Starting phenix.real_space_refine on Thu Jul 2 07:43:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w3v_32294/07_2026/7w3v_32294.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w3v_32294/07_2026/7w3v_32294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7w3v_32294/07_2026/7w3v_32294.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w3v_32294/07_2026/7w3v_32294.cif" model { file = "/net/cci-nas-00/data/ceres_data/7w3v_32294/07_2026/7w3v_32294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w3v_32294/07_2026/7w3v_32294.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w3v_32294/07_2026/7w3v_32294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w3v_32294/07_2026/7w3v_32294.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4755 2.51 5 N 1197 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7480 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1675 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 5, 'TRANS': 216} Chain: "C" Number of atoms: 5487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 696, 5487 Classifications: {'peptide': 696} Link IDs: {'PTRANS': 29, 'TRANS': 666} Chain breaks: 2 Chain: "B" 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 chiralities: 2 Chain: "D" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "E" 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 chiralities: 2 Chain: "F" 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 chiralities: 2 Chain: "G" 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 chiralities: 2 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 1.56, per 1000 atoms: 0.21 Number of scatterers: 7480 At special positions: 0 Unit cell: (92.307, 90.185, 120.954, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1499 8.00 N 1197 7.00 C 4755 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 644 " 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 ALPHA1-2 " MAN D 5 " - " MAN D 6 " ALPHA1-3 " BMA D 3 " - " MAN D 8 " " MAN D 4 " - " MAN D 7 " ALPHA1-6 " BMA D 3 " - " MAN D 4 " " MAN D 4 " - " MAN D 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 1 " - " ASN C 73 " " NAG C1001 " - " ASN C 159 " " NAG C1002 " - " ASN C 234 " " NAG C1003 " - " ASN C 261 " " NAG C1004 " - " ASN C 532 " " NAG C1005 " - " ASN C 542 " " NAG C1006 " - " ASN C 562 " " NAG C1007 " - " ASN C 591 " " NAG C1008 " - " ASN C 660 " " NAG D 1 " - " ASN C 143 " " NAG E 1 " - " ASN C 311 " " NAG F 1 " - " ASN C 481 " " NAG G 1 " - " ASN C 647 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 401.3 milliseconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1710 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 16.6% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.511A pdb=" N GLY C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 45 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 105 through 111 removed outlier: 3.849A pdb=" N LEU C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.900A pdb=" N ILE C 133 " --> pdb=" O PRO C 130 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 136 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.667A pdb=" N PHE C 157 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 158 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 184 removed outlier: 3.782A pdb=" N SER C 182 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS C 183 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 256 through 263 removed outlier: 4.134A pdb=" N SER C 263 " --> pdb=" O PHE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 337 through 340 removed outlier: 3.855A pdb=" N ARG C 340 " --> pdb=" O SER C 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 340' Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 428 through 434 removed outlier: 3.914A pdb=" N GLY C 432 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 434 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 458 removed outlier: 3.634A pdb=" N MET C 454 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 455 " --> pdb=" O GLU C 452 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 457 " --> pdb=" O MET C 454 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER C 458 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.551A pdb=" N HIS C 478 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 480 " --> pdb=" O SER C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 621 removed outlier: 3.687A pdb=" N CYS C 621 " --> pdb=" O SER C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 666 through 672 removed outlier: 3.723A pdb=" N LEU C 672 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.891A pdb=" N ALA A 64 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 58 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 