Starting phenix.real_space_refine on Wed Sep 25 19:14:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/09_2024/7c7s_30301.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/09_2024/7c7s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/09_2024/7c7s_30301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/09_2024/7c7s_30301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/09_2024/7c7s_30301.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c7s_30301/09_2024/7c7s_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-5461/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: 6.77, per 1000 atoms: 0.62 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: 2.96 Conformation dependent library (CDL) restraints added in 1.4 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: 1.21 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: 3.28 Time building geometry restraints manager: 3.20 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: 3.060 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: 0.110 Process input model: 26.600 Find NCS groups from input model: 0.170 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:10.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.830 ------------------------------------------------------------------------------- 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 0.092 11170 Z= 0.389 Angle : 0.782 11.105 15152 Z= 0.433 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.296 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: 1.0305 time to fit residues: 241.5487 Evaluate side-chains 137 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11170 Z= 0.218 Angle : 0.655 8.533 15152 Z= 0.337 Chirality : 0.045 0.360 1735 Planarity : 0.005 0.063 1882 Dihedral : 7.934 84.332 1660 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.31 % Allowed : 13.14 % 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 (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: -1.16 (0.22), residues: 1341 helix: 0.01 (0.18), residues: 715 sheet: -1.16 (0.34), residues: 221 loop : -1.73 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 656 HIS 0.005 0.001 HIS B 355 PHE 0.017 0.001 PHE A 375 TYR 0.014 0.001 TYR A 678 ARG 0.008 0.001 ARG B 95 *********************** 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 194 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8006 (tt0) cc_final: 0.7503 (tm-30) REVERT: A 861 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 214 ASP cc_start: 0.7071 (t70) cc_final: 0.6677 (t70) REVERT: B 494 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7467 (tp) REVERT: B 504 ILE cc_start: 0.8539 (tt) cc_final: 0.8333 (tt) REVERT: B 676 TRP cc_start: 0.7709 (t60) cc_final: 0.7329 (t60) outliers start: 39 outliers final: 16 residues processed: 176 average time/residue: 1.0227 time to fit residues: 196.9476 Evaluate side-chains 156 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 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 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 68 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11170 Z= 0.252 Angle : 0.640 8.894 15152 Z= 0.327 Chirality : 0.045 0.336 1735 Planarity : 0.004 0.047 1882 Dihedral : 6.461 62.572 1658 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.39 % Allowed : 17.12 % Favored : 79.49 % 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: -0.57 (0.23), residues: 1341 helix: 0.57 (0.19), residues: 714 sheet: -0.95 (0.34), residues: 221 loop : -1.60 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 708 HIS 0.005 0.001 HIS B 355 PHE 0.019 0.001 PHE A 375 TYR 0.016 0.001 TYR B 123 ARG 0.008 0.001 ARG B 642 *********************** 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 183 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 143 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8062 (tt0) cc_final: 0.7515 (tm-30) REVERT: A 610 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 736 ARG cc_start: 0.8409 (ptm-80) cc_final: 0.8171 (ptm-80) REVERT: A 757 GLN cc_start: 0.7272 (mt0) cc_final: 0.6999 (mt0) REVERT: A 861 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.8002 (mp) REVERT: B 504 ILE cc_start: 0.8539 (tt) cc_final: 0.8316 (tt) REVERT: B 676 TRP cc_start: 0.7693 (t60) cc_final: 0.7334 (t60) outliers start: 40 outliers final: 22 residues processed: 169 average time/residue: 0.9076 time to fit residues: 169.8310 Evaluate side-chains 158 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 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 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 