Starting phenix.real_space_refine on Fri Sep 11 18:53:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c7s_30301/09_2026/7c7s_30301.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c7s_30301/09_2026/7c7s_30301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7c7s_30301/09_2026/7c7s_30301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c7s_30301/09_2026/7c7s_30301.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c7s_30301/09_2026/7c7s_30301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c7s_30301/09_2026/7c7s_30301.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7c7s_30301/09_2026/7c7s_30301.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c7s_30301/09_2026/7c7s_30301.cif" } resolution = 2.9 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 61 5.16 5 Cl 2 4.86 5 C 7062 2.51 5 N 1798 2.21 5 O 1991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10915 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5457 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 28, 'TRANS': 656} Chain breaks: 2 Chain: "B" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5321 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 28, 'TRANS': 641} Chain breaks: 3 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 95 Unusual residues: {'2BV': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.48, per 1000 atoms: 0.23 Number of scatterers: 10915 At special positions: 0 Unit cell: (78.078, 103.428, 172.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 61 16.00 P 1 15.00 O 1991 8.00 N 1798 7.00 C 7062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=2.23 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.02 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.17 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 NAG-ASN " NAG A1001 " - " ASN A 409 " " NAG A1002 " - " ASN A 440 " " NAG A1003 " - " ASN A 482 " " NAG A1004 " - " ASN A 502 " " NAG A1005 " - " ASN A 514 " " NAG B1001 " - " ASN B 389 " " NAG B1002 " - " ASN B 404 " " NAG B1003 " - " ASN B 453 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 430.3 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 54.3% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 184 through 201 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 221 through 234 removed outlier: 4.004A pdb=" N LYS A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 292 through 304 removed outlier: 4.199A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.741A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 367 through 382 removed outlier: 3.657A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS A 376 " --> pdb=" O ARG A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 452 Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 466 through 485 Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.664A pdb=" N SER A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 616 removed outlier: 3.541A pdb=" N ASN A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 649 removed outlier: 3.518A pdb=" N ASN A 630 " --> pdb=" O GLN A 626 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Proline residue: A 646 - end of helix removed outlier: 3.781A pdb=" N LEU A 649 " --> pdb=" O PHE A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 693 removed outlier: 3.966A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 732 removed outlier: 3.846A pdb=" N VAL A 714 " --> pdb=" O LEU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 791 removed outlier: 3.531A pdb=" N ILE A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 773 " --> pdb=" O TRP A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 removed outlier: 4.015A pdb=" N MET A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) Proline residue: A 821 - end of helix removed outlier: 3.910A pdb=" N MET A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 859 Proline residue: A 855 - end of helix Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.531A pdb=" N GLY B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 135 through 146 removed outlier: 3.644A pdb=" N SER B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 205 through 219 Processing helix chain 'B' and resid 238 through 242 removed outlier: 3.692A pdb=" N LYS B 241 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 271 removed outlier: 3.771A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR B 268 " --> pdb=" O PHE B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 removed outlier: 3.694A pdb=" N ALA B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 Processing helix chain 'B' and resid 354 through 374 Processing helix chain 'B' and resid 392 through 404 removed outlier: 3.742A pdb=" N GLY B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 