Starting phenix.real_space_refine on Sun Aug 24 21:12:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sur_40776/08_2025/8sur_40776_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sur_40776/08_2025/8sur_40776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sur_40776/08_2025/8sur_40776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sur_40776/08_2025/8sur_40776.map" model { file = "/net/cci-nas-00/data/ceres_data/8sur_40776/08_2025/8sur_40776_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sur_40776/08_2025/8sur_40776_trim.cif" } resolution = 3.1 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= -0.015 sd= 0.827 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 S 71 5.16 5 C 7697 2.51 5 N 1866 2.21 5 O 2065 1.98 5 H 11381 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23085 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 691, 11021 Classifications: {'peptide': 691} Link IDs: {'PTRANS': 31, 'TRANS': 659} Chain breaks: 6 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 11919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 11919 Classifications: {'peptide': 726} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 693} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 72 Unusual residues: {' CA': 2, 'NAG': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 3, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.34, per 1000 atoms: 0.14 Number of scatterers: 23085 At special positions: 0 Unit cell: (134.24, 90.612, 125.011, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 71 16.00 O 2065 8.00 N 1866 7.00 C 7697 6.00 H 11381 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=1.93 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.04 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 901 " - " ASN A 362 " " NAG A 902 " - " ASN A 785 " " NAG A 904 " - " ASN A 778 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 384.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 64.6% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.931A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.709A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.946A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.827A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 Processing helix chain 'A' and resid 504 through 540 removed outlier: 3.834A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 573 removed outlier: 3.666A pdb=" N TYR A 547 " --> pdb=" O THR A 543 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 626 removed outlier: 3.537A pdb=" N LEU A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 638 removed outlier: 3.851A pdb=" N VAL A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 656 Processing helix chain 'A' and resid 662 through 681 removed outlier: 3.796A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.058A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 4.122A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 857 Processing helix chain 'A' and resid 863 through 871 Processing helix chain 'B' and resid 87 through 109 removed outlier: 4.032A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.959A pdb=" N ARG B 191 " --> pdb=" O GLU B 188 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.641A pdb=" N PHE B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 204' Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.885A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 292 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.561A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.832A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 488 Processing helix chain 'B' and resid 504 through 539 removed outlier: 4.157A pdb=" N SER B 510 " --> pdb=" O GLN B 506 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 539 " --> pdb=" O ILE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 3.582A pdb=" N LEU B 557 " --> pdb=" O MET B 553 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 563 " --> pdb=" O GLN B 559 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE B 570 " --> pdb=" O SER B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 654 removed outlier: 4.096A pdb=" N GLN B 652 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.763A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.090A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 