63 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A 235 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TRP A 71 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N THR A 227 " --> pdb=" O TRP A 71 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS A 105 " --> pdb=" O SER A 234 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE A 236 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 103 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 238 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.561A pdb=" N TYR A 34 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 4.300A pdb=" N LYS A 92 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE A 124 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A 217 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP A 122 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 219 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER A 120 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR A 221 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP A 118 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA A 117 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA A 143 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 119 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU A 136 " --> pdb=" O PHE A 180 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N PHE A 182 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N MET A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA A 184 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TRP A 140 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 158 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 148 Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 71 removed outlier: 6.845A pdb=" N LEU C 82 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 141 through 143 removed outlier: 6.532A pdb=" N LEU C 142 " --> pdb=" O ASP C 167 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU C 166 " --> pdb=" O SER C 191 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU C 190 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU C 215 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 318 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU C 346 " --> pdb=" O TYR C 370 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP C 394 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU C 393 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 416 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 440 " --> pdb=" O ASP C 464 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE C 463 " --> pdb=" O ASP C 489 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU C 488 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE C 512 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU C 536 " --> pdb=" O ASN C 562 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU C 561 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 585 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 630 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU C 654 " --> pdb=" O TYR C 679 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.354A pdb=" N GLY C 151 " --> pdb=" O ILE C 174 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU C 173 " --> pdb=" O ASP C 196 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.408A pdb=" N LEU C 357 " --> pdb=" O MET C 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'C' and resid 569 through 570 removed outlier: 5.632A pdb=" N GLY C 570 " --> pdb=" O SER C 593 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N PHE C 592 " --> pdb=" O GLN C 612 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE C 614 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLY C 594 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE C 613 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER C 638 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY C 615 " --> pdb=" O SER C 638 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N PHE C 637 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER C 662 " --> pdb=" O PHE C 637 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLY C 639 " --> pdb=" O SER C 662 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LYS C 664 " --> pdb=" O GLY C 639 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE C 661 " --> pdb=" O SER C 684 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER C 686 " --> pdb=" O PHE C 661 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLY C 663 " --> pdb=" O SER C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 781 through 789 removed outlier: 3.832A pdb=" N MET C 781 " --> pdb=" O TYR C 798 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY C 