506 Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 516 through 539 removed outlier: 4.047A pdb=" N ILE B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 551 Processing helix chain 'B' and resid 552 through 584 removed outlier: 3.711A pdb=" N THR B 557 " --> pdb=" O CYS B 553 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 619 Processing helix chain 'B' and resid 652 through 678 removed outlier: 4.072A pdb=" N TRP B 656 " --> pdb=" O HIS B 652 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 667 " --> pdb=" O TYR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 713 Processing helix chain 'B' and resid 716 through 741 Processing helix chain 'B' and resid 741 through 749 removed outlier: 4.386A pdb=" N LEU B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 749 " --> pdb=" O ILE B 745 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 216 removed outlier: 12.219A pdb=" N ALA A 169 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 10.580A pdb=" N ILE A 241 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N TYR A 171 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N MET A 243 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY A 173 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE A 240 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N LEU A 265 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 336 through 343 removed outlier: 6.175A pdb=" N ILE A 309 " --> pdb=" O ILE A 337 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 339 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE A 361 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 312 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 425 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN A 541 " --> pdb=" O LYS A 549 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LYS A 549 " --> pdb=" O GLN A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 518 through 520 removed outlier: 3.547A pdb=" N PHE A 518 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 584 removed outlier: 6.276A pdb=" N ILE A 581 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN A 757 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR A 583 " --> pdb=" O GLN A 757 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N GLU A 759 " --> pdb=" O THR A 583 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 105 removed outlier: 6.025A pdb=" N LEU B 56 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG B 102 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE B 58 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N TYR B 104 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY B 60 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N MET B 129 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER B 57 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N PHE B 131 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET B 59 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 152 " --> pdb=" O LEU B 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 225 through 232 removed outlier: 7.227A pdb=" N VAL B 198 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 8.808A pdb=" N GLU B 230 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR B 200 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE B 232 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B 202 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 250 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TRP B 279 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL B 317 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 281 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N PHE B 319 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN B 430 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS B 438 " --> pdb=" O GLN B 430 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLN B 432 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU B 436 " --> pdb=" O GLN B 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 410 Processing sheet with id=AA8, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AA9, first strand: chain 'B' and resid 622 through 627 592 hydrogen bonds defined for protein. 