4.040A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 868 removed outlier: 3.593A pdb=" N ILE B 868 " --> pdb=" O THR B 864 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 116 removed outlier: 3.744A pdb=" N PHE A 246 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 76 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 782 through 785 Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.904A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 221 through 225 removed outlier: 4.436A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 230 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 347 through 348 removed outlier: 3.996A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 784 through 785 685 hydrogen bonds defined for protein. 2016 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: 3.94 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10867 1.04 - 1.23: 948 1.23 - 1.43: 4824 1.43 - 1.63: 6655 1.63 - 1.83: 112 Bond restraints: 23406 Sorted by residual: bond pdb=" C TRP A 359 " pdb=" O TRP A 359 " ideal model delta sigma weight residual 1.236 1.052 0.184 1.19e-02 7.06e+03 2.38e+02 bond pdb=" C CYS A 349 " pdb=" O CYS A 349 " ideal model delta sigma weight residual 1.236 1.090 0.145 1.00e-02 1.00e+04 2.11e+02 bond pdb=" C ARG A 360 " pdb=" O ARG A 360 " ideal model delta sigma weight residual 1.233 1.052 0.181 1.57e-02 4.06e+03 1.33e+02 bond pdb=" C GLU B 405 " pdb=" O GLU B 405 " ideal model delta sigma weight residual 1.237 1.104 0.132 1.17e-02 7.31e+03 1.28e+02 bond pdb=" CA GLN B 506 " pdb=" C GLN B 506 " ideal model delta sigma weight residual 1.523 1.387 0.136 1.41e-02 5.03e+03 9.31e+01 ... (remaining 23401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.11: 42084 7.11 - 14.23: 35 14.23 - 21.34: 1 21.34 - 28.45: 4 28.45 - 35.56: 21 Bond angle restraints: 42145 Sorted by residual: angle pdb=" C CYS A 356 " pdb=" CA CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sigma weight residual 111.00 123.03 -12.03 8.70e-01 1.32e+00 1.91e+02 angle pdb=" C GLU B 405 " pdb=" CA GLU B 405 " pdb=" CB GLU B 405 " ideal model delta sigma weight residual 110.79 88.84 21.95 1.66e+00 3.63e-01 1.75e+02 angle pdb=" C SER A 278 " pdb=" CA SER A 278 " pdb=" HA SER A 278 " ideal model delta sigma weight residual 109.00 73.44 35.56 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.50 35.50 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CB GLN A 94 " pdb=" CA GLN A 94 " pdb=" HA GLN A 94 " ideal model delta sigma weight residual 109.00 73.60 35.40 3.00e+00 1.11e-01 1.39e+02 ... (remaining 42140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 10618 25.61 - 51.22: 535 51.22 - 76.83: 101 76.83 - 102.44: 12 102.44 - 128.05: 3 Dihedral angle restraints: 11269 sinusoidal: 5968 harmonic: 5301 Sorted by residual: dihedral pdb=" C CYS A 356 " pdb=" N CYS A 356 " pdb=" CA CYS A 356 " pdb=" CB CYS A 356 " ideal model delta harmonic sigma weight residual -122.60 -163.73 41.13 0 2.50e+00 1.60e-01 2.71e+02 dihedral pdb=" N CYS A 356 " pdb=" C CYS A 356 " pdb=" CA CYS A 356 " pdb=" CB CYS A 356 " ideal model delta harmonic sigma weight residual 122.80 163.01 -40.21 0 2.50e+00 1.60e-01 2.59e+02 dihedral pdb=" C GLU B 405 " pdb=" N GLU B 405 " pdb=" CA GLU B 405 " pdb=" CB GLU B 405 " ideal model delta harmonic sigma weight residual -122.60 -100.11 -22.49 0 2.50e+00 1.60e-01 8.09e+01 ... (remaining 11266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 1794 0.345 - 0.691: 6 0.691 - 1.036: 0 1.036 - 1.382: 1 1.382 - 1.727: 2 Chirality restraints: 1803 Sorted by residual: chirality pdb=" CA CYS A 356 " pdb=" N CYS A 356 " pdb=" C CYS A 356 " pdb=" CB CYS A 356 " both_signs ideal model delta sigma weight residual False 2.51 0.78 1.73 2.00e-01 2.50e+01 7.46e+01 chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -0.98 -1.55 2.00e-01 2.50e+01 6.00e+01 chirality pdb=" C3 NAG D 2 " pdb=" C2 NAG D 2 " pdb=" C4 NAG D 2 " pdb=" O3 NAG D 2 " both_signs ideal model delta sigma weight residual False 2.45 1.11 1.34 2.00e-01 2.50e+01 4.50e+01 ... (remaining 1800 not shown) Planarity restraints: 3361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 401 " -0.061 