Starting phenix.real_space_refine on Thu May 22 14:28:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sur_40776/05_2025/8sur_40776_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sur_40776/05_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_40776/05_2025/8sur_40776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sur_40776/05_2025/8sur_40776.map" model { file = "/net/cci-nas-00/data/ceres_data/8sur_40776/05_2025/8sur_40776_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sur_40776/05_2025/8sur_40776_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.015 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG: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: {'GLU:plan': 2, 'ARG:plan': 1} 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: 10.97, per 1000 atoms: 0.48 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: 5.12 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.63 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: 9.17 Time building geometry restraints manager: 6.11 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 868 or resid 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.000 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: 0.350 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 45.650 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.890 ------------------------------------------------------------------------------- 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 : 7.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (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 TRP 0.114 0.002 TRP A 359 HIS 0.005 0.001 HIS A 830 PHE 0.016 0.001 PHE B 677 TYR 0.019 0.001 TYR B 406 ARG 0.003 0.000 ARG A 713 Details of bonding type rmsd link_NAG-ASN : bond 0.00254 ( 3) link_NAG-ASN : angle 1.35203 ( 9) link_BETA1-4 : bond 0.00350 ( 2) link_BETA1-4 : angle 1.21274 ( 6) hydrogen bonds : bond 0.14368 ( 685) hydrogen bonds : angle 5.82464 ( 2016) SS BOND : bond 0.03275 ( 10) SS BOND : angle 3.35583 ( 20) covalent geometry : bond 0.00686 (12025) covalent geometry : angle 0.85331 (16320) *********************** 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 : 1.615 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: 0.7142 (mmp-170) REVERT: B 678 VAL cc_start: 0.8695 (p) cc_final: 0.8398 (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: 0.4598 time to fit residues: 153.0633 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 : 1.621 ------------------------------------------------------------------------------- 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 119 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.211106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.162446 restraints weight = 40280.071| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 2.53 r_work: 0.3848 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3718 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12040 Z= 0.135 Angle : 0.556 7.195 16355 Z= 0.299 Chirality : 0.046 0.400 1803 Planarity : 0.005 0.068 2015 Dihedral : 8.109 106.027 1774 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.87 % Favored : 95.84 % Rotamer: Outliers : 0.32 % Allowed : 4.87 % Favored : 94.81 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1395 helix: 2.19 (0.17), residues: 839 sheet: -0.67 (0.69), residues: 55 loop : -1.46 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 359 HIS 0.005 0.001 HIS A 830 PHE 0.014 0.001 PHE B 556 TYR 0.015 0.001 TYR B 77 ARG 0.006 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 3) link_NAG-ASN : angle 1.53107 ( 9) link_BETA1-4 : bond 0.00747 ( 2) link_BETA1-4 : angle 1.64616 ( 6) hydrogen bonds : bond 0.05085 ( 685) hydrogen bonds : angle 4.67884 ( 2016) SS BOND : bond 0.00279 ( 10) SS BOND : angle 1.39350 ( 20) covalent geometry : bond 0.00283 (12025) covalent geometry : angle 0.55215 (16320) *********************** 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 186 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 182 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.8101 (m-30) cc_final: 0.7755 (m-30) REVERT: A 308 GLN cc_start: 0.7146 (tt0) cc_final: 0.6737 (mt0) REVERT: A 718 LYS cc_start: 0.8099 (mptt) cc_final: 0.7397 (mttm) REVERT: B 773 MET cc_start: 0.9304 (tpt) cc_final: 0.8806 (tpt) REVERT: B 855 TYR cc_start: 0.8178 (t80) cc_final: 0.7867 (t80) outliers start: 4 outliers final: 3 residues processed: 184 average time/residue: 0.4469 time to fit residues: 122.2549 Evaluate side-chains 167 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 VAL 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 21 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 100 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** 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 = 0.4412 r_free = 0.4412 target = 0.204532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.158630 restraints weight = 40227.044| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.49 r_work: 0.3762 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12040 Z= 0.161 Angle : 0.545 9.247 16355 Z= 0.292 Chirality : 0.046 0.458 1803 Planarity : 0.005 0.050 2015 Dihedral : 6.169 55.274 1770 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 0.73 % Allowed : 6.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1395 helix: 2.24 (0.17), residues: 839 sheet: -1.42 (0.56), residues: 75 loop : -1.42 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 359 HIS 0.008 0.001 HIS A 830 PHE 0.019 0.001 PHE B 675 TYR 0.018 0.001 TYR B 563 ARG 0.003 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 3) link_NAG-ASN : angle 1.74367 ( 9) link_BETA1-4 : bond 0.00642 ( 2) link_BETA1-4 : angle 2.03587 ( 6) hydrogen bonds : bond 0.04794 ( 685) hydrogen bonds : angle 4.45811 ( 2016) SS BOND : bond 0.00276 ( 10) SS BOND : angle 1.22814 ( 20) covalent geometry : bond 0.00362 (12025) covalent geometry : angle 0.54069 (16320) *********************** 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 184 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ARG cc_start: 0.7251 (ttt-90) cc_final: 0.6937 (ttt-90) REVERT: A 250 ASP cc_start: 0.8175 (m-30) cc_final: 0.7777 (m-30) REVERT: A 289 ARG cc_start: 0.8121 (ptm-80) cc_final: 0.7460 (mtt180) REVERT: A 308 GLN cc_start: 0.7249 (tt0) cc_final: 0.6800 (mt0) REVERT: A 555 MET cc_start: 0.8246 (mmt) cc_final: 0.8028 (mmt) REVERT: A 718 LYS cc_start: 0.8170 (mptt) cc_final: 0.7573 (mttt) REVERT: B 192 MET cc_start: 0.5130 (mmm) cc_final: 0.2905 (ttm) REVERT: B 403 GLU cc_start: 0.7986 (tt0) cc_final: 0.7610 (tp30) REVERT: B 773 MET cc_start: 0.9405 (tpt) cc_final: 0.8781 (tpt) REVERT: B 855 TYR cc_start: 0.8328 (t80) cc_final: 0.7989 (t80) outliers start: 9 outliers final: 8 residues processed: 180 average time/residue: 0.4366 time to fit residues: 118.3088 Evaluate side-chains 172 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 132 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 0.0040 chunk 68 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.202880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.153395 restraints weight = 40508.805| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.43 r_work: 0.3742 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12040 Z= 0.147 Angle : 0.520 7.776 16355 Z= 0.281 Chirality : 0.045 0.430 1803 Planarity : 0.005 0.061 2015 Dihedral : 5.553 55.683 1770 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 0.73 % Allowed : 8.36 % Favored : 90.91 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.22), residues: 1395 helix: 2.29 (0.17), residues: 834 sheet: -1.49 (0.57), residues: 75 loop : -1.35 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 829 HIS 0.009 0.001 HIS B 275 PHE 0.015 0.001 PHE A 253 TYR 0.012 0.001 TYR B 77 ARG 0.003 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 3) link_NAG-ASN : angle 1.79978 ( 9) link_BETA1-4 : bond 0.00862 ( 2) link_BETA1-4 : angle 2.41203 ( 6) hydrogen bonds : bond 0.04621 ( 685) hydrogen bonds : angle 4.33438 ( 2016) SS BOND : bond 0.00271 ( 10) SS BOND : angle 1.19669 ( 20) covalent geometry : bond 0.00328 (12025) covalent geometry : angle 0.51466 (16320) *********************** 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 188 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7250 (tt0) cc_final: 0.6795 (mt0) REVERT: A 479 LEU cc_start: 0.8989 (mm) cc_final: 0.8736 (mm) REVERT: A 555 MET cc_start: 0.8323 (mmt) cc_final: 0.8076 (mmt) REVERT: A 671 MET cc_start: 0.8651 (mmp) cc_final: 0.8317 (mmp) REVERT: A 718 LYS cc_start: 0.8195 (mptt) cc_final: 0.7757 (mttt) REVERT: B 192 MET cc_start: 0.5107 (mmm) cc_final: 0.2943 (ttm) REVERT: B 403 GLU cc_start: 0.7909 (tt0) cc_final: 0.7607 (tp30) REVERT: B 773 MET cc_start: 0.9396 (tpt) cc_final: 0.8746 (tpt) REVERT: B 855 TYR cc_start: 0.8339 (t80) cc_final: 0.8016 (t80) outliers start: 9 outliers final: 7 residues processed: 184 average time/residue: 0.4587 time to fit residues: 125.0113 Evaluate side-chains 179 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 172 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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 604 GLU Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain B residue 107 CYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 479 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.197798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.150958 restraints weight = 40780.495| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.51 r_work: 0.3666 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12040 Z= 0.219 Angle : 0.555 8.421 16355 Z= 0.304 Chirality : 0.047 0.443 1803 Planarity : 0.005 0.057 2015 Dihedral : 5.605 59.546 1770 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 1.38 % Allowed : 9.25 % Favored : 89.37 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1395 helix: 2.14 (0.17), residues: 829 sheet: -1.63 (0.59), residues: 75 loop : -1.43 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 359 HIS 0.007 0.002 HIS A 830 PHE 0.022 0.002 PHE B 675 TYR 0.012 0.001 TYR B 798 ARG 0.002 0.000 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 3) link_NAG-ASN : angle 2.01546 ( 9) link_BETA1-4 : bond 0.00523 ( 2) link_BETA1-4 : angle 2.07952 ( 6) hydrogen bonds : bond 0.05080 ( 685) hydrogen bonds : angle 4.42592 ( 2016) SS BOND : bond 0.00363 ( 10) SS BOND : angle 1.31591 ( 20) covalent geometry : bond 0.00502 (12025) covalent geometry : angle 0.54984 (16320) *********************** 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 201 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8266 (ptm-80) cc_final: 0.8019 (ptt90) REVERT: A 308 GLN cc_start: 0.7237 (tt0) cc_final: 0.7026 (mt0) REVERT: A 479 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8825 (mm) REVERT: A 555 MET cc_start: 0.8355 (mmt) cc_final: 0.8052 (mmt) REVERT: A 718 LYS cc_start: 0.8248 (mptt) cc_final: 0.7788 (mmmt) REVERT: A 795 GLU cc_start: 0.4398 (tm-30) cc_final: 0.4038 (tm-30) REVERT: B 192 MET cc_start: 0.5292 (mmm) cc_final: 0.3108 (ttm) REVERT: B 403 GLU cc_start: 0.7913 (tt0) cc_final: 0.7569 (tp30) REVERT: B 773 MET cc_start: 0.9413 (tpt) cc_final: 0.8755 (tpt) REVERT: B 855 TYR cc_start: 0.8375 (t80) cc_final: 0.8075 (t80) outliers start: 17 outliers final: 12 residues processed: 193 average time/residue: 0.4324 time to fit residues: 125.2419 Evaluate side-chains 179 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 698 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 388 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 694 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.0970 chunk 117 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.199958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.153744 restraints weight = 40544.598| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.47 r_work: 0.3705 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12040 Z= 0.121 Angle : 0.504 7.767 16355 Z= 0.273 Chirality : 0.045 0.432 1803 Planarity : 0.005 0.050 2015 Dihedral : 5.339 59.685 1770 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 0.89 % Allowed : 9.98 % Favored : 89.12 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1395 