Starting phenix.real_space_refine on Thu Jul 2 14:45:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snm_40629/07_2026/8snm_40629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snm_40629/07_2026/8snm_40629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8snm_40629/07_2026/8snm_40629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snm_40629/07_2026/8snm_40629.map" model { file = "/net/cci-nas-00/data/ceres_data/8snm_40629/07_2026/8snm_40629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snm_40629/07_2026/8snm_40629.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.059 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 Ca 1 9.91 5 Zn 1 6.06 5 S 69 5.16 5 C 5719 2.51 5 N 1529 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8986 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3929 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 467} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1406 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 170} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3649 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5195 SG CYS A 184 44.254 25.694 36.116 1.00 74.22 S Time building chain proxies: 1.98, per 1000 atoms: 0.22 Number of scatterers: 8986 At special positions: 0 Unit cell: (70.992, 110.432, 152.83, 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) Zn 1 29.99 Ca 1 19.99 S 69 16.00 O 1667 8.00 N 1529 7.00 C 5719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS C 447 " - pdb=" SG CYS C 611 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 487 " distance=2.03 Simple disulfide: pdb=" SG CYS C 479 " - pdb=" SG CYS C 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 548 " distance=2.03 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 606 " distance=2.03 Simple disulfide: pdb=" SG CYS C 579 " - pdb=" SG CYS C 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 225 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 506 " distance=2.03 Simple disulfide: pdb=" SG CYS B 489 " - pdb=" SG CYS B 502 " distance=2.02 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 514 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 582 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 593 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 641 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 443.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 415 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 409 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 405 " pdb="ZN ZN B 901 " - pdb=" SG CYS A 184 " Number of angles added : 3 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 37.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'C' and resid 343 through 349 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 373 through 395 removed outlier: 3.710A pdb=" N TYR C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'C' and resid 451 through 467 removed outlier: 4.049A pdb=" N ASP C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 537 removed outlier: 3.816A pdb=" N ILE C 537 " --> pdb=" O GLY C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 545 Processing helix chain 'C' and resid 559 through 564 removed outlier: 3.769A pdb=" N CYS C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 590 Processing helix chain 'C' and resid 600 through 604 Processing helix chain 'C' and resid 605 through 612 removed outlier: 4.062A pdb=" N LYS C 609 " --> pdb=" O HIS C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 631 removed outlier: 3.524A pdb=" N SER C 631 " --> pdb=" O ARG C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 660 removed outlier: 4.455A pdb=" N ARG C 653 " --> pdb=" O MET C 649 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP C 654 " --> pdb=" O THR C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 683 Processing helix chain 'C' and resid 691 through 709 Processing helix chain 'C' and resid 715 through 735 removed outlier: 4.210A pdb=" N ALA C 719 " --> pdb=" O ARG C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 756 removed outlier: 3.764A pdb=" N HIS C 744 " --> pdb=" O ASP C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 795 Processing helix chain 'C' and resid 801 through 803 No H-bonds generated for 'chain 'C' and resid 801 through 803' Processing helix chain 'C' and resid 804 through 809 removed outlier: 3.879A pdb=" N THR C 808 " --> pdb=" O ILE C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 820 Processing helix chain 'A' and resid 32 through 39 removed outlier: 4.071A pdb=" N SER A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.827A pdb=" N ARG A 89 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.758A pdb=" N VAL A 156 " --> pdb=" O TRP A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 243 through 265 Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.508A pdb=" N GLY B 346 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 347 " --> pdb=" O ASP B 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 343 through 347' Processing helix chain 'B' and resid 