Starting phenix.real_space_refine on Tue Mar 3 17:39:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w3v_32294/03_2026/7w3v_32294.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w3v_32294/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7w3v_32294/03_2026/7w3v_32294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w3v_32294/03_2026/7w3v_32294.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w3v_32294/03_2026/7w3v_32294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w3v_32294/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 24 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 1.66, per 1000 atoms: 0.22 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 291.3 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: 0.19 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: 1.06 Time building geometry restraints manager: 0.89 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 - 23.00: 4521 23.00 - 45.99: 248 45.99 - 68.99: 34 68.99 - 91.98: 10 91.98 - 114.98: 29 Dihedral angle restraints: 4842 sinusoidal: 2185 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=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " pdb=" C5 NAG E 2 " ideal model delta sinusoidal sigma weight residual -62.96 52.02 -114.98 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 4839 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 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 : 17.079 114.975 3123 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 covalent geometry : bond 0.00366 ( 7638) covalent geometry : angle 0.65429 (10358) SS BOND : bond 0.00284 ( 3) SS BOND : angle 1.00021 ( 6) hydrogen bonds : bond 0.18587 ( 133) hydrogen bonds : angle 6.74611 ( 285) link_ALPHA1-2 : bond 0.00202 ( 1) link_ALPHA1-2 : angle 1.90260 ( 3) link_ALPHA1-3 : bond 0.00462 ( 2) link_ALPHA1-3 : angle 1.53095 ( 6) link_ALPHA1-6 : bond 0.00302 ( 2) link_ALPHA1-6 : angle 1.68255 ( 6) link_BETA1-4 : bond 0.00544 ( 6) link_BETA1-4 : angle 1.90597 ( 18) link_NAG-ASN : bond 0.00314 ( 13) link_NAG-ASN : angle 2.05242 ( 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 : 0.204 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: 0.0920 time to fit residues: 22.1032 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 : 0.234 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3323 r_free = 0.3323 target = 0.099961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089951 restraints weight = 11622.174| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.98 r_work: 0.3083 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.0950 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 : 0.668 8.919 10436 Z= 0.329 Chirality : 0.050 0.342 1241 Planarity : 0.004 0.040 1280 Dihedral : 13.655 110.617 1462 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.99 % Allowed : 8.74 % 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: -2.67 (0.27), residues: 910 helix: -2.24 (0.44), residues: 129 sheet: -2.00 (0.34), residues: 228 loop : -1.55 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.019 0.002 TYR C 170 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 covalent geometry : bond 0.00489 ( 7638) covalent geometry : angle 0.65137 (10358) SS BOND : bond 0.00380 ( 3) SS BOND : angle 1.33820 ( 6) hydrogen bonds : bond 0.04544 ( 133) hydrogen bonds : angle 5.66543 ( 285) link_ALPHA1-2 : bond 0.00077 ( 1) link_ALPHA1-2 : angle 2.09774 ( 3) link_ALPHA1-3 : bond 0.00812 ( 2) link_ALPHA1-3 : angle 1.58249 ( 6) link_ALPHA1-6 : bond 0.00261 ( 2) link_ALPHA1-6 : angle 2.02945 ( 6) link_BETA1-4 : bond 0.00568 ( 6) link_BETA1-4 : angle 1.99604 ( 18) link_NAG-ASN : bond 0.00418 ( 13) link_NAG-ASN : angle 1.83898 ( 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 188 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 