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 121 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 0.0010 overall best weight: 0.9190 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11170 Z= 0.259 Angle : 0.642 9.345 15152 Z= 0.324 Chirality : 0.045 0.334 1735 Planarity : 0.004 0.045 1882 Dihedral : 5.607 42.244 1658 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.64 % Allowed : 18.81 % 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: 0.79 (0.19), residues: 715 sheet: -0.78 (0.36), residues: 203 loop : -1.65 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 708 HIS 0.005 0.001 HIS B 355 PHE 0.029 0.002 PHE A 339 TYR 0.013 0.001 TYR A 678 ARG 0.008 0.000 ARG A 620 *********************** 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 186 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 143 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLN cc_start: 0.8091 (tt0) cc_final: 0.7556 (tm-30) REVERT: A 610 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8221 (tt) REVERT: A 752 VAL cc_start: 0.6513 (m) cc_final: 0.6305 (m) REVERT: A 861 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7898 (mp) REVERT: B 435 ARG cc_start: 0.7973 (pmt170) cc_final: 0.7743 (ppt90) REVERT: B 494 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7286 (tp) REVERT: B 504 ILE cc_start: 0.8557 (tt) cc_final: 0.8327 (tt) REVERT: B 676 TRP cc_start: 0.7676 (t60) cc_final: 0.7333 (t60) outliers start: 43 outliers final: 23 residues processed: 170 average time/residue: 0.9026 time to fit residues: 169.8799 Evaluate side-chains 162 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11170 Z= 0.297 Angle : 0.648 9.765 15152 Z= 0.328 Chirality : 0.046 0.335 1735 Planarity : 0.004 0.045 1882 Dihedral : 5.296 38.586 1658 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.08 % Allowed : 18.22 % Favored : 76.69 % 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: -0.27 (0.23), residues: 1341 helix: 0.84 (0.19), residues: 721 sheet: -0.74 (0.36), residues: 211 loop : -1.61 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 708 HIS 0.006 0.001 HIS B 355 PHE 0.020 0.002 PHE A 375 TYR 0.019 0.002 TYR B 220 ARG 0.004 0.000 ARG A 620 *********************** 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 203 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 143 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: A 340 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6725 (tpp80) REVERT: A 357 GLN cc_start: 0.8226 (tt0) cc_final: 0.7670 (tm-30) REVERT: A 610 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8237 (tt) REVERT: B 494 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7213 (tp) REVERT: B 504 ILE cc_start: 0.8566 (tt) cc_final: 0.8332 (tt) REVERT: B 676 TRP cc_start: 0.7680 (t60) cc_final: 0.7333 (t60) outliers start: 60 outliers final: 31 residues processed: 185 average time/residue: 1.0107 time to fit residues: 207.3626 Evaluate side-chains 171 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 584 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 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 737 THR Chi-restraints excluded: chain A residue 780 LEU 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 68 optimal weight: 0.0870 chunk 125 optimal weight: 4.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11170 Z= 0.211 Angle : 0.637 9.647 15152 Z= 0.319 Chirality : 0.044 0.334 1735 Planarity : 0.004 0.047 1882 Dihedral : 5.032 36.141 1658 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.81 % Allowed : 20.93 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.00 (0.23), residues: 1341 helix: 1.11 (0.20), residues: 716 sheet: -0.72 (0.37), residues: 205 loop : -1.50 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 769 HIS 0.004 0.001 HIS B 355 PHE 0.024 0.001 PHE A 339 TYR 0.014 0.001 TYR A 678 ARG 0.011 0.000 ARG A 356 *********************** 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 191 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: A 357 GLN cc_start: 0.8093 (tt0) cc_final: 0.7548 (tm-30) REVERT: A 610 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8197 (tt) REVERT: A 861 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 494 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7277 (tp) REVERT: B 504 ILE cc_start: 0.8581 (tt) cc_final: 0.8338 (tt) REVERT: B 645 LEU cc_start: 0.6957 (tp) cc_final: 0.6063 (mp) REVERT: B 676 TRP cc_start: 0.7616 (t60) cc_final: 0.7289 (t60) REVERT: B 694 MET cc_start: 0.7524 (mtp) cc_final: 0.7263 (mtm) outliers start: 45 outliers final: 27 residues