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C GLN B 401 " 0.194 2.00e-02 2.50e+03 pdb=" O GLN B 401 " -0.067 2.00e-02 2.50e+03 pdb=" N ALA B 402 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 359 " 0.036 2.00e-02 2.50e+03 7.41e-02 5.49e+01 pdb=" C TRP A 359 " -0.128 2.00e-02 2.50e+03 pdb=" O TRP A 359 " 0.046 2.00e-02 2.50e+03 pdb=" N ARG A 360 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 359 " 0.069 2.00e-02 2.50e+03 3.46e-02 4.78e+01 pdb=" CG TRP A 359 " -0.115 2.00e-02 2.50e+03 pdb=" CD1 TRP A 359 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 359 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP A 359 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 359 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 359 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 359 " 0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 359 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 359 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP A 359 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP A 359 " 0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 359 " 0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 359 " -0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 359 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 359 " 0.001 2.00e-02 2.50e+03 ... (remaining 3358 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.92: 66 1.92 - 2.59: 23702 2.59 - 3.26: 70082 3.26 - 3.93: 83997 3.93 - 4.60: 131261 Nonbonded interactions: 309108 Sorted by model distance: nonbonded pdb=" OD1 ASP B 859 " pdb="CA CA B 904 " model vdw 1.256 2.390 nonbonded pdb=" OE2 GLU B 624 " pdb="CA CA B 902 " model vdw 1.365 2.390 nonbonded pdb=" H SER A 278 " pdb=" HA SER A 278 " model vdw 1.595 1.816 nonbonded pdb=" HA PHE B 215 " pdb=" HB3 PHE B 215 " model vdw 1.598 1.952 nonbonded pdb=" O GLY A 344 " pdb=" HE ARG A 360 " model vdw 1.605 2.450 ... (remaining 309103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 59 through 868 or resid 904 or resid 906 through 907)) selection = (chain 'B' and (resid 59 through 82 or resid 91 through 93 or (resid 94 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 100 or (resid 101 through 107 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 108 throug \ h 115 or (resid 116 through 126 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 127 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 130 \ through 134 or (resid 135 through 137 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 138 through 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 142 or (resid 143 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 144 through 147 or resid 185 through 222 or resid 232 \ through 235 or (resid 236 through 239 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 240 or (resid 241 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 242 throu \ gh 409 or resid 457 through 487 or resid 503 through 589 or (resid 590 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 59 \ 1 through 638 or resid 645 through 660 or (resid 661 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 662 through 777 or ( \ resid 778 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 779 t \ hrough 784 or (resid 785 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) \ or resid 786 through 901 or resid 903 through 904)) } ncs_group { reference = 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.007 0.184 12040 Z= 0.491 Angle : 0.861 21.948 16355 Z= 0.555 Chirality : 0.082 1.727 1803 Planarity : 0.006 0.112 2015 Dihedral : 14.515 128.045 4477 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.94 % Favored : 95.70 % Rotamer: Outliers : 0.65 % Allowed : 0.32 % Favored : 99.03 % Cbeta Deviations : 0.59 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.22), residues: 1395 helix: 2.00 (0.17), residues: 833 sheet: -0.47 (0.66), residues: 63 loop : -1.49 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 713 TYR 0.019 0.001 TYR B 406 PHE 0.016 0.001 PHE B 677 TRP 0.114 0.002 TRP A 359 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00686 (12025) covalent geometry : angle 0.85331 (16320) SS BOND : bond 0.03275 ( 10) SS BOND : angle 3.35583 ( 20) hydrogen bonds : bond 0.14368 ( 685) hydrogen bonds : angle 5.82464 ( 