Starting phenix.real_space_refine on Tue Jul 29 05:29:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c7s_30301/07_2025/7c7s_30301.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c7s_30301/07_2025/7c7s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7c7s_30301/07_2025/7c7s_30301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c7s_30301/07_2025/7c7s_30301.map" model { file = "/net/cci-nas-00/data/ceres_data/7c7s_30301/07_2025/7c7s_30301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c7s_30301/07_2025/7c7s_30301.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 15 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.67, per 1000 atoms: 0.70 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: 2.76 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.26 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: 3.93 Time building geometry restraints manager: 3.15 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 - 21.38: 6307 21.38 - 42.75: 383 42.75 - 64.13: 49 64.13 - 85.51: 10 85.51 - 106.89: 8 Dihedral angle restraints: 6757 sinusoidal: 2820 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 6754 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: 2.110 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.710 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 13.958 106.886 4202 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.002 TRP A 708 HIS 0.007 0.001 HIS B 355 PHE 0.023 0.002 PHE A 375 TYR 0.016 0.002 TYR B 697 ARG 0.009 0.001 ARG B 637 Details of bonding type rmsd link_NAG-ASN : bond 0.00936 ( 8) link_NAG-ASN : angle 3.11006 ( 24) hydrogen bonds : bond 0.13568 ( 592) hydrogen bonds : angle 5.60653 ( 1728) SS BOND : bond 0.09118 ( 7) SS BOND : angle 7.09833 ( 14) covalent geometry : bond 0.00601 (11170) covalent geometry : angle 0.78178 (15152) *********************** 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 : 1.192 Fit side-chains revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8234 (tt0) cc_final: 0.7639 (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: 0.8320 (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: 1.0325 time to fit residues: 241.7016 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 : 1.206 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 0.0970 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 chunk 78 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 254 GLN 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 = 0.3734 r_free = 0.3734 target = 0.095305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076749 restraints weight = 22416.962| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.06 r_work: 0.3189 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1674 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= 0.137 Angle : 0.660 8.994 15190 Z= 0.335 Chirality : 0.045 0.357 1735 Planarity : 0.005 0.062 1882 Dihedral : 7.738 82.200 1660 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.88 % Allowed : 13.47 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1341 helix: 0.08 (0.18), residues: 715 sheet: -1.13 (0.34), residues: 221 loop : -1.71 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 656 HIS 0.004 0.001 HIS B 355 PHE 0.015 0.001 PHE A 375 TYR 0.015 0.001 TYR A 678 ARG 0.011 0.001 ARG A 863 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 8) link_NAG-ASN : angle 2.87746 ( 24) hydrogen bonds : bond 0.04618 ( 592) hydrogen bonds : angle 4.26543 ( 1728) SS BOND : bond 0.00170 ( 7) SS BOND : angle 1.44017 ( 14) covalent geometry : bond 0.00296 (11170) covalent geometry : angle 0.64902 (15152) *********************** 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 190 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8167 (tt0) cc_final: 0.7496 (tm-30) REVERT: A 814 VAL cc_start: 0.8225 (p) cc_final: 0.8024 (t) REVERT: A 861 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8114 (mp) REVERT: A 863 ARG cc_start: 0.7743 (ttp80) cc_final: 0.7514 (tmm160) REVERT: B 214 ASP cc_start: 0.7573 (t70) cc_final: 0.7014 (t70) REVERT: B 275 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8537 (t) REVERT: B 494 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7509 (tp) REVERT: B 524 ILE cc_start: 0.8150 (mm) cc_final: 0.7945 (mt) REVERT: B 656 TRP cc_start: 