helix: 2.30 (0.17), residues: 834 sheet: -1.55 (0.59), residues: 75 loop : -1.29 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 829 HIS 0.005 0.001 HIS B 275 PHE 0.014 0.001 PHE B 556 TYR 0.010 0.001 TYR B 77 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 3) link_NAG-ASN : angle 1.77558 ( 9) link_BETA1-4 : bond 0.00665 ( 2) link_BETA1-4 : angle 1.87165 ( 6) hydrogen bonds : bond 0.04545 ( 685) hydrogen bonds : angle 4.25582 ( 2016) SS BOND : bond 0.00340 ( 10) SS BOND : angle 1.70669 ( 20) covalent geometry : bond 0.00264 (12025) covalent geometry : angle 0.49816 (16320) *********************** 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 185 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 GLN cc_start: 0.7243 (tt0) cc_final: 0.7025 (mt0) REVERT: A 479 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8802 (mm) REVERT: A 555 MET cc_start: 0.8349 (mmt) cc_final: 0.8061 (mmt) REVERT: A 671 MET cc_start: 0.8629 (mmp) cc_final: 0.8338 (mmp) REVERT: A 718 LYS cc_start: 0.8262 (mptt) cc_final: 0.7754 (mmmt) REVERT: A 795 GLU cc_start: 0.4429 (tm-30) cc_final: 0.4051 (tm-30) REVERT: B 192 MET cc_start: 0.5221 (mmm) cc_final: 0.3069 (ttm) REVERT: B 403 GLU cc_start: 0.7878 (tt0) cc_final: 0.7585 (tp30) REVERT: B 855 TYR cc_start: 0.8342 (t80) cc_final: 0.8052 (t80) outliers start: 11 outliers final: 9 residues processed: 178 average time/residue: 0.4720 time to fit residues: 124.3547 Evaluate side-chains 175 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 698 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 67 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.197141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149705 restraints weight = 40781.413| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.51 r_work: 0.3659 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12040 Z= 0.196 Angle : 0.537 8.068 16355 Z= 0.294 Chirality : 0.046 0.441 1803 Planarity : 0.005 0.050 2015 Dihedral : 5.403 58.782 1770 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.80 % Favored : 96.06 % Rotamer: Outliers : 1.30 % Allowed : 10.15 % Favored : 88.56 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1395 helix: 2.24 (0.17), residues: 828 sheet: -1.72 (0.60), residues: 75 loop : -1.39 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 829 HIS 0.005 0.002 HIS A 830 PHE 0.018 0.001 PHE B 675 TYR 0.011 0.001 TYR B 798 ARG 0.007 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 3) link_NAG-ASN : angle 1.90395 ( 9) link_BETA1-4 : bond 0.00451 ( 2) link_BETA1-4 : angle 1.98989 ( 6) hydrogen bonds : bond 0.04877 ( 685) hydrogen bonds : angle 4.32770 ( 2016) SS BOND : bond 0.00356 ( 10) SS BOND : angle 1.73595 ( 20) covalent geometry : bond 0.00452 (12025) covalent geometry : angle 0.53138 (16320) *********************** 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 184 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8207 (ptm-80) cc_final: 0.7828 (ptm-80) REVERT: A 308 GLN cc_start: 0.7205 (tt0) cc_final: 0.7002 (mt0) REVERT: A 479 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8826 (mm) REVERT: A 718 LYS cc_start: 0.8256 (mptt) cc_final: 0.7764 (mmmt) REVERT: A 795 GLU cc_start: 0.4413 (tm-30) cc_final: 0.4040 (tm-30) REVERT: B 192 MET cc_start: 0.5286 (mmm) cc_final: 0.3207 (ttm) REVERT: B 403 GLU cc_start: 0.7930 (tt0) cc_final: 0.7612 (tp30) REVERT: B 855 TYR cc_start: 0.8376 (t80) cc_final: 0.8078 (t80) outliers start: 16 outliers final: 13 residues processed: 176 average time/residue: 0.4494 time to fit residues: 117.6923 Evaluate side-chains 176 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 0.0370 chunk 63 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.5262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.198235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148724 restraints weight = 40789.734| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.38 r_work: 0.3689 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3411 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= 0.138 