787 " --> pdb=" O TYR C 792 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR C 792 " --> pdb=" O GLY C 787 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 285 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: 1.31 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2323 1.34 - 1.46: 1832 1.46 - 1.58: 3441 1.58 - 1.70: 0 1.70 - 1.81: 42 Bond restraints: 7638 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.06e+00 bond pdb=" C1 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.67e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG C1007 " pdb=" O5 NAG C1007 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 7633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 9921 1.44 - 2.89: 356 2.89 - 4.33: 57 4.33 - 5.78: 15 5.78 - 7.22: 9 Bond angle restraints: 10358 Sorted by residual: angle pdb=" N ILE C 620 " pdb=" CA ILE C 620 " pdb=" C ILE C 620 " ideal model delta sigma weight residual 111.91 108.11 3.80 8.90e-01 1.26e+00 1.82e+01 angle pdb=" C PHE C 136 " pdb=" N LYS C 137 " pdb=" CA LYS C 137 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C LEU C 312 " pdb=" N THR C 313 " pdb=" CA THR C 313 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.47e+00 angle pdb=" C ILE A 215 " pdb=" N THR A 216 " pdb=" CA THR A 216 " ideal model delta sigma weight residual 122.73 118.78 3.95 1.62e+00 3.81e-01 5.93e+00 angle pdb=" C PHE C 250 " pdb=" N SER C 251 " pdb=" CA SER C 251 " ideal model delta sigma weight residual 121.54 126.08 -4.54 1.91e+00 2.74e-01 5.65e+00 ... (remaining 10353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3958 17.98 - 35.95: 324 35.95 - 53.93: 54 53.93 - 71.91: 10 71.91 - 89.89: 4 Dihedral angle restraints: 4350 sinusoidal: 1693 harmonic: 2657 Sorted by residual: dihedral pdb=" CB CYS C 30 " pdb=" SG CYS C 30 " pdb=" SG CYS C 64 " pdb=" CB CYS C 64 " ideal model delta sinusoidal sigma weight residual 93.00 46.84 46.16 1 1.00e+01 1.00e-02 2.95e+01 dihedral pdb=" CA PHE C 260 " pdb=" C PHE C 260 " pdb=" N ASN C 261 " pdb=" CA ASN C 261 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE C 284 " pdb=" C PHE C 284 " pdb=" N GLY C 285 " pdb=" CA GLY C 285 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 4347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1048 0.063 - 0.126: 177 0.126 - 0.188: 12 0.188 - 0.251: 0 0.251 - 0.314: 4 Chirality restraints: 1241 Sorted by residual: chirality pdb=" C1 NAG C1003 " pdb=" ND2 ASN C 261 " pdb=" C2 NAG C1003 " pdb=" O5 NAG C1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C1 NAG C1004 " pdb=" ND2 ASN C 532 " pdb=" C2 NAG C1004 " pdb=" O5 NAG C1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN C 481 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 1238 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 792 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO C 793 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 793 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 793 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 261 " -0.017 2.00e-02 2.50e+03 1.58e-02 3.12e+00 pdb=" CG ASN C 261 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 261 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 261 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG C1003 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 614 " 0.006 2.00e-02 2.50e+03 9.66e-03 1.63e+00 pdb=" CG PHE C 614 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE C 614 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE C 614 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 614 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 614 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 614 " -0.000 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1191 2.76 - 3.30: 6969 3.30 - 3.83: 11850 3.83 - 4.37: 14502 4.37 - 4.90: 24817 Nonbonded interactions: 59329 Sorted by model distance: nonbonded pdb=" OG1 THR C 101 " pdb=" OE2 GLU C 123 " model vdw 2.228 3.040 nonbonded pdb=" O CYS C 220 " pdb=" ND2 ASN C 248 " model vdw 2.248 3.120 nonbonded pdb=" OH TYR A 69 " pdb=" OH TYR A 108 " model vdw 2.268 3.040 nonbonded pdb=" NZ LYS A 155 " pdb=" O7 NAG D 2 " model vdw 2.272 3.120 nonbonded pdb=" OD1 ASP C 319 " pdb=" OG SER C 321 " model vdw 2.304 3.040 ... (remaining 59324 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 'B' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 7.