180 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 26 TRP cc_start: 0.8833 (m100) cc_final: 0.8332 (m100) REVERT: A 34 TYR cc_start: 0.8160 (m-80) cc_final: 0.7456 (m-80) REVERT: A 231 MET cc_start: 0.8688 (tmm) cc_final: 0.8440 (ttt) REVERT: C 79 VAL cc_start: 0.7994 (m) cc_final: 0.7039 (t) REVERT: C 201 ASN cc_start: 0.7794 (p0) cc_final: 0.7443 (p0) REVERT: C 270 ASP cc_start: 0.7399 (t0) cc_final: 0.6919 (t0) REVERT: C 493 ASN cc_start: 0.8202 (m-40) cc_final: 0.7963 (m110) REVERT: C 676 GLU cc_start: 0.7387 (pt0) cc_final: 0.6924 (pt0) outliers start: 8 outliers final: 7 residues processed: 182 average time/residue: 0.0849 time to fit residues: 20.7966 Evaluate side-chains 177 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 190 ASN C 510 GLN ** 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 = 0.3319 r_free = 0.3319 target = 0.099761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.089807 restraints weight = 11464.766| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.96 r_work: 0.3076 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 7665 Z= 0.218 Angle : 0.661 9.585 10436 Z= 0.325 Chirality : 0.049 0.213 1241 Planarity : 0.004 0.035 1280 Dihedral : 11.084 107.657 1462 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.85 % Allowed : 11.58 % Favored : 86.58 % 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: -2.71 (0.27), residues: 910 helix: -2.17 (0.44), residues: 127 sheet: -2.03 (0.34), residues: 229 loop : -1.60 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 164 TYR 0.020 0.002 TYR C 533 PHE 0.019 0.002 PHE C 614 TRP 0.013 0.002 TRP A 41 HIS 0.004 0.002 HIS C 609 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 7638) covalent geometry : angle 0.64638 (10358) SS BOND : bond 0.00433 ( 3) SS BOND : angle 1.36271 ( 6) hydrogen bonds : bond 0.04085 ( 133) hydrogen bonds : angle 5.49903 ( 285) link_ALPHA1-2 : bond 0.00006 ( 1) link_ALPHA1-2 : angle 2.01363 ( 3) link_ALPHA1-3 : bond 0.00919 ( 2) link_ALPHA1-3 : angle 1.72278 ( 6) link_ALPHA1-6 : bond 0.00341 ( 2) link_ALPHA1-6 : angle 1.89209 ( 6) link_BETA1-4 : bond 0.00517 ( 6) link_BETA1-4 : angle 2.01880 ( 18) link_NAG-ASN : bond 0.00434 ( 13) link_NAG-ASN : angle 1.59241 ( 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 180 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8190 (m-80) cc_final: 0.7489 (m-80) REVERT: A 231 MET cc_start: 0.8643 (tmm) cc_final: 0.8384 (ttt) REVERT: C 79 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7316 (t) REVERT: C 201 ASN cc_start: 0.7843 (p0) cc_final: 0.7443 (p0) REVERT: C 224 LYS cc_start: 0.8959 (mppt) cc_final: 0.8637 (mmtm) REVERT: C 270 ASP cc_start: 0.7385 (t0) cc_final: 0.6922 (t0) REVERT: C 464 ASP cc_start: 0.7624 (t0) cc_final: 0.7417 (t0) REVERT: C 493 ASN cc_start: 0.8166 (m-40) cc_final: 0.7588 (m-40) REVERT: C 625 THR cc_start: 0.8551 (m) cc_final: 0.8183 (p) REVERT: C 676 GLU cc_start: 0.7413 (pt0) cc_final: 0.6951 (pt0) outliers start: 15 outliers final: 11 residues processed: 173 average time/residue: 0.0861 time to fit residues: 20.0795 Evaluate side-chains 171 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 CYS Chi-restraints excluded: chain A residue 99 SER 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 199 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 286 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 248 ASN C 372 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.099723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.089635 restraints weight = 11778.699| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.01 r_work: 0.3071 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7665 Z= 0.164 Angle : 0.615 7.386 10436 Z= 0.304 Chirality : 0.047 0.229 1241 Planarity : 0.003 0.030 1280 Dihedral : 