1728 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: 2.19 Time building geometry restraints manager: 1.25 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: 3404 1.34 - 1.47: 2775 1.47 - 1.59: 4890 1.59 - 1.71: 0 1.71 - 1.84: 101 Bond restraints: 11170 Sorted by residual: bond pdb=" C5 2BV A1006 " pdb=" C6 2BV A1006 " ideal model delta sigma weight residual 1.394 1.486 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C VAL A 619 " pdb=" N ARG A 620 " ideal model delta sigma weight residual 1.331 1.385 -0.054 1.35e-02 5.49e+03 1.58e+01 bond pdb=" O2 2BV A1006 " pdb=" P 2BV A1006 " ideal model delta sigma weight residual 1.510 1.588 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N LEU B 621 " pdb=" CA LEU B 621 " ideal model delta sigma weight residual 1.457 1.418 0.039 1.30e-02 5.92e+03 9.21e+00 bond pdb=" O1 2BV A1006 " pdb=" P 2BV A1006 " ideal model delta sigma weight residual 1.528 1.471 0.057 2.00e-02 2.50e+03 8.23e+00 ... (remaining 11165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 14809 2.22 - 4.44: 293 4.44 - 6.66: 40 6.66 - 8.88: 7 8.88 - 11.10: 3 Bond angle restraints: 15152 Sorted by residual: angle pdb=" C LEU B 539 " pdb=" N ASP B 540 " pdb=" CA ASP B 540 " ideal model delta sigma weight residual 120.31 127.44 -7.13 1.52e+00 4.33e-01 2.20e+01 angle pdb=" C PHE B 537 " pdb=" N GLY B 538 " pdb=" CA GLY B 538 " ideal model delta sigma weight residual 120.14 125.19 -5.05 1.25e+00 6.40e-01 1.63e+01 angle pdb=" N THR B 468 " pdb=" CA THR B 468 " pdb=" C THR B 468 " ideal model delta sigma weight residual 110.20 104.16 6.04 1.58e+00 4.01e-01 1.46e+01 angle pdb=" N ASN A 502 " pdb=" CA ASN A 502 " pdb=" CB ASN A 502 " ideal model delta sigma weight residual 109.95 115.74 -5.79 1.55e+00 4.16e-01 1.40e+01 angle pdb=" O1 2BV A1006 " pdb=" P 2BV A1006 " pdb=" O2 2BV A1006 " ideal model delta sigma weight residual 117.58 106.48 11.10 3.00e+00 1.11e-01 1.37e+01 ... (remaining 15147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 5836 15.90 - 31.81: 607 31.81 - 47.71: 118 47.71 - 63.62: 18 63.62 - 79.52: 10 Dihedral angle restraints: 6589 sinusoidal: 2652 harmonic: 3937 Sorted by residual: dihedral pdb=" CB CYS A 376 " pdb=" SG CYS A 376 " pdb=" SG CYS A 410 " pdb=" CB CYS A 410 " ideal model delta sinusoidal sigma weight residual -86.00 -151.12 65.12 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CB CYS B 265 " pdb=" SG CYS B 265 " pdb=" SG CYS B 302 " pdb=" CB CYS B 302 " ideal model delta sinusoidal sigma weight residual -86.00 -146.78 60.78 1 1.00e+01 1.00e-02 4.91e+01 dihedral pdb=" CB CYS A 220 " pdb=" SG CYS A 220 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual -86.00 -146.70 60.70 1 1.00e+01 1.00e-02 4.90e+01 ... (remaining 6586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1526 0.076 - 0.153: 195 0.153 - 0.229: 9 0.229 - 0.306: 3 0.306 - 0.382: 2 Chirality restraints: 1735 Sorted by residual: chirality pdb=" C2 2BV A1006 " pdb=" N 2BV A1006 " pdb=" C1 2BV A1006 " pdb=" C3 2BV A1006 " both_signs ideal model delta sigma weight residual False -2.51 -2.13 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 389 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" C1 NAG A1004 " pdb=" ND2 ASN A 502 " pdb=" C2 NAG A1004 " pdb=" O5 NAG A1004 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1732 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 475 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C ARG B 475 " -0.065 2.00e-02 2.50e+03 pdb=" O ARG B 475 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS B 476 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 681 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C MET A 681 " 0.064 2.00e-02 2.50e+03 pdb=" O MET A 681 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A 682 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 190 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C PRO A 190 " 0.052 2.00e-02 2.50e+03 pdb=" O PRO A 190 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA A 191 " -0.018 2.00e-02 2.50e+03 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 346 2.70 - 3.25: 11059 3.25 - 3.80: 17163 3.80 - 4.35: 21786 4.35 - 4.90: 36592 Nonbonded interactions: 86946 Sorted by model distance: nonbonded pdb=" NH1 ARG B 212 " pdb=" OG1 THR B 216 " model vdw 2.153 3.120 nonbonded pdb=" O PRO B 136 " pdb=" OG SER B 140 " model vdw 2.210 3.040 nonbonded pdb=" O CYS A 246 " pdb=" OG SER A 250 " model vdw 2.258 3.040 nonbonded pdb=" O LEU B 471 " pdb=" N ARG B 642 " model vdw 2.262 3.120 nonbonded pdb=" OG SER A 625 " pdb=" OD2 ASP A 801 " model vdw 2.294 3.040 ... (remaining 86941 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.530 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.710 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.006 0.198 11185 Z= 0.291 Angle : 0.819 22.927 15190 Z= 0.447 Chirality : 0.052 0.382 1735 Planarity : 0.005 0.052 1882 Dihedral : 13.111 79.521 4034 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.20), residues: 1341 helix: -1.32 (0.17), residues: 707 sheet: -1.48 (0.33), residues: 216 loop : -2.27 (0.25), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 637 TYR 0.016 0.002 TYR B 697 PHE 0.023 0.002 PHE A 375 TRP 0.026 0.002 TRP A 708 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.27 (11170) covalent geometry : angle 0.78178 / 0.43 (15152) SS BOND : bond 0.09118 / 6.03 ( 7) SS BOND : angle 7.09833 / 5.31 ( 14) hydrogen bonds : bond 0.13568 / 9.22 ( 592) hydrogen bonds : angle 5.60653 / 3.92 ( 1728) link_NAG-ASN : bond 0.00936 / 0.56 ( 8) link_NAG-ASN : angle 3.11006 / 2.43 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8234 (tt0) cc_final: 0.7638 (tm-30) REVERT: B 214 ASP cc_start: 0.7127 (t70) cc_final: 0.6714 (t70) REVERT: B 504 ILE cc_start: 0.8550 (tt) cc_final: 0.8319 (tt) REVERT: B 676 TRP cc_start: 0.7708 (t60) cc_final: 0.7303 (t60) outliers start: 0 outliers final: 1 residues processed: 214 average time/residue: 0.5092 time to fit residues: 118.6736 Evaluate side-chains 137 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 612 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.2980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.0030 chunk 55 optimal weight: 4.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 ASN B 254 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN B 521 ASN B 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.095073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.076425 restraints weight = 22645.464| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.09 r_work: 0.3182 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11185 Z= 0.144 Angle : 0.658 8.862 15190 Z= 0.336 Chirality : 0.045 0.354 1735 Planarity : 0.005 0.061 1882 Dihedral : 4.872 31.726 1492 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.14 % Allowed : 13.31 % Favored : 83.56 % 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: -1.10 (0.22), residues: 1341 helix: 0.07 (0.18), residues: 715 sheet: -1.19 (0.33), residues: 223 loop : -1.71 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.015 0.001 TYR A 678 PHE 0.016 0.001 PHE A 375 TRP 0.026 0.002 TRP B 656 HIS 0.005 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (11170) covalent geometry : angle 0.64808 / 0.33 (15152) SS BOND : bond 0.00505 / 0.37 ( 7) SS BOND : angle 1.49099 / 1.02 ( 14) hydrogen bonds : bond 0.04630 / 3.15 ( 592) hydrogen bonds : angle 4.26516 / 3.02 ( 1728) link_NAG-ASN : bond 0.00694 / 0.46 ( 8) link_NAG-ASN : angle 2.80667 / 2.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8184 (tt0) cc_final: 0.7521 (tm-30) REVERT: A 861 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8114 (mp) REVERT: B 214 ASP cc_start: 0.7608 (t70) cc_final: 0.7055 (t70) REVERT: B 494 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7512 (tp) REVERT: B 504 ILE cc_start: 0.8654 (tt) cc_final: 0.8453 (tt) REVERT: B 524 ILE cc_start: 0.8167 (mm) cc_final: 0.7962 (mt) REVERT: B 571 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.6289 (ptm) REVERT: B 668 MET cc_start: 0.8129 (tmm) cc_final: 0.7886 (tmm) REVERT: B 676 TRP cc_start: 0.8001 (t60) cc_final: 0.7458 (t60) outliers start: 37 outliers final: 17 residues processed: 176 average time/residue: 0.5186 time to fit residues: 99.9180 Evaluate side-chains 158 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 668 TRP Chi-restraints excluded: chain A residue 710 LEU Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 571 MET Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 100 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 123 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.093377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075144 restraints weight = 22961.909| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.14 r_work: 0.3139 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11185 Z= 0.210 Angle : 0.663 8.719 15190 Z= 0.340 Chirality : 0.047 0.339 1735 Planarity : 0.005 0.047 1882 Dihedral : 4.785 21.884 1490 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.73 % Allowed : 17.20 % Favored : 79.07 % 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: -0.67 (0.22), residues: 1341 helix: 0.47 (0.19), residues: 715 sheet: -0.98 (0.34), residues: 221 loop : -1.63 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 620 TYR 0.016 0.002 TYR B 123 PHE 0.021 0.002 PHE A 375 TRP 0.018 0.002 TRP A 708 HIS 0.006 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (11170) covalent geometry : angle 0.65325 / 0.34 (15152) SS BOND : bond 0.00393 / 0.22 ( 7) SS BOND : angle 1.15673 / 0.85 ( 14) hydrogen bonds : bond 0.04694 / 3.23 ( 592) hydrogen bonds : angle 4.21881 / 2.99 ( 1728) link_NAG-ASN : bond 0.00692 / 0.47 ( 8) link_NAG-ASN : angle 2.82449 / 2.