395 through 410 Processing helix chain 'B' and resid 451 through 465 removed outlier: 3.816A pdb=" N SER B 457 " --> pdb=" O CYS B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 647 through 658 removed outlier: 3.596A pdb=" N GLN B 658 " --> pdb=" O ASP B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 671 Processing helix chain 'B' and resid 671 through 698 removed outlier: 3.528A pdb=" N SER B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) Proline residue: B 686 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 403 through 411 Processing sheet with id=AA2, first strand: chain 'C' and resid 481 through 482 Processing sheet with id=AA3, first strand: chain 'C' and resid 579 through 582 removed outlier: 3.515A pdb=" N TYR C 593 " --> pdb=" O CYS C 572 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.829A pdb=" N ARG A 126 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER A 125 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 119 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 104 through 107 removed outlier: 4.355A pdb=" N VAL A 96 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N CYS B 225 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE B 279 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU B 227 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 281 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU B 334 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS B 226 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS B 336 " --> pdb=" O LYS B 226 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 228 " --> pdb=" O HIS B 336 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE B 338 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 230 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 368 through 371 Processing sheet with id=AA7, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AA8, first strand: chain 'B' and resid 522 through 523 Processing sheet with id=AA9, first strand: chain 'B' and resid 533 through 535 Processing sheet with id=AB1, first strand: chain 'B' and resid 589 through 590 removed outlier: 4.111A pdb=" N GLU B 589 " --> pdb=" O ARG B 605 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 612 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 633 through 635 344 hydrogen bonds defined for protein. 984 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2049 1.33 - 1.46: 2684 1.46 - 1.59: 4383 1.59 - 1.72: 0 1.72 - 1.85: 83 Bond restraints: 9199 Sorted by residual: bond pdb=" C TRP B 684 " pdb=" O TRP B 684 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" CA GLY C 517 " pdb=" C GLY C 517 " ideal model delta sigma weight residual 1.509 1.481 0.028 1.04e-02 9.25e+03 7.50e+00 bond pdb=" CA SER C 516 " pdb=" CB SER C 516 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.57e-02 4.06e+03 6.54e+00 bond pdb=" CA SER C 516 " pdb=" C SER C 516 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.24e-02 6.50e+03 5.94e+00 bond pdb=" CA THR C 515 " pdb=" C THR C 515 " ideal model delta sigma weight residual 1.521 1.493 0.029 1.31e-02 5.83e+03 4.77e+00 ... (remaining 9194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 12096 1.99 - 3.98: 316 3.98 - 5.97: 39 5.97 - 7.95: 7 7.95 - 9.94: 5 Bond angle restraints: 12463 Sorted by residual: angle pdb=" N GLY C 517 " pdb=" CA GLY C 517 " pdb=" C GLY C 517 " ideal model delta sigma weight residual 111.09 102.51 8.58 1.33e+00 5.65e-01 4.16e+01 angle pdb=" N ASN A 174 " pdb=" CA ASN A 174 " pdb=" C ASN A 174 " ideal model delta sigma weight residual 108.08 117.42 -9.34 1.69e+00 3.50e-01 3.05e+01 angle pdb=" CA ASN A 174 " pdb=" C ASN A 174 " pdb=" N VAL A 175 " ideal model delta sigma weight residual 119.63 115.16 4.47 8.10e-01 1.52e+00 3.04e+01 angle pdb=" C ASN A 174 " pdb=" CA ASN A 174 " pdb=" CB ASN A 174 " ideal model delta sigma weight residual 116.63 110.23 6.40 1.16e+00 7.43e-01 3.04e+01 angle pdb=" C ALA B 270 " pdb=" CA ALA B 270 " pdb=" CB ALA B 270 " ideal model delta sigma weight residual 116.54 110.56 5.98 1.15e+00 7.56e-01 2.71e+01 ... (remaining 12458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5039 17.72 - 35.44: 401 35.44 - 53.16: 63 53.16 - 70.88: 21 70.88 - 88.60: 8 Dihedral angle restraints: 5532 sinusoidal: 2239 harmonic: 3293 Sorted by residual: dihedral pdb=" CB CYS B 582 " pdb=" SG CYS B 582 " pdb=" SG CYS B 604 " pdb=" CB CYS B 604 " ideal model delta sinusoidal sigma weight residual -86.00 -174.60 88.60 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 591 " pdb=" SG CYS B 591 " pdb=" SG CYS B 611 " pdb=" CB CYS B 611 " ideal model delta sinusoidal sigma weight residual -86.00 -150.88 64.88 1 1.00e+01 1.00e-02 5.52e+01 dihedral pdb=" CB CYS B 514 " pdb=" SG CYS B 514 " pdb=" SG CYS B 522 " pdb=" CB CYS B 522 " ideal model delta sinusoidal sigma weight residual -86.00 -142.84 56.84 1 1.00e+01 1.00e-02 4.35e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1068 0.052 - 0.104: 254 0.104 - 0.156: 39 0.156 - 0.207: 3 0.207 - 0.259: 2 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA ASN A 174 " pdb=" N ASN A 174 " pdb=" C ASN A 174 " pdb=" CB ASN A 174 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA VAL C 430 " pdb=" N VAL C 430 " pdb=" C VAL C 430 " pdb=" CB VAL C 430 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA SER B 608 " pdb=" N SER B 608 " pdb=" C SER B 608 " pdb=" CB SER B 608 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1363 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 612 " -0.089 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO B 613 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO B 613 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 613 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 312 " -0.014 2.00e-02 2.50e+03 1.95e-02 9.55e+00 pdb=" CG TRP B 312 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 312 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 312 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 312 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 312 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 312 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 312 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 312 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 312 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 685 " 0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO B 686 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 686 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 686 " 0.042 5.00e-02 4.00e+02 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 511 2.73 - 3.27: 9305 3.27 - 3.81: 14987 3.81 - 4.36: 18810 4.36 - 4.90: 31509 Nonbonded interactions: 75122 Sorted by model distance: nonbonded pdb=" OE1 GLN C 624 " pdb=" OH TYR C 626 " model vdw 2.183 3.040 nonbonded pdb=" OD2 ASP C 475 " pdb=" OG1 THR A 62 " model vdw 2.187 3.040 nonbonded pdb=" OH TYR B 340 " pdb=" OG1 THR B 393 " model vdw 2.207 3.040 nonbonded pdb=" NH1 ARG A 89 " pdb=" OG1 THR A 116 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THR C 376 " pdb=" OE1 GLU C 656 " model vdw 2.209 3.040 ... (remaining 75117 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 group one per residue 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: 3.470 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 9225 Z= 0.239 Angle : 0.763 15.422 12510 Z= 0.447 Chirality : 0.046 0.259 1366 Planarity : 0.006 0.133 1602 Dihedral : 13.051 83.445 3344 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.24), residues: 1126 helix: 0.98 (0.27), residues: 358 sheet: -0.21 (0.48), residues: 111 loop : -1.36 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 372 TYR 0.012 0.001 TYR C 797 PHE 0.015 0.001 PHE B 323 TRP 0.050 0.002 TRP B 312 HIS 0.009 0.001 HIS B 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.22 ( 9199) covalent geometry : angle 0.74325 / 0.44 (12463) SS BOND : bond 0.00318 / 0.20 ( 22) SS BOND : angle 1.72893 / 1.15 ( 44) hydrogen bonds : bond 0.14106 / 9.56 ( 344) hydrogen bonds : angle 6.41998 / 4.69 ( 984) metal coordination : bond 0.08411 / 4.36 ( 4) metal coordination : angle 9.45740 / 3.62 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 434 SER cc_start: 0.8184 (m) cc_final: 0.7874 (p) REVERT: C 515 THR cc_start: 0.8782 (p) cc_final: 0.8226 (t) REVERT: C 529 GLU cc_start: 0.7223 (tt0) cc_final: 0.6676 (tt0) REVERT: C 694 SER cc_start: 0.8856 (m) cc_final: 0.8547 (p) REVERT: C 728 LEU cc_start: 0.7914 (tp) cc_final: 0.7714 (mm) REVERT: B 224 THR cc_start: 0.9035 (m) cc_final: 0.8532 (p) REVERT: B 564 ASP cc_start: 0.6807 (m-30) cc_final: 0.5907 (t0) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1193 time to fit residues: 41.1800 Evaluate side-chains 110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.0050 chunk 106 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 403 GLN C 555 ASN C 695 GLN A 52 GLN A 92 GLN B 320 GLN B 444 HIS B 621 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.115840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093859 restraints weight = 18443.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096943 restraints weight = 10435.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099073 restraints weight = 7275.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100481 restraints weight = 5744.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101297 restraints weight = 4915.290| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9225 Z= 0.148 Angle : 0.638 9.136 12510 Z= 0.330 Chirality : 0.044 0.167 1366 Planarity : 0.005 0.084 1602 Dihedral : 4.672 24.008 1221 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.72 % Allowed : 10.61 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1126 helix: 1.52 (0.27), residues: 362 sheet: -0.15 (0.47), residues: 118 loop : -1.28 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 412 TYR 0.025 0.001 TYR C 685 PHE 0.017 0.001 PHE B 655 TRP 0.015 0.001 TRP B 312 HIS 0.005 0.001 HIS C 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 9199) covalent geometry : angle 0.62633 / 0.33 (12463) SS BOND : bond 0.00455 / 0.32 ( 22) SS BOND : angle 1.78589 / 1.37 ( 44) hydrogen bonds : bond 0.03921 / 2.60 ( 344) hydrogen bonds : angle 5.12395 / 3.67 ( 984) metal coordination : bond 0.02756 / 1.37 ( 4) metal coordination : angle 4.65308 / 2.