processed: 174 average time/residue: 0.8739 time to fit residues: 169.0264 Evaluate side-chains 171 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 584 PHE 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 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 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 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 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 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11170 Z= 0.240 Angle : 0.640 10.027 15152 Z= 0.321 Chirality : 0.045 0.334 1735 Planarity : 0.004 0.046 1882 Dihedral : 4.934 34.973 1658 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.81 % Allowed : 21.53 % Favored : 74.66 % 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: 0.09 (0.23), residues: 1341 helix: 1.23 (0.20), residues: 709 sheet: -0.65 (0.37), residues: 204 loop : -1.50 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 769 HIS 0.005 0.001 HIS B 355 PHE 0.017 0.001 PHE A 645 TYR 0.013 0.001 TYR A 678 ARG 0.014 0.001 ARG A 863 *********************** 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 192 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7459 (tm-30) REVERT: A 340 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6865 (tpp80) REVERT: A 357 GLN cc_start: 0.8128 (tt0) cc_final: 0.7563 (tm-30) REVERT: A 610 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8203 (tt) REVERT: A 861 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8051 (mp) REVERT: B 494 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7308 (tp) REVERT: B 504 ILE cc_start: 0.8539 (tt) cc_final: 0.8297 (tt) REVERT: B 676 TRP cc_start: 0.7627 (t60) cc_final: 0.7266 (t60) REVERT: B 694 MET cc_start: 0.7518 (mtp) cc_final: 0.7253 (mtm) outliers start: 45 outliers final: 27 residues processed: 175 average time/residue: 0.9328 time to fit residues: 180.7093 Evaluate side-chains 171 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 584 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 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 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 727 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 88 optimal weight: 0.4980 chunk 64 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11170 Z= 0.224 Angle : 0.659 9.789 15152 Z= 0.327 Chirality : 0.044 0.335 1735 Planarity : 0.004 0.062 1882 Dihedral : 4.844 33.636 1658 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.90 % Allowed : 22.46 % Favored : 73.64 % 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: 0.20 (0.23), residues: 1341 helix: 1.32 (0.20), residues: 708 sheet: -0.59 (0.38), residues: 204 loop : -1.47 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 769 HIS 0.004 0.001 HIS B 355 PHE 0.019 0.001 PHE A 645 TYR 0.022 0.001 TYR B 220 ARG 0.011 0.000 ARG A 764 *********************** 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 185 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 139 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: A 340 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6873 (tpp80) REVERT: A 357 GLN cc_start: 0.8116 (tt0) cc_final: 0.7543 (tm-30) REVERT: A 610 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8186 (tt) REVERT: A 861 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 863 ARG cc_start: 0.7885 (tmm160) cc_final: 0.7621 (ttp80) REVERT: B 494 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7313 (tp) REVERT: B 504 ILE cc_start: 0.8540 (tt) cc_final: 0.8300 (tt) REVERT: B 645 LEU cc_start: 0.6984 (tp) cc_final: 0.6115 (mp) REVERT: B 676 TRP cc_start: 0.7485 (t60) cc_final: 0.7211 (t60) REVERT: B 694 MET cc_start: 0.7506 (mtp) cc_final: 0.7245 (mtm) outliers start: 46 outliers final: 24 residues processed: 171 average time/residue: 0.8738 time to fit residues: 165.9981 Evaluate side-chains 170 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 584 PHE 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 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 79 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11170 Z= 0.231 Angle : 0.661 10.041 15152 Z= 0.330 Chirality : 0.044 0.334 1735 Planarity : 0.004 0.056 1882 Dihedral : 4.777 32.443 1658 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.31 % Allowed : 22.97 % 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: 0.23 (0.23), residues: 1341 helix: 1.33 (0.20), residues: 714 sheet: -0.64 (0.37), residues: 204 loop : -1.42 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 769 HIS 0.005 0.001 HIS B 355 PHE 0.018 0.001 PHE A 645 TYR 0.018 0.001 TYR B 