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8326 (tt0) cc_final: 0.7604 (tm-30) REVERT: A 610 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8272 (tt) REVERT: A 757 GLN cc_start: 0.7805 (mt0) cc_final: 0.7525 (mt0) REVERT: A 861 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8084 (mp) REVERT: B 494 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7372 (tp) REVERT: B 504 ILE cc_start: 0.8670 (tt) cc_final: 0.8456 (tt) REVERT: B 524 ILE cc_start: 0.8173 (mm) cc_final: 0.7972 (mt) REVERT: B 668 MET cc_start: 0.8094 (tmm) cc_final: 0.7803 (tmm) REVERT: B 676 TRP cc_start: 0.8038 (t60) cc_final: 0.7504 (t60) outliers start: 44 outliers final: 25 residues processed: 170 average time/residue: 0.4447 time to fit residues: 83.8839 Evaluate side-chains 163 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 668 TRP Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 131 optimal weight: 0.0170 chunk 59 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.093886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.075409 restraints weight = 22750.432| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.07 r_work: 0.3162 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11185 Z= 0.167 Angle : 0.637 8.869 15190 Z= 0.323 Chirality : 0.045 0.336 1735 Planarity : 0.004 0.046 1882 Dihedral : 4.689 21.548 1490 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.98 % Allowed : 18.90 % Favored : 77.12 % 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: -0.40 (0.23), residues: 1341 helix: 0.75 (0.19), residues: 715 sheet: -0.82 (0.36), residues: 208 loop : -1.64 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 863 TYR 0.019 0.002 TYR B 220 PHE 0.026 0.002 PHE A 339 TRP 0.016 0.001 TRP A 708 HIS 0.005 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (11170) covalent geometry : angle 0.62707 / 0.32 (15152) SS BOND : bond 0.00357 / 0.24 ( 7) SS BOND : angle 0.95301 / 0.72 ( 14) hydrogen bonds : bond 0.04290 / 2.94 ( 592) hydrogen bonds : angle 4.11383 / 2.91 ( 1728) link_NAG-ASN : bond 0.00662 / 0.44 ( 8) link_NAG-ASN : angle 2.81064 / 2.11 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8411 (tt0) cc_final: 0.7670 (tm-30) REVERT: A 610 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 736 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8350 (ptm-80) REVERT: A 752 VAL cc_start: 0.6893 (m) cc_final: 0.6670 (m) REVERT: A 814 VAL cc_start: 0.8211 (p) cc_final: 0.7993 (t) REVERT: A 861 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8065 (mp) REVERT: B 504 ILE cc_start: 0.8674 (tt) cc_final: 0.8456 (tt) REVERT: B 668 MET cc_start: 0.8086 (tmm) cc_final: 0.7833 (tmm) REVERT: B 676 TRP cc_start: 0.8001 (t60) cc_final: 0.7488 (t60) outliers start: 47 outliers final: 23 residues processed: 171 average time/residue: 0.4198 time to fit residues: 79.4810 Evaluate side-chains 164 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 668 TRP Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 736 ARG Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 91 optimal weight: 0.3980 chunk 98 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 0.0000 chunk 53 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.094352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075844 restraints weight = 22779.788| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.09 r_work: 0.3174 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11185 Z= 0.137 Angle : 0.618 9.057 15190 Z= 0.311 Chirality : 0.044 0.336 1735 Planarity : 0.004 0.045 1882 Dihedral : 4.536 20.487 1490 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.32 % Allowed : 19.15 % Favored : 76.53 % 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: -0.17 (0.23), residues: 1341 helix: 0.95 (0.19), residues: 720 sheet: -0.70 (0.36), residues: 203 loop : -1.60 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 863 TYR 0.014 0.001 TYR A 678 PHE 0.017 0.001 PHE A 375 TRP 0.015 0.001 TRP A 708 HIS 0.004 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (11170) covalent geometry : angle 0.60822 / 0.31 (15152) SS BOND : bond 0.00259 / 0.16 ( 7) SS BOND : angle 0.96124 / 0.79 ( 14) hydrogen bonds : bond 0.04015 / 2.74 ( 592) hydrogen bonds : angle 4.01813 / 2.84 ( 1728) link_NAG-ASN : bond 0.00658 / 0.44 ( 8) link_NAG-ASN : angle 2.75291 / 2.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8299 (tt0) cc_final: 0.7566 (tm-30) REVERT: A 610 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8227 (tt) REVERT: A 740 THR cc_start: 0.8940 (t) cc_final: 0.8729 (m) REVERT: A 752 VAL cc_start: 0.6832 (m) cc_final: 0.6623 (m) REVERT: A 758 LEU cc_start: 0.7555 (mm) cc_final: 0.7161 (mm) REVERT: A 814 VAL cc_start: 0.8176 (p) cc_final: 0.7833 (t) REVERT: B 494 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7289 (tp) REVERT: B 504 ILE cc_start: 0.8687 (tt) cc_final: 0.8449 (tt) REVERT: B 668 MET cc_start: 0.8082 (tmm) cc_final: 0.7667 (tmm) REVERT: B 676 TRP cc_start: 0.7968 (t60) cc_final: 0.7436 (t60) outliers start: 51 outliers final: 25 residues processed: 