9.969 99.507 1462 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.22 % Allowed : 12.19 % Favored : 85.59 % 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: -2.15 (0.44), residues: 127 sheet: -1.99 (0.34), residues: 229 loop : -1.57 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 164 TYR 0.018 0.002 TYR C 533 PHE 0.021 0.001 PHE C 614 TRP 0.014 0.001 TRP A 41 HIS 0.004 0.001 HIS C 609 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7638) covalent geometry : angle 0.59801 (10358) SS BOND : bond 0.00383 ( 3) SS BOND : angle 1.28920 ( 6) hydrogen bonds : bond 0.03504 ( 133) hydrogen bonds : angle 5.33148 ( 285) link_ALPHA1-2 : bond 0.00023 ( 1) link_ALPHA1-2 : angle 1.88574 ( 3) link_ALPHA1-3 : bond 0.00946 ( 2) link_ALPHA1-3 : angle 1.79027 ( 6) link_ALPHA1-6 : bond 0.00489 ( 2) link_ALPHA1-6 : angle 1.83397 ( 6) link_BETA1-4 : bond 0.00566 ( 6) link_BETA1-4 : angle 2.21266 ( 18) link_NAG-ASN : bond 0.00384 ( 13) link_NAG-ASN : angle 1.60049 ( 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 186 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8202 (m-80) cc_final: 0.7427 (m-80) REVERT: C 79 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7059 (t) REVERT: C 150 SER cc_start: 0.8920 (t) cc_final: 0.8483 (m) REVERT: C 224 LYS cc_start: 0.8973 (mppt) cc_final: 0.8670 (mmtm) REVERT: C 270 ASP cc_start: 0.7213 (t0) cc_final: 0.6781 (t0) REVERT: C 464 ASP cc_start: 0.7640 (t0) cc_final: 0.7401 (t0) REVERT: C 493 ASN cc_start: 0.8196 (m-40) cc_final: 0.7719 (m110) REVERT: C 612 GLN cc_start: 0.7765 (mt0) cc_final: 0.7325 (mt0) REVERT: C 676 GLU cc_start: 0.7444 (pt0) cc_final: 0.6953 (pt0) outliers start: 18 outliers final: 12 residues processed: 178 average time/residue: 0.0928 time to fit residues: 22.1238 Evaluate side-chains 177 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 87 LEU 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 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 598 LEU Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 653 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.0870 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 86 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.102299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.092300 restraints weight = 11423.603| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.96 r_work: 0.3110 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7665 Z= 0.105 Angle : 0.586 6.968 10436 Z= 0.289 Chirality : 0.045 0.292 1241 Planarity : 0.003 0.028 1280 Dihedral : 9.497 96.192 1462 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.59 % Allowed : 12.93 % Favored : 84.48 % 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: -2.59 (0.27), residues: 910 helix: -2.13 (0.44), residues: 127 sheet: -1.95 (0.34), residues: 228 loop : -1.50 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 164 TYR 0.013 0.001 TYR C 170 PHE 0.021 0.001 PHE C 614 TRP 0.012 0.001 TRP A 41 HIS 0.003 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 7638) covalent geometry : angle 0.56894 (10358) SS BOND : bond 0.00349 ( 3) SS BOND : angle 1.15065 ( 6) hydrogen bonds : bond 0.02982 ( 133) hydrogen bonds : angle 5.11280 ( 285) link_ALPHA1-2 : bond 0.00035 ( 1) link_ALPHA1-2 : angle 1.81980 ( 3) link_ALPHA1-3 : bond 0.00943 ( 2) link_ALPHA1-3 : angle 1.88172 ( 6) link_ALPHA1-6 : bond 0.00667 ( 2) link_ALPHA1-6 : angle 1.71276 ( 6) link_BETA1-4 : bond 0.00546 ( 6) link_BETA1-4 : angle 2.10026 ( 18) link_NAG-ASN : bond 0.00349 ( 13) link_NAG-ASN : angle 1.58885 ( 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 191 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8154 (m-80) cc_final: 0.7396 (m-80) REVERT: C 79 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.6553 (t) REVERT: C 150 SER cc_start: 0.8860 (t) cc_final: 0.8442 (m) REVERT: C 270 ASP cc_start: 0.7182 (t0) cc_final: 0.6760 (t0) REVERT: C 337 SER cc_start: 0.8522 (m) cc_final: 0.8305 (m) REVERT: C 464 ASP cc_start: 0.7601 (t0) cc_final: 0.7302 (t0) REVERT: C 493 ASN cc_start: 0.8159 (m-40) cc_final: 0.7617 (m110) REVERT: C 612 GLN cc_start: 0.7813 (mt0) cc_final: 0.7403 (mt0) REVERT: C 676 GLU cc_start: 0.7452 (pt0) cc_final: 0.6949 (pt0) outliers start: 21 outliers final: 13 residues processed: 180 average time/residue: 0.0912 time to fit residues: 21.9918 Evaluate side-chains 183 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 99 SER 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 535 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 86 ASN C 510 GLN ** 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 = 0.3289 r_free = 0.3289 target = 0.097832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.087692 restraints weight = 11652.011| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.01 r_work: 0.3060 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7665 Z= 0.239 Angle : 0.662 7.504 10436 Z= 0.325 Chirality : 0.049 0.250 1241 Planarity : 0.004 0.034 1280 Dihedral : 9.341 94.018 1462 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.71 % Allowed : 13.55 % Favored : 83.74 % 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: -2.10 (0.45), residues: 127 sheet: -1.95 (0.34), residues: 229 loop : -1.57 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 164 TYR 0.022 0.002 TYR C 533 PHE 0.024 0.002 PHE C 384 TRP 0.016 0.002 TRP A 28 HIS 0.009 0.002 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00546 ( 7638) covalent geometry : angle 0.64260 (10358) SS BOND : bond 0.00424 ( 3) SS BOND : angle 1.35343 ( 6) hydrogen bonds : bond 0.03776 ( 133) hydrogen bonds : angle 5.33522 ( 285) link_ALPHA1-2 : bond 0.00079 ( 1) link_ALPHA1-2 : angle 1.99931 ( 3) link_ALPHA1-3 : bond 0.00835 ( 2) link_ALPHA1-3 : angle 1.74666 ( 6) link_ALPHA1-6 : bond 0.00461 ( 2) link_ALPHA1-6 : angle 1.99570 ( 6) link_BETA1-4 : bond 0.00497 ( 6) link_BETA1-4 : angle 2.47330 ( 18) link_NAG-ASN : bond 0.00470 ( 13) link_NAG-ASN : angle 1.77193 ( 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 201 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8243 (m-80) cc_final: 0.7507 (m-80) REVERT: C 79 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7267 (t) REVERT: C 224 LYS cc_start: 0.8935 (mptt) cc_final: 0.8691 (mmtm) REVERT: C 270 ASP cc_start: 0.7256 (t0) cc_final: 0.6829 (t0) REVERT: C 464 ASP cc_start: 0.7716 (t0) cc_final: 0.7438 (t0) REVERT: C 493 ASN cc_start: 0.8174 (m-40) cc_final: 0.7580 (m-40) REVERT: C 612 GLN cc_start: 0.7796 (mt0) cc_final: 0.7358 (mt0) REVERT: C 676 GLU cc_start: 0.7475 (pt0) cc_final: 0.6957 (pt0) outliers start: 22 outliers final: 14 residues processed: 191 average time/residue: 0.0893 time to fit residues: 22.9761 Evaluate side-chains 189 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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 649 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 29 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 351 ASN C 650 ASN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.098958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.088729 restraints weight = 11730.918| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.05 r_work: 0.3084 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1423 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= 0.135 Angle : 0.615 8.347 10436 Z= 0.301 Chirality : 0.047 0.323 1241 Planarity : 0.003 0.032 1280 Dihedral : 9.091 93.461 1462 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.83 % Allowed : 13.67 % 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: -2.61 (0.27), residues: 910 helix: -2.14 (0.44), residues: 