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7665 Z= 0.178 Angle : 0.672 7.220 10436 Z= 0.321 Chirality : 0.048 0.314 1241 Planarity : 0.004 0.057 1280 Dihedral : 13.423 89.886 2631 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.12 % Allowed : 0.62 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.27), residues: 910 helix: -2.30 (0.43), residues: 133 sheet: -2.16 (0.36), residues: 200 loop : -1.50 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 164 TYR 0.021 0.002 TYR A 108 PHE 0.022 0.001 PHE C 614 TRP 0.021 0.001 TRP A 28 HIS 0.002 0.001 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 ( 7638) covalent geometry : angle 0.65429 / 0.32 (10358) SS BOND : bond 0.00284 / 0.15 ( 3) SS BOND : angle 1.00021 / 0.47 ( 6) hydrogen bonds : bond 0.18587 / 12.32 ( 133) hydrogen bonds : angle 6.74611 / 4.65 ( 285) link_ALPHA1-2 : bond 0.00202 / 0.13 ( 1) link_ALPHA1-2 : angle 1.90260 / 1.04 ( 3) link_ALPHA1-3 : bond 0.00462 / 0.27 ( 2) link_ALPHA1-3 : angle 1.53095 / 0.91 ( 6) link_ALPHA1-6 : bond 0.00302 / 0.18 ( 2) link_ALPHA1-6 : angle 1.68255 / 0.97 ( 6) link_BETA1-4 : bond 0.00544 / 0.42 ( 6) link_BETA1-4 : angle 1.90597 / 1.28 ( 18) link_NAG-ASN : bond 0.00314 / 0.23 ( 13) link_NAG-ASN : angle 2.05242 / 1.22 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.282 Fit side-chains REVERT: A 96 ASN cc_start: 0.7605 (m-40) cc_final: 0.7399 (m110) REVERT: A 114 THR cc_start: 0.7936 (m) cc_final: 0.7516 (p) REVERT: C 270 ASP cc_start: 0.6854 (t0) cc_final: 0.6343 (t0) REVERT: C 676 GLU cc_start: 0.7134 (pt0) cc_final: 0.6780 (pt0) outliers start: 1 outliers final: 0 residues processed: 179 average time/residue: 0.0821 time to fit residues: 19.9590 Evaluate side-chains 160 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS C 86 ASN C 122 ASN C 493 ASN C 530 GLN C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089883 restraints weight = 11635.450| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.98 r_work: 0.3082 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 7665 Z= 0.217 Angle : 0.644 7.481 10436 Z= 0.323 Chirality : 0.048 0.299 1241 Planarity : 0.004 0.039 1280 Dihedral : 4.995 18.639 970 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.11 % Allowed : 8.62 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.27), residues: 910 helix: -2.26 (0.43), residues: 129 sheet: -1.97 (0.34), residues: 227 loop : -1.56 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 99 TYR 0.020 0.002 TYR C 533 PHE 0.013 0.002 PHE C 410 TRP 0.013 0.002 TRP A 41 HIS 0.005 0.002 HIS C 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 ( 7638) covalent geometry : angle 0.62882 / 0.32 (10358) SS BOND : bond 0.00385 / 0.20 ( 3) SS BOND : angle 1.32457 / 0.69 ( 6) hydrogen bonds : bond 0.04336 / 2.94 ( 133) hydrogen bonds : angle 5.65701 / 3.90 ( 285) link_ALPHA1-2 : bond 0.00002 / 0.00 ( 1) link_ALPHA1-2 : angle 1.98578 / 1.07 ( 3) link_ALPHA1-3 : bond 0.00544 / 0.32 ( 2) link_ALPHA1-3 : angle 1.36632 / 0.80 ( 6) link_ALPHA1-6 : bond 0.00239 / 0.13 ( 2) link_ALPHA1-6 : angle 1.73555 / 0.95 ( 6) link_BETA1-4 : bond 0.00549 / 0.42 ( 6) link_BETA1-4 : angle 1.67463 / 1.11 ( 18) link_NAG-ASN : bond 0.00398 / 0.27 ( 13) link_NAG-ASN : angle 1.81126 / 1.09 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 181 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.8830 (m100) cc_final: 0.8329 (m100) REVERT: A 34 TYR cc_start: 0.8165 (m-80) cc_final: 0.7457 (m-80) REVERT: A 231 MET cc_start: 0.8694 (tmm) cc_final: 0.8428 (ttt) REVERT: C 79 VAL cc_start: 0.7999 (m) cc_final: 0.7036 (t) REVERT: C 150 SER cc_start: 0.8964 (t) cc_final: 0.8534 (m) REVERT: C 201 ASN cc_start: 0.7805 (p0) cc_final: 0.7421 (p0) REVERT: C 270 ASP cc_start: 0.7397 (t0) cc_final: 0.6914 (t0) REVERT: C 493 ASN cc_start: 0.8228 (m-40) cc_final: 0.7983 (m110) REVERT: C 559 LYS cc_start: 0.8705 (tttp) cc_final: 0.8504 (tttt) REVERT: C 676 GLU cc_start: 0.7389 (pt0) cc_final: 0.6930 (pt0) outliers start: 9 outliers final: 8 residues processed: 183 average time/residue: 0.0765 time to fit residues: 18.8842 Evaluate side-chains 178 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 170 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 649 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS C 510 GLN C 609 HIS ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091880 restraints weight = 11419.764| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.96 r_work: 0.3105 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7665 Z= 0.139 Angle : 0.593 8.628 10436 Z= 0.296 Chirality : 0.045 0.220 1241 Planarity : 0.003 0.032 1280 Dihedral : 4.837 17.742 970 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.35 % Allowed : 11.58 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.27), residues: 910 helix: -2.21 (0.44), residues: 127 sheet: -2.01 (0.34), residues: 229 loop : -1.51 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 164 TYR 0.016 0.002 TYR C 533 PHE 0.018 0.001 PHE C 614 TRP 0.012 0.001 TRP A 41 HIS 0.004 0.001 HIS C 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 