0.7441 (m100) cc_final: 0.6276 (m-10) REVERT: B 668 MET cc_start: 0.8115 (tmm) cc_final: 0.7889 (tmm) REVERT: B 676 TRP cc_start: 0.7996 (t60) cc_final: 0.7440 (t60) outliers start: 34 outliers final: 12 residues processed: 174 average time/residue: 1.0615 time to fit residues: 202.5350 Evaluate side-chains 155 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 559 ASP 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 827 SER Chi-restraints excluded: chain A residue 861 ILE Chi-restraints excluded: chain B residue 275 SER 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 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 133 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.076703 restraints weight = 22778.538| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.11 r_work: 0.3176 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11185 Z= 0.145 Angle : 0.628 8.841 15190 Z= 0.317 Chirality : 0.044 0.336 1735 Planarity : 0.004 0.045 1882 Dihedral : 6.200 59.265 1658 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.88 % Allowed : 17.12 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.23), residues: 1341 helix: 0.67 (0.19), residues: 715 sheet: -0.93 (0.34), residues: 221 loop : -1.60 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 708 HIS 0.004 0.001 HIS B 355 PHE 0.017 0.001 PHE A 375 TYR 0.018 0.001 TYR B 220 ARG 0.008 0.000 ARG B 642 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 8) link_NAG-ASN : angle 2.82381 ( 24) hydrogen bonds : bond 0.04237 ( 592) hydrogen bonds : angle 4.10459 ( 1728) SS BOND : bond 0.00297 ( 7) SS BOND : angle 0.99909 ( 14) covalent geometry : bond 0.00332 (11170) covalent geometry : angle 0.61819 (15152) *********************** 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 179 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8242 (tt0) cc_final: 0.7530 (tm-30) REVERT: A 610 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8179 (tt) REVERT: A 757 GLN cc_start: 0.7746 (mt0) cc_final: 0.7430 (mt0) REVERT: A 814 VAL cc_start: 0.8246 (p) cc_final: 0.8029 (t) REVERT: A 861 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7993 (mp) REVERT: B 435 ARG cc_start: 0.8327 (pmt170) cc_final: 0.8081 (ppt90) REVERT: B 668 MET cc_start: 0.8091 (tmm) cc_final: 0.7790 (tmm) REVERT: B 676 TRP cc_start: 0.7979 (t60) cc_final: 0.7448 (t60) REVERT: B 694 MET cc_start: 0.7901 (mtp) cc_final: 0.7630 (mtm) outliers start: 34 outliers final: 17 residues processed: 167 average time/residue: 0.9767 time to fit residues: 179.1977 Evaluate side-chains 154 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 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 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 470 ILE Chi-restraints excluded: chain B residue 491 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3708 r_free = 0.3708 target = 0.093742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.075232 restraints weight = 22728.157| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.07 r_work: 0.3156 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11185 Z= 0.189 Angle : 0.657 8.826 15190 Z= 0.329 Chirality : 0.046 0.331 1735 Planarity : 0.005 0.044 1882 Dihedral : 5.522 41.299 1658 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.81 % Allowed : 18.64 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.23), residues: 1341 helix: 0.80 (0.19), residues: 714 sheet: -0.77 (0.36), residues: 203 loop : -1.68 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 708 HIS 0.006 0.001 HIS B 355 PHE 0.026 0.002 PHE A 339 TYR 0.012 0.002 TYR A 678 ARG 0.011 0.001 ARG A 863 Details of bonding type rmsd link_NAG-ASN : bond 0.00698 ( 8) link_NAG-ASN : angle 2.99796 ( 24) hydrogen bonds : bond 0.04393 ( 592) hydrogen bonds : angle 4.12021 ( 1728) SS BOND : bond 0.00355 ( 7) SS BOND : angle 0.89959 ( 14) covalent geometry : bond 0.00453 (11170) covalent geometry : angle 0.64592 (15152) *********************** 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 191 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 146 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8316 (tt0) cc_final: 0.7577 (tm-30) REVERT: A 610 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8253 (tt) REVERT: A 814 VAL cc_start: 0.8205 (p) cc_final: 0.8003 (t) REVERT: A 861 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 435 ARG cc_start: 0.8402 (pmt170) cc_final: 0.8150 (ppt90) REVERT: B 494 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7234 (tp) REVERT: B 668 MET cc_start: 0.8082 (tmm) cc_final: 0.7826 (tmm) REVERT: B 676 TRP cc_start: 0.8018 (t60) cc_final: 0.7505 (t60) outliers start: 45 outliers final: 23 residues processed: 175 average time/residue: 0.8749 time to fit residues: 170.5674 Evaluate side-chains 162 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 617 SER Chi-restraints excluded: chain A residue 662 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 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 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 484 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE 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 83 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 117 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 119 optimal weight: 0.0270 chunk 39 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.076215 restraints weight = 22625.837| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.09 r_work: 0.3181 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2390 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= 0.135 Angle : 0.627 8.943 15190 Z= 0.312 Chirality : 0.044 0.334 1735 Planarity : 0.004 0.041 1882 Dihedral : 5.049 37.746 1658 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.31 % Allowed : 19.83 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1341 helix: 1.12 (0.20), residues: 716 sheet: -0.67 (0.37), residues: 203 loop : -1.51 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 708 HIS 0.004 0.001 HIS B 355 PHE 0.019 0.001 PHE A 375 TYR 0.014 0.001 TYR A 678 ARG 0.004 0.000 ARG A 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 8) link_NAG-ASN : angle 3.03239 ( 24) hydrogen bonds : bond 0.03916 ( 592) hydrogen bonds : angle 3.97448 ( 1728) SS BOND : bond 0.00375 ( 7) SS BOND : angle 0.83814 ( 14) covalent geometry : bond 0.00312 (11170) covalent geometry : angle 0.61536 (15152) *********************** 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 187 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 308 LYS cc_start: 0.8411 (pttt) cc_final: 0.8170 (pttm) REVERT: A 357 GLN cc_start: 0.8299 (tt0) cc_final: 0.7563 (tm-30) REVERT: A 610 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8146 (tt) REVERT: A 758 LEU cc_start: 0.7627 (mm) cc_final: 0.7224 (mm) REVERT: A 814 VAL cc_start: 0.8146 (p) cc_final: 0.7806 (t) REVERT: B 494 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7301 (tp) REVERT: B 645 LEU cc_start: 0.7023 (tp) cc_final: 0.6107 (mp) REVERT: B 668 MET cc_start: 0.8070 (tmm) cc_final: 0.7678 (tmm) REVERT: B 676 TRP cc_start: 0.7958 (t60) cc_final: 0.7442 (t60) REVERT: B 694 MET cc_start: 0.7891 (mtp) cc_final: 0.7638 (mtm) outliers start: 39 outliers final: 19 residues processed: 177 average time/residue: 0.9355 time to fit residues: 182.8227 Evaluate side-chains 163 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 662 VAL 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 327 ILE 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 470 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 728 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 23 optimal weight: 0.0020 chunk 62 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3727 r_free = 0.3727 target = 0.094728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.076560 restraints weight = 22708.504| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.15 r_work: 0.3178 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11185 Z= 0.134 Angle : 0.633 9.864 15190 Z= 0.312 Chirality : 0.044 0.333 1735 Planarity : 0.004 0.039 1882 Dihedral : 4.861 35.454 1658 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.31 % Allowed : 21.10 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1341 helix: 1.24 (0.20), residues: 715 sheet: -0.61 (0.37), residues: 203 loop : -1.47 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 769 HIS 0.004 0.001 HIS B 355 PHE 0.023 0.001 PHE A 339 TYR 0.021 0.001 TYR B 220 ARG 0.012 0.000 ARG A 863 Details of bonding type rmsd link_NAG-ASN : bond 0.00685 ( 8) link_NAG-ASN : angle 3.02142 ( 24) hydrogen