181 average time/residue: 0.4544 time to fit residues: 90.8621 Evaluate side-chains 171 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 107 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.094190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076137 restraints weight = 22809.074| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.16 r_work: 0.3163 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11185 Z= 0.158 Angle : 0.637 9.568 15190 Z= 0.320 Chirality : 0.045 0.335 1735 Planarity : 0.004 0.049 1882 Dihedral : 4.525 19.903 1490 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.90 % Allowed : 20.17 % Favored : 75.93 % 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: 0.02 (0.23), residues: 1341 helix: 1.12 (0.20), residues: 714 sheet: -0.62 (0.37), residues: 204 loop : -1.52 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 863 TYR 0.020 0.001 TYR B 220 PHE 0.023 0.001 PHE A 339 TRP 0.015 0.001 TRP A 708 HIS 0.005 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (11170) covalent geometry : angle 0.62801 / 0.32 (15152) SS BOND : bond 0.00292 / 0.19 ( 7) SS BOND : angle 0.94905 / 0.83 ( 14) hydrogen bonds : bond 0.04047 / 2.78 ( 592) hydrogen bonds : angle 3.99148 / 2.81 ( 1728) link_NAG-ASN : bond 0.00660 / 0.44 ( 8) link_NAG-ASN : angle 2.73257 / 2.06 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8403 (pttt) cc_final: 0.8143 (pttm) REVERT: A 340 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7317 (tpp80) REVERT: A 357 GLN cc_start: 0.8318 (tt0) cc_final: 0.7594 (tm-30) REVERT: A 610 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8229 (tt) REVERT: A 814 VAL cc_start: 0.8203 (p) cc_final: 0.7966 (t) REVERT: A 861 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8111 (mp) REVERT: B 435 ARG cc_start: 0.8421 (pmt170) cc_final: 0.8166 (ppt90) REVERT: B 494 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7345 (tp) REVERT: B 504 ILE cc_start: 0.8697 (tt) cc_final: 0.8454 (tt) REVERT: B 645 LEU cc_start: 0.7025 (tp) cc_final: 0.6095 (mp) REVERT: B 668 MET cc_start: 0.8096 (tmm) cc_final: 0.7716 (tmm) REVERT: B 669 LEU cc_start: 0.8942 (mm) cc_final: 0.8643 (mm) REVERT: B 676 TRP cc_start: 0.7973 (t60) cc_final: 0.7466 (t60) REVERT: B 694 MET cc_start: 0.7901 (mtp) cc_final: 0.7632 (mtm) outliers start: 46 outliers final: 31 residues processed: 183 average time/residue: 0.4549 time to fit residues: 91.6856 Evaluate side-chains 181 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 16 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.0020 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.094935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.076088 restraints weight = 22563.945| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.14 r_work: 0.3168 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11185 Z= 0.143 Angle : 0.635 9.710 15190 Z= 0.318 Chirality : 0.044 0.334 1735 Planarity : 0.005 0.067 1882 Dihedral : 4.504 22.963 1490 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.64 % Allowed : 21.19 % Favored : 75.17 % 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: 0.12 (0.23), residues: 1341 helix: 1.22 (0.20), residues: 714 sheet: -0.59 (0.37), residues: 204 loop : -1.50 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 863 TYR 0.013 0.001 TYR A 678 PHE 0.019 0.001 PHE A 586 TRP 0.017 0.001 TRP A 769 HIS 0.004 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (11170) covalent geometry : angle 0.62604 / 0.32 (15152) SS BOND : bond 0.00279 / 0.20 ( 7) SS BOND : angle 0.82215 / 0.70 ( 14) hydrogen bonds : bond 0.03911 / 2.68 ( 592) hydrogen bonds : angle 3.93804 / 2.77 ( 1728) link_NAG-ASN : bond 0.00655 / 0.44 ( 8) link_NAG-ASN : angle 2.70115 / 2.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8062 (t0) cc_final: 0.7862 (t0) REVERT: A 340 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7367 (tpp80) REVERT: A 357 GLN cc_start: 0.8358 (tt0) cc_final: 0.7618 (tm-30) REVERT: A 610 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8231 (tt) REVERT: A 758 LEU cc_start: 0.7520 (mm) cc_final: 0.7125 (mm) REVERT: A 814 VAL cc_start: 0.8158 (p) cc_final: 0.7921 (t) REVERT: A 861 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8086 (mp) REVERT: B 494 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7357 (tp) REVERT: B 504 ILE cc_start: 0.8703 (tt) cc_final: 0.8454 (tt) REVERT: B 668 MET cc_start: 0.8124 (tmm) cc_final: 0.7721 (tmm) REVERT: B 676 TRP cc_start: 0.7965 (t60) cc_final: 0.7422 (t60) REVERT: B 694 MET cc_start: 0.7929 (mtp) cc_final: 0.7676 (mtm) outliers start: 43 outliers final: 29 residues processed: 175 average time/residue: 0.4054 time to fit residues: 79.2034 Evaluate side-chains 174 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 