7638) covalent geometry : angle 0.57953 / 0.29 (10358) SS BOND : bond 0.00387 / 0.21 ( 3) SS BOND : angle 1.22839 / 0.62 ( 6) hydrogen bonds : bond 0.03615 / 2.47 ( 133) hydrogen bonds : angle 5.40515 / 3.71 ( 285) link_ALPHA1-2 : bond 0.00048 / 0.03 ( 1) link_ALPHA1-2 : angle 1.77833 / 0.93 ( 3) link_ALPHA1-3 : bond 0.00653 / 0.38 ( 2) link_ALPHA1-3 : angle 1.36218 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00269 / 0.16 ( 2) link_ALPHA1-6 : angle 1.43753 / 0.82 ( 6) link_BETA1-4 : bond 0.00536 / 0.41 ( 6) link_BETA1-4 : angle 1.61155 / 1.11 ( 18) link_NAG-ASN : bond 0.00336 / 0.25 ( 13) link_NAG-ASN : angle 1.60959 / 0.98 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.8843 (m100) cc_final: 0.8302 (m100) REVERT: A 34 TYR cc_start: 0.8143 (m-80) cc_final: 0.7437 (m-80) REVERT: C 150 SER cc_start: 0.8927 (t) cc_final: 0.8489 (m) REVERT: C 270 ASP cc_start: 0.7353 (t0) cc_final: 0.6885 (t0) REVERT: C 493 ASN cc_start: 0.8170 (m-40) cc_final: 0.7748 (m110) REVERT: C 559 LYS cc_start: 0.8649 (tttp) cc_final: 0.8437 (tttt) REVERT: C 676 GLU cc_start: 0.7411 (pt0) cc_final: 0.6963 (pt0) outliers start: 11 outliers final: 8 residues processed: 171 average time/residue: 0.0827 time to fit residues: 19.0914 Evaluate side-chains 172 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 598 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 190 ASN C 372 GLN C 510 GLN C 530 GLN C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.100227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090313 restraints weight = 11750.807| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.98 r_work: 0.3042 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7665 Z= 0.205 Angle : 0.620 6.953 10436 Z= 0.311 Chirality : 0.048 0.221 1241 Planarity : 0.004 0.032 1280 Dihedral : 5.056 19.403 970 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 2.46 % Allowed : 12.07 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.27), residues: 910 helix: -2.21 (0.44), residues: 127 sheet: -1.96 (0.34), residues: 229 loop : -1.60 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 164 TYR 0.020 0.002 TYR C 170 PHE 0.020 0.002 PHE C 614 TRP 0.013 0.002 TRP A 41 HIS 0.006 0.002 HIS C 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 7638) covalent geometry : angle 0.60723 / 0.31 (10358) SS BOND : bond 0.00401 / 0.21 ( 3) SS BOND : angle 1.31596 / 0.67 ( 6) hydrogen bonds : bond 0.03753 / 2.56 ( 133) hydrogen bonds : angle 5.35861 / 3.69 ( 285) link_ALPHA1-2 : bond 0.00017 / 0.01 ( 1) link_ALPHA1-2 : angle 1.85662 / 0.96 ( 3) link_ALPHA1-3 : bond 0.00558 / 0.33 ( 2) link_ALPHA1-3 : angle 1.33700 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00155 / 0.10 ( 2) link_ALPHA1-6 : angle 1.57802 / 0.89 ( 6) link_BETA1-4 : bond 0.00437 / 0.34 ( 6) link_BETA1-4 : angle 1.66621 / 1.14 ( 18) link_NAG-ASN : bond 0.00382 / 0.26 ( 13) link_NAG-ASN : angle 1.52722 / 0.90 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8171 (m-80) cc_final: 0.7488 (m-80) REVERT: C 79 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7243 (t) REVERT: C 224 LYS cc_start: 0.8925 (mppt) cc_final: 0.8660 (mmtm) REVERT: C 270 ASP cc_start: 0.7370 (t0) cc_final: 0.6924 (t0) REVERT: C 493 ASN cc_start: 0.8157 (m-40) cc_final: 0.7592 (m-40) REVERT: C 559 LYS cc_start: 0.8662 (tttp) cc_final: 0.8456 (tttt) REVERT: C 676 GLU cc_start: 0.7415 (pt0) cc_final: 0.6976 (pt0) outliers start: 20 outliers final: 14 residues processed: 178 average time/residue: 0.0807 time to fit residues: 19.1853 Evaluate side-chains 175 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 650 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS C 372 GLN C 510 GLN C 565 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.100557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090589 restraints weight = 11513.747| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.98 r_work: 0.3098 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7665 Z= 0.132 Angle : 0.583 7.019 10436 Z= 0.293 Chirality : 0.045 0.221 1241 Planarity : 0.003 0.029 1280 Dihedral : 4.828 17.214 970 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.34 % Allowed : 12.44 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.27), residues: 910 helix: -2.17 (0.44), residues: 127 sheet: -1.99 (0.34), residues: 229 loop : -1.53 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 164 TYR 0.016 0.002 TYR C 533 PHE 0.020 0.001 PHE C 614 TRP 0.015 0.001 TRP A 28 HIS 0.005 0.001 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7638) covalent geometry : angle 0.57088 / 0.29 (10358) SS BOND : bond 0.00384 / 0.21 ( 3) SS BOND : angle 1.21089 / 0.62 ( 6) hydrogen bonds : bond 0.03223 / 2.19 ( 133) hydrogen bonds : angle 5.20123 / 3.56 ( 285) link_ALPHA1-2 : bond 0.00039 / 0.02 ( 1) link_ALPHA1-2 : angle 1.79184 / 0.96 ( 3) link_ALPHA1-3 : bond 0.00560 / 0.33 ( 2) link_ALPHA1-3 : angle 1.37535 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00262 / 0.16 ( 2) link_ALPHA1-6 : angle 1.41351 / 0.80 ( 6) link_BETA1-4 : bond 0.00511 / 0.38 ( 6) link_BETA1-4 : angle 1.60708 / 1.12 ( 18) link_NAG-ASN : bond 0.00354 / 0.25 ( 13) link_NAG-ASN : angle 1.50762 / 0.97 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8174 (m-80) cc_final: 0.7400 (m-80) REVERT: C 79 VAL cc_start: 0.7917 (OUTLIER) cc_final: 0.6884 (t) REVERT: C 132 PHE cc_start: 0.8219 (p90) cc_final: 0.8014 (p90) REVERT: C 150 SER cc_start: 0.8898 (t) cc_final: 0.8486 (m) REVERT: C 270 ASP cc_start: 0.7192 (t0) cc_final: 0.6756 (t0) REVERT: C 337 SER cc_start: 0.8579 (m) cc_final: 0.8349 (m) REVERT: C 493 ASN cc_start: 0.8167 (m-40) cc_final: 0.7721 (m-40) REVERT: C 559 LYS cc_start: 0.8666 (tttp) cc_final: 0.8448 (tttt) REVERT: C 612 GLN cc_start: 0.7775 (mt0) cc_final: 0.7345 (mt0) REVERT: C 676 GLU cc_start: 0.7469 (pt0) cc_final: 0.6977 (pt0) outliers start: 19 outliers final: 14 residues processed: 174 average time/residue: 0.0813 time to fit residues: 19.0594 Evaluate side-chains 177 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 649 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS C 510 GLN C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.098436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.088642 restraints weight = 11574.668| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.94 r_work: 0.3047 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 7665 Z= 0.315 Angle : 0.716 8.783 10436 Z= 0.352 Chirality : 0.052 0.349 1241 Planarity : 0.004 0.037 1280 Dihedral : 5.475 21.441 970 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 3.69 % Allowed : 12.19 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.27), residues: 910 helix: -2.17 (0.44), residues: 129 sheet: -1.89 (0.35), residues: 222 loop : -1.74 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 164 TYR 0.024 0.002 TYR C 170 PHE 0.022 0.002 PHE C 614 TRP 0.020 0.002 TRP A 28 HIS 0.011 0.002 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.31 ( 7638) covalent geometry : angle 0.69564 / 0.35 (10358) SS BOND : bond 0.00489 / 0.26 ( 3) SS BOND : angle 1.49949 / 0.78 ( 6) hydrogen bonds : bond 0.04260 / 2.89 ( 133) hydrogen bonds : angle 5.53948 / 3.80 ( 285) link_ALPHA1-2 : bond 0.00195 / 0.12 ( 1) link_ALPHA1-2 : angle 2.05977 / 1.03 ( 3) link_ALPHA1-3 : bond 0.00498 / 0.29 ( 2) link_ALPHA1-3 : angle 1.35276 / 0.78 ( 6) link_ALPHA1-6 : bond 0.00273 / 0.15 ( 2) link_ALPHA1-6 : angle 1.75219 / 0.97 ( 6) link_BETA1-4 : bond 0.00449 / 0.36 ( 6) link_BETA1-4 : angle 2.09123 / 1.34 ( 18) link_NAG-ASN : bond 0.00603 / 0.42 ( 13) link_NAG-ASN : angle 2.25018 / 1.59 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8262 (m-80) cc_final: 0.7591 (m-80) REVERT: C 79 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.7480 (t) REVERT: C 89 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7906 (p) REVERT: C 224 LYS cc_start: 0.8923 (mptt) cc_final: 0.8687 (mmtm) REVERT: C 270 ASP cc_start: 0.7426 (t0) cc_final: 0.6957 (t0) REVERT: C 559 LYS cc_start: 0.8658 (tttp) cc_final: 0.8445 (tttt) REVERT: C 676 GLU cc_start: 0.7443 (pt0) cc_final: 0.6933 (pt0) outliers start: 30 outliers final: 19 residues processed: 190 average time/residue: 0.0843 time to fit residues: 21.6077 Evaluate side-chains 187 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 673 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS C 351 ASN C 510 GLN C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089277 restraints weight = 11667.393| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.99 r_work: 0.3076 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7665 Z= 0.165 Angle : 0.627 9.235 10436 Z= 0.312 Chirality : 0.047 0.223 1241 Planarity : 0.004 0.033 1280 Dihedral : 5.170 19.467 970 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.08 % Allowed : 13.42 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.27), residues: 910 helix: -2.11 (0.45), residues: 127 sheet: -1.97 (0.35), residues: 219 loop : -1.64 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 164 TYR 0.018 0.002 TYR A 201 PHE 0.024 0.002 PHE C 384 TRP 0.013 0.001 TRP A 28 HIS 0.006 0.002 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 7638) covalent geometry : angle 0.61310 / 0.31 (10358) SS BOND : bond 0.00428 / 0.23 ( 3) SS BOND : angle 1.26906 / 0.66 ( 6) hydrogen bonds : bond 0.03454 / 2.35 ( 133) hydrogen bonds : angle 5.38473 / 3.67 ( 285) link_ALPHA1-2 : bond 0.00005 / 0.00 ( 1) link_ALPHA1-2 : angle 1.86103 / 0.97 ( 3) link_ALPHA1-3 : bond 0.00517 / 0.30 ( 2) link_ALPHA1-3 : angle 1.38038 / 0.81 ( 6) link_ALPHA1-6 : bond 0.00218 / 0.13 ( 2) link_ALPHA1-6 : angle 1.44279 / 0.83 ( 6) link_BETA1-4 : bond 0.00446 / 0.34 ( 6) link_BETA1-4 : angle 1.70860 / 1.17 ( 18) link_NAG-ASN : bond 0.00379 / 0.27 ( 13) link_NAG-ASN : angle 1.67498 / 1.12 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8228 (m-80) cc_final: 0.7506 (m-80) REVERT: C 79 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7240 (t) REVERT: C 270 ASP cc_start: 0.7246 (t0) cc_final: 0.6780 (t0) REVERT: C 493 ASN cc_start: 0.8172 (m-40) cc_final: 0.7596 (m-40) REVERT: C 535 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8318 (t) REVERT: C 559 LYS cc_start: 0.8657 (tttp) cc_final: 0.8433 (tttt) REVERT: C 612 GLN cc_start: 0.7748 (mt0) cc_final: 0.7300 (mt0) REVERT: C 676 GLU cc_start: 0.7460 (pt0) cc_final: 0.6960 (pt0) outliers start: 25 outliers final: 16 residues processed: 187 average time/residue: 0.0869 time to fit residues: 21.8427 Evaluate side-chains 191 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 137 LYS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 531 ASN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 650 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088679 restraints weight = 11660.251| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.96 r_work: 0.3057 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 7665 Z= 0.270 Angle : 0.705 9.764 10436 Z= 0.345 Chirality : 0.050 0.235 1241 Planarity : 0.004 0.039 1280 Dihedral : 5.403 20.813 970 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.96 % Allowed : 15.15 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.27), residues: 910 helix: -2.13 (0.44), residues: 127 sheet: -1.97 (0.35), residues: 223 loop : -1.72 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 164 TYR 0.022 0.002 TYR C 533 PHE 0.029 0.002 PHE C 384 TRP 0.017 0.002 TRP A 28 HIS 0.008 0.002 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 ( 7638) covalent geometry : angle 0.68861 / 0.34 (10358) SS BOND : bond 0.00476 / 0.26 ( 3) SS BOND : angle 1.41409 / 0.73 ( 6) hydrogen bonds : bond 0.03900 / 2.64 ( 133) hydrogen bonds : angle 5.47764 / 3.74 ( 285) link_ALPHA1-2 : bond 0.00170 / 0.11 ( 1) link_ALPHA1-2 : angle 1.99183 / 1.00 ( 3) link_ALPHA1-3 : bond 0.00479 / 0.28 ( 2) link_ALPHA1-3 : angle 1.35847 / 0.79 ( 6) link_ALPHA1-6 : bond 0.00157 / 0.09 ( 2) link_ALPHA1-6 : angle 1.65668 / 0.93 ( 6) link_BETA1-4 : bond 0.00402 / 0.32 ( 6) link_BETA1-4 : angle 1.83758 / 1.22 ( 18) link_NAG-ASN : bond 0.00471 / 0.32 ( 13) link_NAG-ASN : angle 2.08563 / 1.31 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8258 (m-80) cc_final: 0.7530 (m-80) REVERT: C 79 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7391 (t) REVERT: C 270 ASP cc_start: 0.7395 (t0) cc_final: 0.6918 (t0) REVERT: C 559 LYS cc_start: 0.8668 (tttp) cc_final: 0.8451 (tttt) REVERT: C 612 GLN cc_start: 0.7795 (mt0) cc_final: 0.7351 (mt0) REVERT: C 676 GLU cc_start: 0.7463 (pt0) cc_final: 0.6963 (pt0) outliers start: 24 outliers final: 18 residues processed: 186 average time/residue: 0.0801 time to fit residues: 20.0006 Evaluate side-chains 193 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 649 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 58 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.091311 restraints weight = 11407.711| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.94 r_work: 0.3097 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7665 Z= 0.131 Angle : 0.643 9.451 10436 Z= 0.313 Chirality : 0.048 0.281 1241 Planarity : 0.003 0.036 1280 Dihedral : 5.081 24.235 970 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.59 % Allowed : 15.89 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.27), residues: 910 helix: -2.09 (0.45), residues: 127 sheet: -1.93 (0.36), residues: 218 loop : -1.66 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 164 TYR 0.017 0.002 TYR A 201 PHE 0.029 0.001 PHE C 384 TRP 0.016 0.001 TRP A 41 HIS 0.004 0.001 HIS C 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7638) covalent geometry : angle 0.62373 / 0.31 (10358) SS BOND : bond 0.00377 / 0.20 ( 3) SS BOND : angle 1.23170 / 0.63 ( 6) hydrogen bonds : bond 0.03255 / 2.27 ( 133) hydrogen bonds : angle 5.22469 / 3.56 ( 285) link_ALPHA1-2 : bond 0.00027 / 0.02 ( 1) link_ALPHA1-2 : angle 1.68548 / 0.89 ( 3) link_ALPHA1-3 : bond 0.00517 / 0.30 ( 2) link_ALPHA1-3 : angle 1.41048 / 0.83 ( 6) link_ALPHA1-6 : bond 0.00317 / 0.19 ( 2) link_ALPHA1-6 : angle 1.36892 / 0.79 ( 6) link_BETA1-4 : bond 0.00470 / 0.35 ( 6) link_BETA1-4 : angle 1.61445 / 1.12 ( 18) link_NAG-ASN : bond 0.00505 / 0.39 ( 13) link_NAG-ASN : angle 2.21404 / 1.33 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 26 TRP cc_start: 0.8867 (m100) cc_final: 0.8335 (m100) REVERT: A 34 TYR cc_start: 0.8199 (m-80) cc_final: 0.7491 (m-80) REVERT: A 114 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.7962 (p) REVERT: C 150 SER cc_start: 0.8945 (t) cc_final: 0.8514 (m) REVERT: C 270 ASP cc_start: 0.7225 (t0) cc_final: 0.6771 (t0) REVERT: C 337 SER cc_start: 0.8565 (m) cc_final: 0.8326 (m) REVERT: C 493 ASN cc_start: 0.8174 (m-40) cc_final: 0.7620 (m110) REVERT: C 559 LYS cc_start: 0.8661 (tttp) cc_final: 0.8440 (tttt) REVERT: C 612 GLN cc_start: 0.7776 (mt0) cc_final: 0.7358 (mt0) outliers start: 21 outliers final: 13 residues processed: 186 average time/residue: 0.0864 time to fit residues: 21.4345 Evaluate side-chains 188 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 650 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089276 restraints weight = 11574.677| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.97 r_work: 0.3074 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7665 Z= 0.167 Angle : 0.676 15.383 10436 Z= 0.325 Chirality : 0.055 0.951 1241 Planarity : 0.004 0.041 1280 Dihedral : 5.099 24.272 970 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.34 % Allowed : 16.38 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.27), residues: 910 helix: -2.10 (0.44), residues: 127 sheet: -1.90 (0.36), residues: 219 loop : -1.66 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 164 TYR 0.018 0.002 TYR C 533 PHE 0.030 0.002 PHE C 384 TRP 0.014 0.001 TRP A 41 HIS 0.005 0.001 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 7638) covalent geometry : angle 0.63903 / 0.32 (10358) SS BOND : bond 0.00402 / 0.22 ( 3) SS BOND : angle 1.35221 / 0.69 ( 6) hydrogen bonds : bond 0.03384 / 2.31 ( 133) hydrogen bonds : angle 5.20536 / 3.54 ( 285) link_ALPHA1-2 : bond 0.00086 / 0.05 ( 1) link_ALPHA1-2 : angle 1.81290 / 0.96 ( 3) link_ALPHA1-3 : bond 0.00496 / 0.29 ( 2) link_ALPHA1-3 : angle 1.39158 / 0.82 ( 6) link_ALPHA1-6 : bond 0.00179 / 0.11 ( 2) link_ALPHA1-6 : angle 1.49976 / 0.85 ( 6) link_BETA1-4 : bond 0.00471 / 0.36 ( 6) link_BETA1-4 : angle 1.65186 / 1.14 ( 18) link_NAG-ASN : bond 0.00794 / 0.64 ( 13) link_NAG-ASN : angle 3.37384 / 1.88 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 26 TRP cc_start: 0.8857 (m100) cc_final: 0.8333 (m100) REVERT: A 34 TYR cc_start: 0.8217 (m-80) cc_final: 0.7494 (m-80) REVERT: A 231 MET cc_start: 0.8653 (tmm) cc_final: 0.8338 (ttt) REVERT: C 79 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.6996 (t) REVERT: C 150 SER cc_start: 0.8961 (t) cc_final: 0.8533 (m) REVERT: C 270 ASP cc_start: 0.7236 (t0) cc_final: 0.6783 (t0) REVERT: C 337 SER cc_start: 0.8610 (m) cc_final: 0.8363 (m) REVERT: C 493 ASN cc_start: 0.8195 (m-40) cc_final: 0.7631 (m110) REVERT: C 559 LYS cc_start: 0.8620 (tttp) cc_final: 0.8403 (tttt) REVERT: C 612 GLN cc_start: 0.7797 (mt0) cc_final: 0.7372 (mt0) outliers start: 19 outliers final: 16 residues processed: 184 average time/residue: 0.0786 time to fit residues: 19.3449 Evaluate side-chains 191 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 650 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089308 restraints weight = 11529.565| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.97 r_work: 0.3075 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 7665 Z= 0.237 Angle : 1.074 59.161 10436 Z= 0.588 Chirality : 0.056 0.884 1241 Planarity : 0.004 0.068 1280 Dihedral : 5.093 19.162 970 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.85 % Allowed : 17.12 % Favored : 81.03 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.27), residues: 910 helix: -2.10 (0.44), residues: 127 sheet: -1.90 (0.36), residues: 219 loop : -1.67 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 164 TYR 0.017 0.002 TYR C 533 PHE 0.028 0.002 PHE C 384 TRP 0.013 0.001 TRP A 41 HIS 0.005 0.001 HIS C 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 ( 7638) covalent geometry : angle 1.04471 / 0.58 (10358) SS BOND : bond 0.00408 / 0.22 ( 3) SS BOND : angle 1.34732 / 0.68 ( 6) hydrogen bonds : bond 0.03312 / 2.25 ( 133) hydrogen bonds : angle 5.20352 / 3.54 ( 285) link_ALPHA1-2 : bond 0.00275 / 0.17 ( 1) link_ALPHA1-2 : angle 1.79165 / 0.93 ( 3) link_ALPHA1-3 : bond 0.00489 / 0.29 ( 2) link_ALPHA1-3 : angle 1.39031 / 0.82 ( 6) link_ALPHA1-6 : bond 0.00208 / 0.13 ( 2) link_ALPHA1-6 : angle 1.49674 / 0.84 ( 6) link_BETA1-4 : bond 0.00378 / 0.29 ( 6) link_BETA1-4 : angle 1.64967 / 1.12 ( 18) link_NAG-ASN : bond 0.03949 / 3.26 ( 13) link_NAG-ASN : angle 4.06194 / 2.37 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1866.68 seconds wall clock time: 32 minutes 44.78 seconds (1964.78 seconds total)