bonds : bond 0.03837 ( 592) hydrogen bonds : angle 3.91133 ( 1728) SS BOND : bond 0.00233 ( 7) SS BOND : angle 0.83057 ( 14) covalent geometry : bond 0.00311 (11170) covalent geometry : angle 0.62162 (15152) *********************** 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 186 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8327 (tt0) cc_final: 0.7570 (tm-30) REVERT: A 610 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8131 (tt) REVERT: A 758 LEU cc_start: 0.7620 (mm) cc_final: 0.7152 (mm) REVERT: A 814 VAL cc_start: 0.8194 (p) cc_final: 0.7909 (t) REVERT: A 861 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8073 (mp) REVERT: B 494 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7302 (tp) REVERT: B 668 MET cc_start: 0.8073 (tmm) cc_final: 0.7684 (tmm) REVERT: B 669 LEU cc_start: 0.8941 (mm) cc_final: 0.8637 (mm) REVERT: B 676 TRP cc_start: 0.7979 (t60) cc_final: 0.7405 (t60) REVERT: B 694 MET cc_start: 0.7871 (mtp) cc_final: 0.7630 (mtm) outliers start: 39 outliers final: 22 residues processed: 175 average time/residue: 0.9042 time to fit residues: 174.6066 Evaluate side-chains 164 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 693 THR 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 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 229 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 391 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 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 657 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 25 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.094356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076247 restraints weight = 23031.708| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.19 r_work: 0.3159 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2570 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= 0.162 Angle : 0.650 9.950 15190 Z= 0.323 Chirality : 0.045 0.335 1735 Planarity : 0.005 0.061 1882 Dihedral : 4.854 33.813 1658 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.73 % Allowed : 22.20 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1341 helix: 1.21 (0.20), residues: 715 sheet: -0.61 (0.37), residues: 204 loop : -1.42 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 769 HIS 0.005 0.001 HIS B 355 PHE 0.017 0.001 PHE A 375 TYR 0.013 0.001 TYR A 678 ARG 0.011 0.000 ARG A 620 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 8) link_NAG-ASN : angle 3.10374 ( 24) hydrogen bonds : bond 0.03993 ( 592) hydrogen bonds : angle 3.93514 ( 1728) SS BOND : bond 0.00249 ( 7) SS BOND : angle 0.69618 ( 14) covalent geometry : bond 0.00386 (11170) covalent geometry : angle 0.63895 (15152) *********************** 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: 44 poor density : 145 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8309 (tt0) cc_final: 0.7589 (tm-30) REVERT: A 610 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8202 (tt) REVERT: A 814 VAL cc_start: 0.8079 (p) cc_final: 0.7846 (t) REVERT: A 861 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8047 (mp) REVERT: B 494 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7333 (tp) REVERT: B 645 LEU cc_start: 0.7105 (tp) cc_final: 0.6207 (mp) REVERT: B 668 MET cc_start: 0.8101 (tmm) cc_final: 0.7678 (tmm) REVERT: B 676 TRP cc_start: 0.7992 (t60) cc_final: 0.7428 (t60) REVERT: B 694 MET cc_start: 0.7862 (mtp) cc_final: 0.7616 (mtm) outliers start: 44 outliers final: 32 residues processed: 177 average time/residue: 0.8971 time to fit residues: 176.8657 Evaluate side-chains 175 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 PHE 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 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 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 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 494 ILE Chi-restraints excluded: chain B residue 524 ILE Chi-restraints excluded: chain B residue 530 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 58 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 49 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3733 r_free = 0.3733 target = 0.095151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.076585 restraints weight = 22527.408| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.09 