2016) link_BETA1-4 : bond 0.00350 ( 2) link_BETA1-4 : angle 1.21274 ( 6) link_NAG-ASN : bond 0.00254 ( 3) link_NAG-ASN : angle 1.35203 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 221 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 271 ARG cc_start: 0.7365 (mmt90) cc_final: 0.7144 (mmp-170) REVERT: B 678 VAL cc_start: 0.8695 (p) cc_final: 0.8397 (m) REVERT: B 855 TYR cc_start: 0.7856 (t80) cc_final: 0.7639 (t80) outliers start: 8 outliers final: 2 residues processed: 227 average time/residue: 0.1811 time to fit residues: 60.3430 Evaluate side-chains 173 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 624 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 695 ASN B 562 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.211507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.162975 restraints weight = 40517.781| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.51 r_work: 0.3856 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12040 Z= 0.132 Angle : 0.556 7.382 16355 Z= 0.299 Chirality : 0.046 0.419 1803 Planarity : 0.005 0.069 2015 Dihedral : 8.125 105.939 1774 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.87 % Favored : 95.84 % Rotamer: Outliers : 0.41 % Allowed : 4.71 % Favored : 94.89 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.22), residues: 1395 helix: 2.19 (0.17), residues: 839 sheet: -0.67 (0.69), residues: 55 loop : -1.47 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 211 TYR 0.015 0.001 TYR B 77 PHE 0.014 0.001 PHE B 556 TRP 0.018 0.001 TRP A 359 HIS 0.006 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00276 (12025) covalent geometry : angle 0.55253 (16320) SS BOND : bond 0.00273 ( 10) SS BOND : angle 1.27272 ( 20) hydrogen bonds : bond 0.05054 ( 685) hydrogen bonds : angle 4.68975 ( 2016) link_BETA1-4 : bond 0.00756 ( 2) link_BETA1-4 : angle 1.60809 ( 6) link_NAG-ASN : bond 0.00305 ( 3) link_NAG-ASN : angle 1.52353 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 185 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8117 (m-30) cc_final: 0.7755 (m-30) REVERT: A 308 GLN cc_start: 0.7137 (tt0) cc_final: 0.6732 (mt0) REVERT: A 718 LYS cc_start: 0.8089 (mptt) cc_final: 0.7392 (mttm) REVERT: B 678 VAL cc_start: 0.8957 (p) cc_final: 0.8746 (t) REVERT: B 773 MET cc_start: 0.9297 (tpt) cc_final: 0.8817 (tpt) REVERT: B 855 TYR cc_start: 0.8198 (t80) cc_final: 0.7933 (t80) outliers start: 5 outliers final: 4 residues processed: 187 average time/residue: 0.1808 time to fit residues: 50.5583 Evaluate side-chains 169 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 165 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 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 283 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.203420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.160183 restraints weight = 40298.851| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.54 r_work: 0.3730 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12040 Z= 0.171 Angle : 0.556 9.201 16355 Z= 0.298 Chirality : 0.046 0.443 1803 Planarity : 0.005 0.050 2015 Dihedral : 6.242 56.595 1770 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 0.81 % Allowed : 6.66 % Favored : 92.53 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.22), residues: 1395 helix: 2.21 (0.17), residues: 838 sheet: -1.43 (0.57), residues: 75 loop : -1.45 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 354 TYR 0.013 0.001 TYR B 563 PHE 0.021 0.001 PHE B 675 TRP 0.009 0.001 TRP B 359 HIS 0.009 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00384 (12025) covalent geometry : angle 0.55169 (16320) SS BOND : bond 0.00284 ( 10) SS BOND : angle 1.29330 ( 20) hydrogen bonds : bond 0.04891 ( 685) hydrogen bonds : angle 4.47243 ( 2016) link_BETA1-4 : bond 0.00860 ( 2) link_BETA1-4 : angle 2.29144 ( 6) link_NAG-ASN : bond 0.00014 ( 3) link_NAG-ASN : angle 1.88760 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8216 (m-30) cc_final: 0.7821 (m-30) REVERT: A 281 LYS cc_start: 0.8643 (mptt) cc_final: 0.8325 (mptt) REVERT: A 289 ARG cc_start: 0.8133 (ptm-80) cc_final: 0.7444 (mtt-85) REVERT: A 308 GLN cc_start: 0.7274 (tt0) cc_final: 0.6820 (mt0) REVERT: A 555 MET cc_start: 0.8270 (mmt) cc_final: 0.8060 (mmt) REVERT: A 718 LYS cc_start: 