Angle : 0.505 7.781 16355 Z= 0.274 Chirality : 0.045 0.438 1803 Planarity : 0.005 0.050 2015 Dihedral : 5.170 53.754 1770 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 1.54 % Allowed : 10.23 % Favored : 88.23 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.22), residues: 1395 helix: 2.32 (0.17), residues: 834 sheet: -1.66 (0.60), residues: 75 loop : -1.33 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 829 HIS 0.005 0.001 HIS B 275 PHE 0.013 0.001 PHE B 556 TYR 0.009 0.001 TYR B 798 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 3) link_NAG-ASN : angle 1.79031 ( 9) link_BETA1-4 : bond 0.00616 ( 2) link_BETA1-4 : angle 1.83357 ( 6) hydrogen bonds : bond 0.04572 ( 685) hydrogen bonds : angle 4.22358 ( 2016) SS BOND : bond 0.00253 ( 10) SS BOND : angle 1.35164 ( 20) covalent geometry : bond 0.00307 (12025) covalent geometry : angle 0.50049 (16320) *********************** 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 188 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8169 (ptm-80) cc_final: 0.7962 (ptm-80) REVERT: A 308 GLN cc_start: 0.7196 (tt0) cc_final: 0.6992 (mt0) REVERT: A 479 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8797 (mm) REVERT: A 555 MET cc_start: 0.8331 (mmt) cc_final: 0.7993 (mmt) REVERT: A 718 LYS cc_start: 0.8332 (mptt) cc_final: 0.7842 (mmmt) REVERT: A 795 GLU cc_start: 0.4412 (tm-30) cc_final: 0.4040 (tm-30) REVERT: B 192 MET cc_start: 0.5375 (mmm) cc_final: 0.3360 (ttm) REVERT: B 403 GLU cc_start: 0.7878 (tt0) cc_final: 0.7607 (tp30) REVERT: B 855 TYR cc_start: 0.8375 (t80) cc_final: 0.8061 (t80) outliers start: 19 outliers final: 15 residues processed: 176 average time/residue: 0.4756 time to fit residues: 125.3897 Evaluate side-chains 182 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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 631 MET 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 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 762 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 130 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.198254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.151792 restraints weight = 40464.145| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.41 r_work: 0.3688 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12040 Z= 0.137 Angle : 0.504 7.812 16355 Z= 0.272 Chirality : 0.045 0.442 1803 Planarity : 0.005 0.050 2015 Dihedral : 4.829 53.256 1770 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.20 % Rotamer: Outliers : 1.54 % Allowed : 10.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.23), residues: 1395 helix: 2.40 (0.17), residues: 825 sheet: -1.51 (0.61), residues: 75 loop : -1.31 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 829 HIS 0.004 0.001 HIS A 830 PHE 0.015 0.001 PHE A 253 TYR 0.011 0.001 TYR B 798 ARG 0.005 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00094 ( 3) link_NAG-ASN : angle 1.70621 ( 9) link_BETA1-4 : bond 0.00536 ( 2) link_BETA1-4 : angle 1.74972 ( 6) hydrogen bonds : bond 0.04431 ( 685) hydrogen bonds : angle 4.17943 ( 2016) SS BOND : bond 0.00241 ( 10) SS BOND : angle 1.30329 ( 20) covalent geometry : bond 0.00307 (12025) covalent geometry : angle 0.49982 (16320) *********************** 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 190 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8160 (ptm-80) cc_final: 0.7940 (ptm-80) REVERT: A 308 GLN cc_start: 0.7221 (tt0) cc_final: 0.7012 (mt0) REVERT: A 479 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8836 (mm) REVERT: A 534 MET cc_start: 0.6445 (mtp) cc_final: 0.6178 (mtm) REVERT: A 555 MET cc_start: 0.8315 (mmt) cc_final: 0.7967 (mmt) REVERT: A 718 LYS cc_start: 0.8385 (mptt) cc_final: 0.7877 (mmmt) REVERT: A 795 GLU cc_start: 0.4534 (tm-30) cc_final: 0.4142 (tm-30) REVERT: B 192 MET cc_start: 0.5289 (mmm) cc_final: 0.3315 (ttm) REVERT: B 403 GLU cc_start: 0.7877 (tt0) cc_final: 0.7649 (tp30) REVERT: B 855 TYR cc_start: 0.8389 (t80) cc_final: 0.8119 (t80) outliers start: 19 outliers final: 16 residues processed: 177 average