663 ARG 0.010 0.000 ARG A 764 *********************** 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 184 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: A 340 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6875 (tpp80) REVERT: A 357 GLN cc_start: 0.8154 (tt0) cc_final: 0.7605 (tm-30) REVERT: A 610 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8185 (tt) REVERT: A 861 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7848 (mp) REVERT: B 494 ILE cc_start: 0.7609 (OUTLIER) cc_final: 0.7308 (tp) REVERT: B 504 ILE cc_start: 0.8543 (tt) cc_final: 0.8299 (tt) REVERT: B 645 LEU cc_start: 0.6941 (tp) cc_final: 0.6111 (mp) REVERT: B 676 TRP cc_start: 0.7477 (t60) cc_final: 0.7217 (t60) REVERT: B 694 MET cc_start: 0.7499 (mtp) cc_final: 0.7236 (mtm) outliers start: 39 outliers final: 29 residues processed: 172 average time/residue: 0.8641 time to fit residues: 166.1576 Evaluate side-chains 176 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 366 PHE 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 608 VAL Chi-restraints excluded: chain A residue 610 LEU 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 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 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 601 VAL Chi-restraints excluded: chain B residue 652 HIS 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 128 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 134 optimal weight: 0.0000 chunk 123 optimal weight: 0.0770 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS B 652 HIS B 698 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11170 Z= 0.191 Angle : 0.675 12.891 15152 Z= 0.331 Chirality : 0.044 0.336 1735 Planarity : 0.004 0.050 1882 Dihedral : 4.600 30.563 1658 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.12 % Allowed : 25.08 % 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: 0.34 (0.24), residues: 1341 helix: 1.44 (0.20), residues: 717 sheet: -0.66 (0.37), residues: 203 loop : -1.39 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 769 HIS 0.004 0.001 HIS B 652 PHE 0.021 0.001 PHE A 645 TYR 0.024 0.001 TYR B 220 ARG 0.009 0.000 ARG A 764 ********************** 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 171 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 340 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.7000 (tpp80) REVERT: A 357 GLN cc_start: 0.8130 (tt0) cc_final: 0.7575 (tm-30) REVERT: A 610 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8071 (tt) REVERT: A 861 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7803 (mp) REVERT: B 214 ASP cc_start: 0.6959 (t70) cc_final: 0.6587 (t70) REVERT: B 494 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7292 (tp) REVERT: B 504 ILE cc_start: 0.8539 (tt) cc_final: 0.8295 (tt) REVERT: B 645 LEU cc_start: 0.6922 (tp) cc_final: 0.6105 (mp) REVERT: B 653 MET cc_start: 0.6551 (ppp) cc_final: 0.5831 (tmm) REVERT: B 676 TRP cc_start: 0.7411 (t60) cc_final: 0.7167 (t60) REVERT: B 694 MET cc_start: 0.7379 (mtp) cc_final: 0.7119 (mtm) outliers start: 25 outliers final: 16 residues processed: 164 average time/residue: 0.8582 time to fit residues: 157.0001 Evaluate side-chains 159 residues out of total 1180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 139 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ARG 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 662 VAL 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 160 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 437 VAL Chi-restraints excluded: chain B residue 470 ILE 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 727 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.094871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.076374 restraints weight = 22652.976| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.09 r_work: 0.3179 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11170 Z= 0.232 Angle : 0.674 12.355 15152 Z= 0.335 Chirality : 0.045 0.336 1735 Planarity : 0.004 0.049 1882 Dihedral : 4.616 29.722 1658 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.12 % Allowed : 25.17 % Favored : 72.71 % 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: 0.31 (0.23), residues: 1341 helix: 1.44 (0.20), residues: 707 sheet: -0.62 (0.37), residues: 202 loop : -1.42 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 769 HIS 0.005 0.001 HIS B 355 PHE 0.025 0.001 PHE A 586 TYR 0.020 0.002 TYR B 268 ARG 0.009 0.000 ARG A 764 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3905.84 seconds wall clock time: 69 minutes 39.73 seconds (4179.73 seconds total)