728 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 88 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 595 GLN B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.094214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.075597 restraints weight = 22594.195| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.07 r_work: 0.3165 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11185 Z= 0.167 Angle : 0.663 11.017 15190 Z= 0.331 Chirality : 0.045 0.334 1735 Planarity : 0.004 0.057 1882 Dihedral : 4.548 21.897 1490 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.98 % Allowed : 21.69 % Favored : 74.32 % 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: 0.12 (0.23), residues: 1341 helix: 1.25 (0.20), residues: 708 sheet: -0.61 (0.37), residues: 204 loop : -1.50 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 863 TYR 0.022 0.002 TYR B 220 PHE 0.019 0.002 PHE A 339 TRP 0.017 0.002 TRP A 769 HIS 0.005 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (11170) covalent geometry : angle 0.65446 / 0.33 (15152) SS BOND : bond 0.00324 / 0.23 ( 7) SS BOND : angle 0.81934 / 0.68 ( 14) hydrogen bonds : bond 0.04046 / 2.77 ( 592) hydrogen bonds : angle 3.96649 / 2.79 ( 1728) link_NAG-ASN : bond 0.00646 / 0.43 ( 8) link_NAG-ASN : angle 2.69695 / 2.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 144 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.8078 (t0) cc_final: 0.7851 (t0) REVERT: A 340 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7384 (tpp80) REVERT: A 357 GLN cc_start: 0.8332 (tt0) cc_final: 0.7560 (tm-30) REVERT: A 456 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7741 (ptm160) REVERT: A 610 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 814 VAL cc_start: 0.8127 (p) cc_final: 0.7906 (t) REVERT: A 861 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8085 (mp) REVERT: B 472 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7513 (mm-30) REVERT: B 494 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7360 (tp) REVERT: B 504 ILE cc_start: 0.8662 (tt) cc_final: 0.8419 (tt) REVERT: B 645 LEU cc_start: 0.7082 (tp) cc_final: 0.6411 (mm) REVERT: B 668 MET cc_start: 0.8055 (tmm) cc_final: 0.7686 (tmm) REVERT: B 669 LEU cc_start: 0.8924 (mm) cc_final: 0.8665 (mm) REVERT: B 676 TRP cc_start: 0.7991 (t60) cc_final: 0.7436 (t60) REVERT: B 694 MET cc_start: 0.7902 (mtp) cc_final: 0.7646 (mtm) outliers start: 47 outliers final: 35 residues processed: 178 average time/residue: 0.4193 time to fit residues: 83.2612 Evaluate side-chains 179 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 57 optimal weight: 0.0770 chunk 117 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 664 GLN B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.094528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075992 restraints weight = 22576.653| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.08 r_work: 0.3174 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11185 Z= 0.149 Angle : 0.661 11.202 15190 Z= 0.328 Chirality : 0.044 0.332 1735 Planarity : 0.004 0.052 1882 Dihedral : 4.474 23.659 1490 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.47 % Allowed : 22.63 % Favored : 73.90 % 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: 0.25 (0.23), residues: 1341 helix: 1.41 (0.20), residues: 703 sheet: -0.59 (0.37), residues: 204 loop : -1.50 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 863 TYR 0.014 0.001 TYR A 678 PHE 0.021 0.001 PHE A 645 TRP 0.019 0.001 TRP A 769 HIS 0.005 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (11170) covalent geometry : angle 0.65242 / 0.33 (15152) SS BOND : bond 0.00294 / 0.22 ( 7) SS BOND : angle 0.87376 / 0.77 ( 14) hydrogen bonds : bond 0.03902 / 2.68 ( 592) hydrogen bonds : angle 3.92329 / 2.77 ( 1728) link_NAG-ASN : bond 0.00660 / 0.45 ( 8) link_NAG-ASN : angle 2.65936 / 2.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7388 (tpp80) REVERT: A 357 GLN cc_start: 0.8325 (tt0) cc_final: 0.7603 (tm-30) REVERT: A 456 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7779 (ptm160) REVERT: A 610 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8223 (tt) REVERT: A 656 ARG cc_start: 0.8263 (tmm160) cc_final: 0.7991 (tmm160) REVERT: A 657 ASN cc_start: 0.8772 (t0) cc_final: 0.8418 (m-40) REVERT: A 727 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7414 (tp) REVERT: A 766 MET cc_start: 0.7267 (ttp) cc_final: 0.6996 (tmm) REVERT: A 814 VAL cc_start: 0.8130 (p) cc_final: 0.7914 (t) REVERT: A 861 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8113 (mp) REVERT: B 87 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: B 494 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7341 (tp) REVERT: B 504 ILE cc_start: 0.8664 (tt) cc_final: 0.8420 (tt) REVERT: B 645 LEU cc_start: 0.7042 (tp) cc_final: 0.6393 (mm) REVERT: B 668 MET cc_start: 0.8027 (tmm) cc_final: 0.7657 (tmm) REVERT: B 669 LEU cc_start: 0.8930 (mm) cc_final: 0.8593 (mm) REVERT: B 676 TRP cc_start: 0.7830 (t60) cc_final: 0.7356 (t60) REVERT: B 694 MET cc_start: 0.7732 (mtp) cc_final: 0.7466 (mtm) outliers start: 41 outliers final: 29 residues processed: 173 average time/residue: 0.3786 time to fit residues: 73.2527 Evaluate side-chains 173 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 107 optimal weight: 0.1980 chunk 93 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.094467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075951 restraints weight = 22687.752| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.07 r_work: 0.3171 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11185 Z= 0.155 Angle : 0.675 11.567 15190 Z= 0.335 Chirality : 0.045 0.333 1735 Planarity : 0.005 0.073 1882 Dihedral : 4.499 23.111 1490 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.47 % Allowed : 23.05 % Favored : 73.47 % 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: 0.25 (0.23), residues: 1341 helix: 1.44 (0.20), residues: 705 sheet: -0.59 (0.37), residues: 205 loop : -1.56 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 620 TYR 0.024 0.001 TYR B 220 PHE 0.027 0.001 PHE A 586 TRP 0.034 0.001 TRP A 769 HIS 0.006 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (11170) covalent geometry : angle 0.66724 / 0.33 (15152) SS BOND : bond 0.00292 / 0.21 ( 7) SS BOND : angle 0.82895 / 0.72 ( 14) hydrogen bonds : bond 0.03930 / 2.69 ( 592) hydrogen bonds : angle 3.93076 / 2.77 ( 1728) link_NAG-ASN : bond 0.00655 / 0.44 ( 8) link_NAG-ASN : angle 2.63846 / 1.98 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7422 (tpp80) REVERT: A 357 GLN cc_start: 0.8314 (tt0) cc_final: 0.7595 (tm-30) REVERT: A 456 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7771 (ptm160) REVERT: A 610 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 656 ARG cc_start: 0.8287 (tmm160) cc_final: 0.8044 (tmm160) REVERT: A 657 ASN cc_start: 0.8770 (t0) cc_final: 0.8359 (m-40) REVERT: A 727 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7328 (tp) REVERT: A 814 VAL cc_start: 0.8123 (p) cc_final: 0.7909 (t) REVERT: A 861 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8101 (mp) REVERT: B 87 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: B 494 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7365 (tp) REVERT: B 504 ILE cc_start: 0.8667 (tt) cc_final: 0.8420 (tt) REVERT: B 645 LEU cc_start: 0.7038 (tp) cc_final: 0.6388 (mm) REVERT: B 668 MET cc_start: 0.8043 (tmm) cc_final: 0.7669 (tmm) REVERT: B 669 LEU cc_start: 0.8934 (mm) cc_final: 0.8661 (mm) REVERT: B 676 TRP cc_start: 0.7821 (t60) cc_final: 0.7344 (t60) REVERT: B 694 MET cc_start: 0.7729 (mtp) cc_final: 0.7464 (mtm) outliers start: 41 outliers final: 30 residues processed: 173 average time/residue: 0.3826 time to fit residues: 73.8170 Evaluate side-chains 175 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 456 ARG Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 654 ILE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 727 ILE Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 827 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 705 ILE Chi-restraints excluded: chain B residue 727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 82 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.094597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076037 restraints weight = 22750.400| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.08 r_work: 0.3172 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11185 Z= 0.156 Angle : 0.677 11.448 15190 Z= 0.337 Chirality : 0.045 0.333 1735 Planarity : 0.005 0.074 1882 Dihedral : 4.494 22.414 1490 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.14 % Allowed : 23.81 % Favored : 73.05 % 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: 0.30 (0.23), residues: 1341 helix: 1.48 (0.20), residues: 700 sheet: -0.59 (0.37), residues: 205 loop : -1.49 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 620 TYR 0.014 0.001 TYR A 678 PHE 0.021 0.001 PHE A 645 TRP 0.030 0.001 TRP A 769 HIS 0.006 0.001 HIS B 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (11170) covalent geometry : angle 0.66929 / 0.34 (15152) SS BOND : bond 0.00298 / 0.21 ( 7) SS BOND : angle 0.83152 / 0.72 ( 14) hydrogen bonds : bond 0.03933 / 2.70 ( 592) hydrogen bonds : angle 3.92628 / 2.77 ( 1728) link_NAG-ASN : bond 0.00652 / 0.44 ( 8) link_NAG-ASN : angle 2.62138 / 1.97 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4226.63 seconds wall clock time: 72 minutes 46.31 seconds (4366.31 seconds total)