94 - 95: 13.644 distance: 95 - 96: 17.820 distance: 96 - 97: 28.161 distance: 97 - 98: 22.064 distance: 99 - 100: 24.413 distance: 100 - 101: 45.255 distance: 100 - 103: 10.690 distance: 101 - 102: 20.035 distance: 101 - 111: 40.160 distance: 103 - 104: 30.503 distance: 104 - 105: 23.091 distance: 104 - 106: 18.738 distance: 105 - 107: 4.245 distance: 107 - 109: 7.383 distance: 108 - 109: 6.996 distance: 111 - 112: 37.553 distance: 112 - 113: 49.631 distance: 112 - 115: 17.502 distance: 113 - 114: 8.365 distance: 113 - 119: 23.567 distance: 115 - 116: 3.294 distance: 116 - 117: 30.601 distance: 116 - 118: 48.055 distance: 119 - 120: 16.809 distance: 120 - 121: 20.483 distance: 120 - 123: 43.569 distance: 121 - 122: 9.972 distance: 121 - 126: 32.432 distance: 123 - 124: 18.315 distance: 123 - 125: 13.898