0.8161 (mptt) cc_final: 0.7728 (mttt) REVERT: B 192 MET cc_start: 0.5133 (mmm) cc_final: 0.2909 (ttm) REVERT: B 403 GLU cc_start: 0.8024 (tt0) cc_final: 0.7675 (tp30) REVERT: B 773 MET cc_start: 0.9402 (tpt) cc_final: 0.8772 (tpt) REVERT: B 855 TYR cc_start: 0.8354 (t80) cc_final: 0.8016 (t80) outliers start: 10 outliers final: 8 residues processed: 188 average time/residue: 0.1649 time to fit residues: 47.1806 Evaluate side-chains 175 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 694 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 10 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.196787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150192 restraints weight = 40618.913| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.47 r_work: 0.3658 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12040 Z= 0.237 Angle : 0.596 7.634 16355 Z= 0.326 Chirality : 0.048 0.407 1803 Planarity : 0.005 0.050 2015 Dihedral : 6.121 59.787 1770 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.70 % Rotamer: Outliers : 1.22 % Allowed : 8.77 % Favored : 90.02 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.22), residues: 1395 helix: 1.90 (0.17), residues: 825 sheet: -1.60 (0.59), residues: 75 loop : -1.61 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 211 TYR 0.013 0.002 TYR B 798 PHE 0.022 0.002 PHE B 675 TRP 0.010 0.002 TRP B 132 HIS 0.014 0.002 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00535 (12025) covalent geometry : angle 0.59019 (16320) SS BOND : bond 0.00358 ( 10) SS BOND : angle 1.49945 ( 20) hydrogen bonds : bond 0.05433 ( 685) hydrogen bonds : angle 4.55988 ( 2016) link_BETA1-4 : bond 0.00941 ( 2) link_BETA1-4 : angle 2.79518 ( 6) link_NAG-ASN : bond 0.00257 ( 3) link_NAG-ASN : angle 2.07792 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.7249 (ttt-90) cc_final: 0.7000 (ttp80) REVERT: A 289 ARG cc_start: 0.8217 (ptm-80) cc_final: 0.7876 (ptt90) REVERT: A 308 GLN cc_start: 0.7238 (tt0) cc_final: 0.7022 (mt0) REVERT: A 479 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8792 (mm) REVERT: A 534 MET cc_start: 0.6834 (mtp) cc_final: 0.6550 (mtt) REVERT: A 555 MET cc_start: 0.8360 (mmt) cc_final: 0.8094 (mmt) REVERT: A 795 GLU cc_start: 0.4418 (tm-30) cc_final: 0.4052 (tm-30) REVERT: B 192 MET cc_start: 0.5105 (mmm) cc_final: 0.2883 (ttm) REVERT: B 403 GLU cc_start: 0.7945 (tt0) cc_final: 0.7529 (tp30) REVERT: B 773 MET cc_start: 0.9400 (tpt) cc_final: 0.8772 (tpt) REVERT: B 855 TYR cc_start: 0.8401 (t80) cc_final: 0.8094 (t80) outliers start: 15 outliers final: 8 residues processed: 190 average time/residue: 0.1868 time to fit residues: 53.3341 Evaluate side-chains 174 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 165 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 694 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 283 GLN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 674 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.197689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152180 restraints weight = 40334.465| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.32 r_work: 0.3687 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12040 Z= 0.157 Angle : 0.529 8.304 16355 Z= 0.288 Chirality : 0.046 0.439 1803 Planarity : 0.005 0.050 2015 Dihedral : 5.567 57.120 1770 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.91 % Rotamer: Outliers : 1.14 % Allowed : 9.90 % Favored : 88.96 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.22), residues: 1395 helix: 2.06 (0.17), residues: 840 sheet: -1.59 (0.59), residues: 75 loop : -1.47 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.009 0.001 TYR B 798 PHE 0.013 0.001 PHE B 675 TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00355 (12025) covalent geometry : angle 0.52274 (16320) SS BOND : bond 0.00237 ( 10) SS BOND : angle 1.78694 ( 20) hydrogen bonds : bond 0.04916 ( 685) hydrogen bonds : angle 4.38090 ( 2016) link_BETA1-4 : bond 0.00608 ( 2) link_BETA1-4 : angle 2.09323 ( 6) link_NAG-ASN : bond 0.00137 ( 3) link_NAG-ASN : angle 1.88450 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7248 (tt0) cc_final: 0.7034 (mt0) REVERT: A 479 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8796 (mm) REVERT: A 555 MET cc_start: 0.8355 (mmt) cc_final: 0.8047 (mmt) REVERT: B 192 MET cc_start: 0.5156 (mmm) cc_final: 0.2985 (ttm) REVERT: B 403 GLU cc_start: 0.7927 (tt0) cc_final: 0.7612 (tp30) REVERT: B 855 TYR cc_start: 0.8417 (t80) cc_final: 0.8125 (t80) outliers start: 14 outliers final: 10 residues processed: 178 average time/residue: 0.1825 time to fit residues: 48.7335 Evaluate side-chains 173 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 108 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 401 GLN A 674 GLN A 695 ASN B 730 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.198483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148101 restraints weight = 40953.547| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.43 r_work: 0.3680 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12040 Z= 0.163 Angle : 0.525 7.701 16355 Z= 0.286 Chirality : 0.046 0.429 1803 Planarity : 0.005 0.050 2015 Dihedral : 5.230 53.964 1770 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.91 % Rotamer: Outliers : 1.22 % Allowed : 10.71 % Favored : 88.07 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.22), residues: 1395 helix: 2.14 (0.17), residues: 833 sheet: -1.58 (0.61), residues: 75 loop : -1.42 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.010 0.001 TYR B 798 PHE 0.015 0.001 PHE A 253 TRP 0.009 0.001 TRP A 829 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00369 (12025) covalent geometry : angle 0.51922 (16320) SS BOND : bond 0.00295 ( 10) SS BOND : angle 1.48311 ( 20) hydrogen bonds : bond 0.04781 ( 685) hydrogen bonds : angle 4.32159 ( 2016) link_BETA1-4 : bond 0.00589 ( 2) link_BETA1-4 : angle 2.05630 ( 6) link_NAG-ASN : bond 0.00074 ( 3) link_NAG-ASN : angle 1.86495 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8303 (ptm-80) cc_final: 0.8077 (ptt90) REVERT: A 294 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 308 GLN cc_start: 0.7244 (tt0) cc_final: 0.7037 (mt0) REVERT: A 479 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8813 (mm) REVERT: A 555 MET cc_start: 0.8358 (mmt) cc_final: 0.8026 (mmt) REVERT: A 730 GLN cc_start: 0.8081 (mp10) cc_final: 0.7876 (mm-40) REVERT: A 795 GLU cc_start: 0.4470 (tm-30) cc_final: 0.4120 (tm-30) REVERT: B 192 MET cc_start: 0.5297 (mmm) cc_final: 0.3132 (ttm) REVERT: B 272 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: B 403 GLU cc_start: 0.7863 (tt0) cc_final: 0.7589 (tp30) REVERT: B 855 TYR cc_start: 0.8400 (t80) cc_final: 0.8089 (t80) outliers start: 15 outliers final: 12 residues processed: 179 average time/residue: 0.1766 time to fit residues: 48.1097 Evaluate side-chains 182 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 118 optimal weight: 8.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN A 674 GLN A 695 ASN B 730 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.196992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.150546 restraints weight = 40643.072| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.39 r_work: 0.3674 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12040 Z= 0.156 Angle : 0.517 8.073 16355 Z= 0.282 Chirality : 0.046 0.443 1803 Planarity : 0.005 0.050 2015 Dihedral : 5.028 52.245 1770 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 1.79 % Allowed : 10.23 % Favored : 87.99 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.22), residues: 1395 helix: 2.18 (0.17), residues: 833 sheet: -1.59 (0.60), residues: 75 loop : -1.41 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.010 0.001 TYR B 798 PHE 0.013 0.001 PHE A 253 TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00352 (12025) covalent geometry : angle 0.51287 (16320) SS BOND : bond 0.00265 ( 10) SS BOND : angle 1.24128 ( 20) hydrogen bonds : bond 0.04707 ( 685) hydrogen bonds : angle 4.27814 ( 2016) link_BETA1-4 : bond 0.00488 ( 2) link_BETA1-4 : angle 1.89474 ( 6) link_NAG-ASN : bond 0.00129 ( 3) link_NAG-ASN : angle 1.72859 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8225 (ptm-80) cc_final: 0.7913 (ptt90) REVERT: A 308 GLN cc_start: 0.7248 (tt0) cc_final: 0.7043 (mt0) REVERT: A 479 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8819 (mm) REVERT: A 555 MET cc_start: 0.8357 (mmt) cc_final: 0.8011 (mmt) REVERT: A 703 ASP cc_start: 0.8408 (m-30) cc_final: 0.8186 (m-30) REVERT: A 795 