127 sheet: -1.97 (0.34), residues: 230 loop : -1.51 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 164 TYR 0.015 0.001 TYR C 170 PHE 0.028 0.001 PHE C 384 TRP 0.013 0.001 TRP A 41 HIS 0.004 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7638) covalent geometry : angle 0.59369 (10358) SS BOND : bond 0.00379 ( 3) SS BOND : angle 1.21604 ( 6) hydrogen bonds : bond 0.03144 ( 133) hydrogen bonds : angle 5.19898 ( 285) link_ALPHA1-2 : bond 0.00068 ( 1) link_ALPHA1-2 : angle 1.84019 ( 3) link_ALPHA1-3 : bond 0.00901 ( 2) link_ALPHA1-3 : angle 1.91746 ( 6) link_ALPHA1-6 : bond 0.00661 ( 2) link_ALPHA1-6 : angle 1.76357 ( 6) link_BETA1-4 : bond 0.00444 ( 6) link_BETA1-4 : angle 2.31778 ( 18) link_NAG-ASN : bond 0.00354 ( 13) link_NAG-ASN : angle 1.92810 ( 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 206 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 26 TRP cc_start: 0.8872 (m100) cc_final: 0.8354 (m100) REVERT: A 34 TYR cc_start: 0.8206 (m-80) cc_final: 0.7442 (m-80) REVERT: C 79 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7202 (t) REVERT: C 150 SER cc_start: 0.8887 (t) cc_final: 0.8483 (m) REVERT: C 165 ILE cc_start: 0.8526 (mm) cc_final: 0.8309 (mm) REVERT: C 224 LYS cc_start: 0.8929 (mptt) cc_final: 0.8680 (mmtm) REVERT: C 270 ASP cc_start: 0.7235 (t0) cc_final: 0.6790 (t0) REVERT: C 337 SER cc_start: 0.8597 (m) cc_final: 0.8368 (m) REVERT: C 343 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8218 (tp) REVERT: C 464 ASP cc_start: 0.7648 (t0) cc_final: 0.7360 (t0) REVERT: C 493 ASN cc_start: 0.8175 (m-40) cc_final: 0.7613 (m110) REVERT: C 612 GLN cc_start: 0.7807 (mt0) cc_final: 0.7387 (mt0) REVERT: C 676 GLU cc_start: 0.7476 (pt0) cc_final: 0.6969 (pt0) outliers start: 23 outliers final: 16 residues processed: 196 average time/residue: 0.0902 time to fit residues: 23.8297 Evaluate side-chains 198 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 650 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 69 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.0050 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.088941 restraints weight = 11696.122| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.02 r_work: 0.3081 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7665 Z= 0.156 Angle : 0.641 9.496 10436 Z= 0.311 Chirality : 0.049 0.427 1241 Planarity : 0.003 0.037 1280 Dihedral : 8.962 92.808 1462 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.83 % Allowed : 14.16 % Favored : 83.00 % 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: -2.60 (0.27), residues: 910 helix: -2.14 (0.44), residues: 127 sheet: -1.95 (0.34), residues: 230 loop : -1.51 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 164 TYR 0.017 0.002 TYR C 170 PHE 0.031 0.002 PHE C 384 TRP 0.018 0.001 TRP A 28 HIS 0.005 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 7638) covalent geometry : angle 0.61921 (10358) SS BOND : bond 0.00385 ( 3) SS BOND : angle 1.26423 ( 6) hydrogen bonds : bond 0.03253 ( 133) hydrogen bonds : angle 5.18416 ( 285) link_ALPHA1-2 : bond 0.00035 ( 1) link_ALPHA1-2 : angle 1.85985 ( 3) link_ALPHA1-3 : bond 0.00881 ( 2) link_ALPHA1-3 : angle 1.86389 ( 6) link_ALPHA1-6 : bond 0.00624 ( 2) link_ALPHA1-6 : angle 1.83375 ( 6) link_BETA1-4 : bond 0.00462 ( 6) link_BETA1-4 : angle 2.31079 ( 18) link_NAG-ASN : bond 0.00392 ( 13) link_NAG-ASN : angle 1.99932 ( 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 198 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 26 TRP cc_start: 0.8860 (m100) cc_final: 0.8345 (m100) REVERT: A 34 TYR cc_start: 0.8210 (m-80) cc_final: 0.7492 (m-80) REVERT: C 79 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7165 (t) REVERT: C 150 SER cc_start: 0.8905 (t) cc_final: 0.8508 (m) REVERT: C 224 LYS cc_start: 0.8924 (mptt) cc_final: 