r_work: 0.3191 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11185 Z= 0.128 Angle : 0.640 9.700 15190 Z= 0.316 Chirality : 0.044 0.335 1735 Planarity : 0.004 0.060 1882 Dihedral : 4.691 32.162 1658 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.88 % Allowed : 23.39 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1341 helix: 1.38 (0.20), residues: 714 sheet: -0.58 (0.38), residues: 203 loop : -1.39 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 769 HIS 0.003 0.001 HIS B 355 PHE 0.019 0.001 PHE A 645 TYR 0.022 0.001 TYR B 220 ARG 0.017 0.001 ARG A 863 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 8) link_NAG-ASN : angle 3.08077 ( 24) hydrogen bonds : bond 0.03713 ( 592) hydrogen bonds : angle 3.87351 ( 1728) SS BOND : bond 0.00238 ( 7) SS BOND : angle 0.66986 ( 14) covalent geometry : bond 0.00293 (11170) covalent geometry : angle 0.62894 (15152) *********************** 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 177 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLU cc_start: 0.7541 (pm20) cc_final: 0.7020 (pm20) REVERT: A 357 GLN cc_start: 0.8297 (tt0) cc_final: 0.7569 (tm-30) REVERT: A 610 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8098 (tt) REVERT: A 747 LYS cc_start: 0.8681 (tppt) cc_final: 0.8452 (tppt) REVERT: A 814 VAL cc_start: 0.8120 (p) cc_final: 0.7867 (t) REVERT: A 861 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8081 (mp) REVERT: B 494 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7278 (tp) REVERT: B 645 LEU cc_start: 0.7008 (tp) cc_final: 0.6373 (mm) REVERT: B 668 MET cc_start: 0.8066 (tmm) cc_final: 0.7665 (tmm) REVERT: B 669 LEU cc_start: 0.8925 (mm) cc_final: 0.8602 (mm) REVERT: B 676 TRP cc_start: 0.7819 (t60) cc_final: 0.7332 (t60) REVERT: B 694 MET cc_start: 0.7822 (mtp) cc_final: 0.7583 (mtm) outliers start: 34 outliers final: 23 residues processed: 170 average time/residue: 0.8959 time to fit residues: 169.2502 Evaluate side-chains 162 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 668 TRP 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 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 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 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 657 LEU Chi-restraints excluded: chain B residue 727 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 1 optimal weight: 0.0570 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 HIS B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.096405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077763 restraints weight = 22773.392| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.15 r_work: 0.3199 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11185 Z= 0.135 Angle : 0.644 10.735 15190 Z= 0.320 Chirality : 0.044 0.335 1735 Planarity : 0.005 0.056 1882 Dihedral : 4.623 30.658 1658 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.71 % Allowed : 24.07 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1341 helix: 1.48 (0.20), residues: 709 sheet: -0.60 (0.36), residues: 214 loop : -1.37 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 769 HIS 0.005 0.001 HIS B 652 PHE 0.020 0.001 PHE A 645 TYR 0.016 0.001 TYR B 663 ARG 0.016 0.001 ARG A 656 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 8) link_NAG-ASN : angle 3.06810 ( 24) hydrogen bonds : bond 0.03733 ( 592) hydrogen bonds : angle 3.85623 ( 1728) SS BOND : bond 0.00225 ( 7) SS BOND : angle 0.66851 ( 14) covalent geometry : bond 0.00315 (11170) covalent geometry : angle 0.63316 (15152) *********************** 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 175 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8373 (tt0) cc_final: 0.7611 (tm-30) REVERT: A 610 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 747 LYS cc_start: 0.8621 (tppt) cc_final: 0.8386 (tppt) REVERT: A 766 MET cc_start: 0.7339 (ttp) cc_final: 0.7047 (tmm) REVERT: A 814 VAL cc_start: 0.8231 (p) cc_final: 0.7931 (t) REVERT: A 861 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.8075 (mp) REVERT: B 494 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7364 (tp) REVERT: B 645 LEU cc_start: 0.7157 (tp) cc_final: 0.6494 (mm) REVERT: B 668 MET cc_start: 0.7967 (tmm) cc_final: 0.7576 (tmm) REVERT: B 669 LEU cc_start: 0.8947 (mm) cc_final: 