GLU cc_start: 0.4465 (tm-30) cc_final: 0.4118 (tm-30) REVERT: B 192 MET cc_start: 0.5307 (mmm) cc_final: 0.3184 (ttm) REVERT: B 272 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: B 403 GLU cc_start: 0.7865 (tt0) cc_final: 0.7604 (tp30) REVERT: B 653 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8788 (m-30) REVERT: B 855 TYR cc_start: 0.8398 (t80) cc_final: 0.8124 (t80) outliers start: 22 outliers final: 16 residues processed: 180 average time/residue: 0.1733 time to fit residues: 46.9561 Evaluate side-chains 184 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 62 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 15 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.198825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152540 restraints weight = 40560.765| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 2.46 r_work: 0.3689 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12040 Z= 0.116 Angle : 0.494 7.629 16355 Z= 0.266 Chirality : 0.045 0.434 1803 Planarity : 0.004 0.050 2015 Dihedral : 4.794 53.911 1770 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.77 % Rotamer: Outliers : 1.46 % Allowed : 10.88 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.23), residues: 1395 helix: 2.32 (0.17), residues: 827 sheet: -1.44 (0.59), residues: 77 loop : -1.35 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.009 0.001 TYR B 798 PHE 0.014 0.001 PHE B 556 TRP 0.010 0.001 TRP B 397 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00251 (12025) covalent geometry : angle 0.48969 (16320) SS BOND : bond 0.00233 ( 10) SS BOND : angle 1.15060 ( 20) hydrogen bonds : bond 0.04371 ( 685) hydrogen bonds : angle 4.18066 ( 2016) link_BETA1-4 : bond 0.00548 ( 2) link_BETA1-4 : angle 1.69640 ( 6) link_NAG-ASN : bond 0.00127 ( 3) link_NAG-ASN : angle 1.70633 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9076 (mm) cc_final: 0.8825 (mm) REVERT: A 534 MET cc_start: 0.6400 (mtp) cc_final: 0.6091 (mtm) REVERT: A 555 MET cc_start: 0.8349 (mmt) cc_final: 0.7986 (mmt) REVERT: A 703 ASP cc_start: 0.8367 (m-30) cc_final: 0.8134 (m-30) REVERT: A 795 GLU cc_start: 0.4432 (tm-30) cc_final: 0.4090 (tm-30) REVERT: B 192 MET cc_start: 0.5315 (mmm) cc_final: 0.3284 (ttm) REVERT: B 279 ILE cc_start: 0.9049 (tp) cc_final: 0.8818 (tp) REVERT: B 403 GLU cc_start: 0.7846 (tt0) cc_final: 0.7613 (tp30) REVERT: B 653 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8764 (m-30) REVERT: B 855 TYR cc_start: 0.8368 (t80) cc_final: 0.8093 (t80) outliers start: 18 outliers final: 16 residues processed: 181 average time/residue: 0.1800 time to fit residues: 49.6005 Evaluate side-chains 186 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 695 ASN B 730 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.196294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.149865 restraints weight = 40859.638| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.41 r_work: 0.3657 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12040 Z= 0.177 Angle : 0.528 7.971 16355 Z= 0.287 Chirality : 0.046 0.435 1803 Planarity : 0.005 0.050 2015 Dihedral : 4.814 50.272 1770 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.30 % Favored : 95.56 % Rotamer: Outliers : 1.46 % Allowed : 11.04 % Favored : 87.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.22), residues: 1395 helix: 2.26 (0.17), residues: 827 sheet: -1.55 (0.60), residues: 77 loop : -1.43 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 289 TYR 0.011 0.001 TYR B 798 PHE 0.017 0.001 PHE A 253 TRP 0.008 0.001 TRP A 829 HIS 0.004 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00405 (12025) covalent geometry : angle 0.52308 (16320) SS BOND : bond 0.00306 ( 10) SS BOND : angle 1.27211 ( 20) hydrogen bonds : bond 0.04745 ( 685) hydrogen bonds : angle 4.26966 ( 2016) link_BETA1-4 : bond 0.00413 ( 2) link_BETA1-4 : angle 1.84367 ( 6) link_NAG-ASN : bond 0.00097 ( 3) link_NAG-ASN : angle 1.90794 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8262 (ptm-80) cc_final: 0.7776 (ptm-80) REVERT: A 479 LEU cc_start: 0.9097 (mm) cc_final: 0.8842 (mm) REVERT: A 534 MET cc_start: 0.6567 (mtp) cc_final: 0.6255 (mtm) REVERT: A 555 MET cc_start: 0.8311 (mmt) cc_final: 0.7944 (mmt) REVERT: A 703 ASP cc_start: 0.8349 (m-30) cc_final: 