0.8669 (mmtm) REVERT: C 270 ASP cc_start: 0.7235 (t0) cc_final: 0.6781 (t0) REVERT: C 337 SER cc_start: 0.8606 (m) cc_final: 0.8366 (m) REVERT: C 464 ASP cc_start: 0.7645 (t0) cc_final: 0.7358 (t0) REVERT: C 493 ASN cc_start: 0.8177 (m-40) cc_final: 0.7618 (m110) REVERT: C 530 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7934 (mm110) REVERT: C 612 GLN cc_start: 0.7783 (mt0) cc_final: 0.7369 (mt0) REVERT: C 676 GLU cc_start: 0.7464 (pt0) cc_final: 0.6950 (pt0) outliers start: 23 outliers final: 16 residues processed: 189 average time/residue: 0.0878 time to fit residues: 22.3602 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 : 0.279 ------------------------------------------------------------------------------- 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 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 531 ASN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 559 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.0030 chunk 43 optimal weight: 2.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3332 r_free = 0.3332 target = 0.100610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.090523 restraints weight = 11481.797| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.97 r_work: 0.3098 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7665 Z= 0.134 Angle : 0.643 16.093 10436 Z= 0.311 Chirality : 0.048 0.354 1241 Planarity : 0.003 0.036 1280 Dihedral : 8.762 92.069 1462 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.46 % Allowed : 14.29 % Favored : 83.25 % 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: -2.53 (0.28), residues: 910 helix: -2.09 (0.46), residues: 121 sheet: -1.90 (0.35), residues: 228 loop : -1.48 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 164 TYR 0.015 0.001 TYR C 170 PHE 0.030 0.001 PHE C 384 TRP 0.012 0.001 TRP A 41 HIS 0.004 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7638) covalent geometry : angle 0.60004 (10358) SS BOND : bond 0.00370 ( 3) SS BOND : angle 1.22328 ( 6) hydrogen bonds : bond 0.03039 ( 133) hydrogen bonds : angle 5.10410 ( 285) link_ALPHA1-2 : bond 0.00086 ( 1) link_ALPHA1-2 : angle 1.82188 ( 3) link_ALPHA1-3 : bond 0.00895 ( 2) link_ALPHA1-3 : angle 1.93330 ( 6) link_ALPHA1-6 : bond 0.00711 ( 2) link_ALPHA1-6 : angle 1.77914 ( 6) link_BETA1-4 : bond 0.00456 ( 6) link_BETA1-4 : angle 2.21147 ( 18) link_NAG-ASN : bond 0.00504 ( 13) link_NAG-ASN : angle 3.35767 ( 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: 20 poor density : 176 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 26 TRP cc_start: 0.8863 (m100) cc_final: 0.8328 (m100) REVERT: A 34 TYR cc_start: 0.8192 (m-80) cc_final: 0.7481 (m-80) REVERT: C 150 SER cc_start: 0.8888 (t) cc_final: 0.8491 (m) REVERT: C 270 ASP cc_start: 0.7237 (t0) cc_final: 0.6747 (t0) REVERT: C 337 SER cc_start: 0.8577 (m) cc_final: 0.8343 (m) REVERT: C 464 ASP cc_start: 0.7621 (t0) cc_final: 0.7322 (t0) REVERT: C 493 ASN cc_start: 0.8149 (m-40) cc_final: 0.7618 (m110) REVERT: C 612 GLN cc_start: 0.7811 (mt0) cc_final: 0.7401 (mt0) outliers start: 20 outliers final: 16 residues processed: 188 average time/residue: 0.0928 time to fit residues: 23.3829 Evaluate side-chains 189 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 173 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 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 531 ASN Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 609 HIS 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: 2.