0.8592 (mm) REVERT: B 676 TRP cc_start: 0.7783 (t60) cc_final: 0.7328 (t60) REVERT: B 694 MET cc_start: 0.7731 (mtp) cc_final: 0.7464 (mtm) outliers start: 32 outliers final: 24 residues processed: 168 average time/residue: 0.9062 time to fit residues: 169.2500 Evaluate side-chains 165 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER 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 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 576 TRP Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 663 TYR 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 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 70 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.096214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077690 restraints weight = 22579.659| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.11 r_work: 0.3202 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11185 Z= 0.144 Angle : 0.673 13.028 15190 Z= 0.332 Chirality : 0.044 0.336 1735 Planarity : 0.004 0.054 1882 Dihedral : 4.605 29.702 1658 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.63 % Allowed : 24.07 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1341 helix: 1.47 (0.20), residues: 709 sheet: -0.64 (0.35), residues: 214 loop : -1.35 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 769 HIS 0.007 0.001 HIS B 652 PHE 0.022 0.001 PHE A 586 TYR 0.024 0.001 TYR B 220 ARG 0.012 0.001 ARG A 863 Details of bonding type rmsd link_NAG-ASN : bond 0.00663 ( 8) link_NAG-ASN : angle 3.07352 ( 24) hydrogen bonds : bond 0.03765 ( 592) hydrogen bonds : angle 3.85206 ( 1728) SS BOND : bond 0.00231 ( 7) SS BOND : angle 0.68286 ( 14) covalent geometry : bond 0.00336 (11170) covalent geometry : angle 0.66251 (15152) ********************** 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 174 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8417 (tt0) cc_final: 0.7663 (tm-30) REVERT: A 610 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8069 (tt) REVERT: A 727 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7200 (tp) REVERT: A 747 LYS cc_start: 0.8607 (tppt) cc_final: 0.8386 (tppt) REVERT: A 814 VAL cc_start: 0.8188 (p) cc_final: 0.7908 (t) REVERT: A 861 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7926 (mp) REVERT: B 233 SER cc_start: 0.8892 (m) cc_final: 0.8686 (t) REVERT: B 645 LEU cc_start: 0.7163 (tp) cc_final: 0.6247 (mp) REVERT: B 668 MET cc_start: 0.7997 (tmm) cc_final: 0.7592 (tmm) REVERT: B 669 LEU cc_start: 0.8969 (mm) cc_final: 0.8606 (mm) REVERT: B 676 TRP cc_start: 0.7762 (t60) cc_final: 0.7317 (t60) REVERT: B 694 MET cc_start: 0.7696 (mtp) cc_final: 0.7432 (mtm) outliers start: 31 outliers final: 21 residues processed: 167 average time/residue: 0.8460 time to fit residues: 157.1196 Evaluate side-chains 162 residues out of total 1180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 617 SER 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 391 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 727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 HIS B 698 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.095708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.077146 restraints weight = 22483.735| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.12 r_work: 0.3188 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11185 Z= 0.164 Angle : 0.685 12.000 15190 Z= 0.339 Chirality : 0.045 0.335 1735 Planarity : 0.005 0.084 1882 Dihedral : 4.650 28.656 1658 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.54 % Allowed : 24.66 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1341 helix: 1.47 (0.20), residues: 704 sheet: -0.71 (0.34), residues: 224 loop : -1.32 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 769 HIS 0.006 0.001 HIS B 652 PHE 0.020 0.001 PHE A 645 TYR 0.027 0.002 TYR B 663 ARG 0.019 0.001 ARG A 656 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 8) link_NAG-ASN : angle 3.10688 ( 24) hydrogen bonds : bond 0.03952 ( 592) hydrogen bonds : angle 3.88270 ( 1728) SS BOND : bond 0.00266 ( 7) SS BOND : angle 0.71266 ( 14) covalent geometry : bond 0.00390 (11170) covalent geometry : angle 0.67404 (15152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9213.21 seconds wall clock time: 158 minutes 59.20 seconds (9539.20 seconds total)