0.8125 (m-30) REVERT: A 795 GLU cc_start: 0.4499 (tm-30) cc_final: 0.4126 (tm-30) REVERT: B 192 MET cc_start: 0.5343 (mmm) cc_final: 0.3346 (ttm) REVERT: B 279 ILE cc_start: 0.9071 (tp) cc_final: 0.8840 (tp) REVERT: B 403 GLU cc_start: 0.7879 (tt0) cc_final: 0.7607 (tp30) REVERT: B 855 TYR cc_start: 0.8386 (t80) cc_final: 0.8120 (t80) outliers start: 18 outliers final: 17 residues processed: 174 average time/residue: 0.1977 time to fit residues: 51.9825 Evaluate side-chains 184 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN A 695 ASN ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.198181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.149435 restraints weight = 40736.271| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.35 r_work: 0.3699 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12040 Z= 0.116 Angle : 0.496 7.613 16355 Z= 0.268 Chirality : 0.045 0.438 1803 Planarity : 0.004 0.050 2015 Dihedral : 4.630 52.363 1770 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.77 % Rotamer: Outliers : 1.46 % Allowed : 11.12 % Favored : 87.42 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.23), residues: 1395 helix: 2.36 (0.17), residues: 827 sheet: -1.40 (0.60), residues: 77 loop : -1.36 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 289 TYR 0.009 0.001 TYR B 798 PHE 0.014 0.001 PHE B 556 TRP 0.010 0.001 TRP B 397 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00251 (12025) covalent geometry : angle 0.49227 (16320) SS BOND : bond 0.00206 ( 10) SS BOND : angle 1.08261 ( 20) hydrogen bonds : bond 0.04359 ( 685) hydrogen bonds : angle 4.15879 ( 2016) link_BETA1-4 : bond 0.00483 ( 2) link_BETA1-4 : angle 1.62559 ( 6) link_NAG-ASN : bond 0.00149 ( 3) link_NAG-ASN : angle 1.67900 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2790 Ramachandran restraints generated. 1395 Oldfield, 0 Emsley, 1395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8196 (ptm-80) cc_final: 0.7687 (ptm-80) REVERT: A 479 LEU cc_start: 0.9090 (mm) cc_final: 0.8817 (mm) REVERT: A 534 MET cc_start: 0.6554 (mtp) cc_final: 0.6244 (mtm) REVERT: A 555 MET cc_start: 0.8326 (mmt) cc_final: 0.7963 (mmt) REVERT: A 674 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8729 (tt0) REVERT: A 703 ASP cc_start: 0.8350 (m-30) cc_final: 0.8123 (m-30) REVERT: A 795 GLU cc_start: 0.4489 (tm-30) cc_final: 0.4122 (tm-30) REVERT: B 192 MET cc_start: 0.5367 (mmm) cc_final: 0.3339 (ttm) REVERT: B 279 ILE cc_start: 0.9046 (tp) cc_final: 0.8809 (tp) REVERT: B 855 TYR cc_start: 0.8381 (t80) cc_final: 0.8111 (t80) outliers start: 18 outliers final: 17 residues processed: 183 average time/residue: 0.2015 time to fit residues: 56.2869 Evaluate side-chains 187 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 674 GLN Chi-restraints excluded: chain A residue 682 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain B residue 99 GLN Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.197996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152135 restraints weight = 40900.159| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.34 r_work: 0.3694 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 12040 Z= 0.141 Angle : 0.778 59.195 16355 Z= 0.470 Chirality : 0.045 0.418 1803 Planarity : 0.004 0.050 2015 Dihedral : 4.628 52.352 1770 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.09 % Favored : 95.77 % Rotamer: Outliers : 1.46 % Allowed : 11.04 % Favored : 87.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.23), residues: 1395 helix: 2.36 (0.17), residues: 827 sheet: -1.40 (0.60), residues: 77 loop : -1.36 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 289 TYR 0.008 0.001 TYR B 77 PHE 0.013 0.001 PHE B 556 TRP 0.009 0.001 TRP B 397 HIS 0.003 0.001 HIS A 830 Details of bonding type rmsd covalent geometry : bond 0.00294 (12025) covalent geometry : angle 0.77633 (16320) SS BOND : bond 0.00209 ( 10) SS BOND : angle 1.07839 ( 20) hydrogen bonds : bond 0.04390 ( 685) hydrogen bonds : angle 4.15898 ( 2016) link_BETA1-4 : bond 0.00486 ( 2) link_BETA1-4 : angle 1.91556 ( 6) link_NAG-ASN : bond 0.00144 ( 3) link_NAG-ASN : angle 1.67731 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6233.89 seconds wall clock time: 106 minutes 3.60 seconds (6363.60 seconds total)