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 174 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.100182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.090044 restraints weight = 11570.281| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.98 r_work: 0.3089 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7665 Z= 0.157 Angle : 0.656 11.864 10436 Z= 0.317 Chirality : 0.050 0.550 1241 Planarity : 0.004 0.041 1280 Dihedral : 8.710 91.751 1462 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.97 % Allowed : 15.02 % Favored : 83.00 % 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: -2.52 (0.28), residues: 910 helix: -2.07 (0.46), residues: 121 sheet: -1.90 (0.34), residues: 228 loop : -1.47 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 164 TYR 0.017 0.002 TYR C 580 PHE 0.030 0.002 PHE C 384 TRP 0.014 0.001 TRP A 28 HIS 0.005 0.001 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7638) covalent geometry : angle 0.62171 (10358) SS BOND : bond 0.00381 ( 3) SS BOND : angle 1.26159 ( 6) hydrogen bonds : bond 0.03133 ( 133) hydrogen bonds : angle 5.11108 ( 285) link_ALPHA1-2 : bond 0.00046 ( 1) link_ALPHA1-2 : angle 1.82794 ( 3) link_ALPHA1-3 : bond 0.00847 ( 2) link_ALPHA1-3 : angle 1.88933 ( 6) link_ALPHA1-6 : bond 0.00671 ( 2) link_ALPHA1-6 : angle 1.83257 ( 6) link_BETA1-4 : bond 0.00431 ( 6) link_BETA1-4 : angle 2.24114 ( 18) link_NAG-ASN : bond 0.00945 ( 13) link_NAG-ASN : angle 2.92228 ( 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 193 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 TRP cc_start: 0.8854 (m100) cc_final: 0.8336 (m100) REVERT: A 34 TYR cc_start: 0.8213 (m-80) cc_final: 0.7494 (m-80) REVERT: A 231 MET cc_start: 0.8631 (tmm) cc_final: 0.8297 (ttt) REVERT: C 150 SER cc_start: 0.8903 (t) cc_final: 0.8512 (m) REVERT: C 270 ASP cc_start: 0.7247 (t0) cc_final: 0.6793 (t0) REVERT: C 337 SER cc_start: 0.8593 (m) cc_final: 0.8355 (m) REVERT: C 464 ASP cc_start: 0.7659 (t0) cc_final: 0.7363 (t0) REVERT: C 493 ASN cc_start: 0.8160 (m-40) cc_final: 0.7617 (m110) REVERT: C 612 GLN cc_start: 0.7818 (mt0) cc_final: 0.7405 (mt0) REVERT: C 650 ASN cc_start: 0.8145 (t0) cc_final: 0.7770 (t0) outliers start: 16 outliers final: 16 residues processed: 186 average time/residue: 0.0898 time to fit residues: 22.3649 Evaluate side-chains 193 residues out of total 812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 531 ASN Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 559 LYS Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 609 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 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 66 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.088076 restraints weight = 11608.394| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.97 r_work: 0.3051 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7665 Z= 0.275 Angle : 0.733 11.092 10436 Z= 0.355 Chirality : 0.054 0.496 1241 Planarity : 0.004 0.043 1280 Dihedral : 9.099 93.644 1462 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.09 % Allowed : 15.27 % Favored : 82.64 % 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: -2.16 (0.44), residues: 127 sheet: -1.83 (0.35), residues: 223 loop : -1.67 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 164 TYR 0.022 0.002 TYR C 170 PHE 0.030 0.002 PHE C 384 TRP 0.019 0.002 TRP A 28 HIS 0.009 0.002 HIS C 417 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 7638) covalent geometry : angle 0.70080 (10358) SS BOND : bond 0.00452 ( 3) SS BOND : angle 1.44011 ( 6) hydrogen bonds : bond 0.03882 ( 133) hydrogen bonds : angle 5.44718 ( 285) link_ALPHA1-2 : bond 0.00153 ( 1) link_ALPHA1-2 : angle 2.10082 ( 3) link_ALPHA1-3 : bond 0.00767 ( 2) link_ALPHA1-3 : angle 1.75379 ( 6) link_ALPHA1-6 : bond 0.00535 ( 2) link_ALPHA1-6 : angle 1.98381 ( 6) link_BETA1-4 : bond 0.00374 ( 6) link_BETA1-4 : angle 2.46963 ( 18) link_NAG-ASN : bond 0.00938 ( 13) link_NAG-ASN : angle 2.96525 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.36 seconds wall clock time: 33 minutes 32.64 seconds (2012.64 seconds total)