time/residue: 0.4340 time to fit residues: 114.3557 Evaluate side-chains 181 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 631 MET 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 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 762 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.197914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.148972 restraints weight = 40790.410| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.36 r_work: 0.3692 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12040 Z= 0.139 Angle : 0.505 7.684 16355 Z= 0.273 Chirality : 0.045 0.433 1803 Planarity : 0.005 0.050 2015 Dihedral : 4.705 52.242 1770 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 1.38 % Allowed : 10.31 % Favored : 88.31 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1395 helix: 2.38 (0.17), residues: 825 sheet: -1.43 (0.61), residues: 77 loop : -1.32 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 829 HIS 0.004 0.001 HIS B 275 PHE 0.014 0.001 PHE A 253 TYR 0.010 0.001 TYR B 798 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 3) link_NAG-ASN : angle 1.68354 ( 9) link_BETA1-4 : bond 0.00499 ( 2) link_BETA1-4 : angle 1.74872 ( 6) hydrogen bonds : bond 0.04450 ( 685) hydrogen bonds : angle 4.17467 ( 2016) SS BOND : bond 0.00255 ( 10) SS BOND : angle 1.30321 ( 20) covalent geometry : bond 0.00313 (12025) covalent geometry : angle 0.50094 (16320) ********************** 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 182 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8166 (ptm-80) cc_final: 0.7943 (ptm-80) REVERT: A 479 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8840 (mm) REVERT: A 534 MET cc_start: 0.6519 (mtp) cc_final: 0.6240 (mtm) REVERT: A 555 MET cc_start: 0.8322 (mmt) cc_final: 0.7980 (mmt) REVERT: A 718 LYS cc_start: 0.8388 (mptt) cc_final: 0.7901 (mmmt) REVERT: A 795 GLU cc_start: 0.4571 (tm-30) cc_final: 0.4165 (tm-30) REVERT: B 192 MET cc_start: 0.5366 (mmm) cc_final: 0.3413 (ttm) REVERT: B 855 TYR cc_start: 0.8387 (t80) cc_final: 0.8117 (t80) outliers start: 17 outliers final: 16 residues processed: 171 average time/residue: 0.4631 time to fit residues: 117.9435 Evaluate side-chains 183 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 631 MET 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 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 20 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 24 optimal weight: 0.0030 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.1394 ------------------------------------------------------------------------------- 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 778 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 = 0.4347 r_free = 0.4347 target = 0.198532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152580 restraints weight = 40772.225| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.44 r_work: 0.3689 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3692 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= 0.120 Angle : 0.495 7.635 16355 Z= 0.267 Chirality : 0.045 0.439 1803 Planarity : 0.004 0.050 2015 Dihedral : 4.563 52.854 1770 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.87 % Favored : 95.99 % Rotamer: Outliers : 1.46 % Allowed : 10.47 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1395 helix: 2.45 (0.17), residues: 821 sheet: -1.37 (0.61), residues: 77 loop : -1.32 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 397 HIS 0.003 0.001 HIS A 830 PHE 0.013 0.001 PHE B 556 TYR 0.009 0.001 TYR B 798 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 3) link_NAG-ASN : angle 1.62481 ( 9) link_BETA1-4 : bond 0.00486 ( 2) link_BETA1-4 : angle 1.63632 ( 6) hydrogen bonds : bond 0.04297 ( 685) hydrogen bonds : angle 4.12496 ( 2016) SS BOND : bond 0.00224 ( 10) SS BOND : angle 1.20981 ( 20) covalent geometry : bond 0.00264 (12025) covalent geometry : angle 0.49166 (16320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13275.94 seconds wall clock time: 227 minutes 21.29 seconds (13641.29 seconds total)