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 412 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.7978 (mmm-85) REVERT: C 515 THR cc_start: 0.8346 (p) cc_final: 0.8024 (t) REVERT: C 555 ASN cc_start: 0.8334 (OUTLIER) cc_final: 0.7946 (t0) REVERT: C 618 ASN cc_start: 0.8772 (t0) cc_final: 0.8422 (t0) REVERT: C 694 SER cc_start: 0.8901 (m) cc_final: 0.8486 (p) REVERT: C 740 ASP cc_start: 0.6143 (p0) cc_final: 0.5666 (p0) REVERT: A 61 GLN cc_start: 0.8338 (tt0) cc_final: 0.7962 (tm-30) REVERT: B 232 ASP cc_start: 0.8458 (t0) cc_final: 0.8206 (t0) REVERT: B 267 TRP cc_start: 0.7647 (m100) cc_final: 0.7283 (m100) REVERT: B 564 ASP cc_start: 0.6474 (m-30) cc_final: 0.5503 (t0) REVERT: B 652 PHE cc_start: 0.8555 (t80) cc_final: 0.8339 (t80) REVERT: B 693 CYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7703 (t) outliers start: 17 outliers final: 5 residues processed: 141 average time/residue: 0.1006 time to fit residues: 19.8074 Evaluate side-chains 102 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 1 optimal weight: 0.0770 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.0570 chunk 56 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 555 ASN C 676 ASN C 800 ASN A 92 GLN B 621 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.114838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093006 restraints weight = 18245.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096132 restraints weight = 10229.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098236 restraints weight = 7079.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.099607 restraints weight = 5574.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100578 restraints weight = 4771.156| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9225 Z= 0.119 Angle : 0.574 9.199 12510 Z= 0.295 Chirality : 0.042 0.145 1366 Planarity : 0.005 0.067 1602 Dihedral : 4.475 24.002 1221 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.02 % Allowed : 13.33 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.24), residues: 1126 helix: 1.88 (0.27), residues: 357 sheet: -0.16 (0.47), residues: 122 loop : -1.27 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 610 TYR 0.014 0.001 TYR C 685 PHE 0.011 0.001 PHE C 668 TRP 0.012 0.001 TRP A 153 HIS 0.005 0.001 HIS C 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 9199) covalent geometry : angle 0.56354 / 0.29 (12463) SS BOND : bond 0.00318 / 0.22 ( 22) SS BOND : angle 1.61818 / 1.25 ( 44) hydrogen bonds : bond 0.03478 / 2.32 ( 344) hydrogen bonds : angle 4.81005 / 3.44 ( 984) metal coordination : bond 0.02138 / 1.06 ( 4) metal coordination : angle 3.72660 / 1.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.7871 (t0) cc_final: 0.6872 (p0) REVERT: C 515 THR cc_start: 0.8238 (p) cc_final: 0.7889 (t) REVERT: C 562 MET cc_start: 0.8314 (mmm) cc_final: 0.8086 (ttm) REVERT: C 618 ASN cc_start: 0.8640 (t0) cc_final: 0.8404 (t0) REVERT: B 435 MET cc_start: 0.8909 (mmm) cc_final: 0.8207 (mmm) REVERT: B 693 CYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7731 (t) outliers start: 20 outliers final: 10 residues processed: 119 average time/residue: 0.0937 time to fit residues: 16.1640 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 762 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 92 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 555 ASN C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 HIS C 648 GLN C 800 ASN A 65 HIS A 92 GLN ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 497 ASN B 535 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.105807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.084136 restraints weight = 18834.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.086847 restraints weight = 10956.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088683 restraints weight = 7795.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089563 restraints weight = 6266.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.090533 restraints weight = 5553.395| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9225 Z= 0.250 Angle : 0.702 9.831 12510 Z= 0.362 Chirality : 0.047 0.164 1366 Planarity : 0.005 0.052 1602 Dihedral : 4.906 24.004 1221 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.54 % Allowed : 14.34 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1126 helix: 1.54 (0.27), residues: 357 sheet: -0.01 (0.47), residues: 114 loop : -1.37 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 412 TYR 0.016 0.002 TYR C 685 PHE 0.022 0.002 PHE B 655 TRP 0.014 0.002 TRP C 738 HIS 0.005 0.001 HIS B 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 ( 9199) covalent geometry : angle 0.69348 / 0.36 (12463) SS BOND : bond 0.00439 / 0.30 ( 22) SS BOND : angle 1.51351 / 1.18 ( 44) hydrogen bonds : bond 0.04633 / 3.13 ( 344) hydrogen bonds : angle 5.00210 / 3.56 ( 984) metal coordination : bond 0.03891 / 1.93 ( 4) metal coordination : angle 4.57711 / 2.34 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8504 (t0) cc_final: 0.7509 (p0) REVERT: C 436 ASP cc_start: 0.8186 (m-30) cc_final: 0.7910 (m-30) REVERT: C 515 THR cc_start: 0.8298 (p) cc_final: 0.7994 (t) REVERT: C 562 MET cc_start: 0.8666 (mmm) cc_final: 0.8372 (ttm) REVERT: B 583 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: B 689 ILE cc_start: 0.8922 (mm) cc_final: 0.8666 (mt) REVERT: B 693 CYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7689 (t) outliers start: 35 outliers final: 16 residues processed: 140 average time/residue: 0.0960 time to fit residues: 19.1135 Evaluate side-chains 110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 555 ASN ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.113281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.090554 restraints weight = 18619.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.093328 restraints weight = 11212.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.095218 restraints weight = 8148.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096139 restraints weight = 6624.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.097180 restraints weight = 5893.658| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9225 Z= 0.166 Angle : 0.639 14.965 12510 Z= 0.323 Chirality : 0.043 0.151 1366 Planarity : 0.004 0.052 1602 Dihedral : 4.644 23.787 1221 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.53 % Allowed : 16.16 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1126 helix: 1.63 (0.28), residues: 358 sheet: -0.04 (0.48), residues: 112 loop : -1.33 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 412 TYR 0.011 0.001 TYR C 593 PHE 0.012 0.001 PHE C 668 TRP 0.021 0.001 TRP B 267 HIS 0.008 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 ( 9199) covalent geometry : angle 0.63114 / 0.32 (12463) SS BOND : bond 0.00290 / 0.21 ( 22) SS BOND : angle 1.60906 / 1.24 ( 44) hydrogen bonds : bond 0.03854 / 2.61 ( 344) hydrogen bonds : angle 4.78872 / 3.41 ( 984) metal coordination : bond 0.02596 / 1.28 ( 4) metal coordination : angle 2.97520 / 1.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8390 (t0) cc_final: 0.7692 (p0) REVERT: C 515 THR cc_start: 0.8208 (p) cc_final: 0.7912 (t) REVERT: C 562 MET cc_start: 0.8634 (mmm) cc_final: 0.8328 (ttm) REVERT: C 618 ASN cc_start: 0.8538 (t0) cc_final: 0.8189 (t0) REVERT: B 689 ILE cc_start: 0.8944 (mm) cc_final: 0.8654 (mt) outliers start: 25 outliers final: 15 residues processed: 117 average time/residue: 0.0954 time to fit residues: 15.8281 Evaluate side-chains 108 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 43 optimal weight: 0.0020 chunk 8 optimal weight: 0.9980 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090308 restraints weight = 18684.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093095 restraints weight = 11198.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094952 restraints weight = 8145.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096172 restraints weight = 6633.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.096887 restraints weight = 5803.906| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9225 Z= 0.161 Angle : 0.624 12.606 12510 Z= 0.312 Chirality : 0.043 0.169 1366 Planarity : 0.004 0.051 1602 Dihedral : 4.491 24.100 1221 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.63 % Allowed : 17.68 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1126 helix: 1.75 (0.28), residues: 358 sheet: -0.06 (0.48), residues: 108 loop : -1.27 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.010 0.001 TYR C 593 PHE 0.023 0.001 PHE B 652 TRP 0.058 0.002 TRP C 738 HIS 0.005 0.001 HIS C 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 9199) covalent geometry : angle 0.61751 / 0.31 (12463) SS BOND : bond 0.00282 / 0.19 ( 22) SS BOND : angle 1.34500 / 1.04 ( 44) hydrogen bonds : bond 0.03664 / 2.49 ( 344) hydrogen bonds : angle 4.69532 / 3.33 ( 984) metal coordination : bond 0.02488 / 1.23 ( 4) metal coordination : angle 3.48588 / 1.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8430 (t0) cc_final: 0.7805 (p0) REVERT: C 515 THR cc_start: 0.8149 (p) cc_final: 0.7869 (t) REVERT: C 562 MET cc_start: 0.8609 (mmm) cc_final: 0.8304 (ttm) REVERT: A 170 GLU cc_start: 0.8192 (mp0) cc_final: 0.7856 (mp0) REVERT: B 583 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: B 689 ILE cc_start: 0.8916 (mm) cc_final: 0.8703 (mt) outliers start: 26 outliers final: 19 residues processed: 117 average time/residue: 0.0984 time to fit residues: 15.8427 Evaluate side-chains 109 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 694 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 555 ASN C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087315 restraints weight = 18948.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090174 restraints weight = 11116.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092132 restraints weight = 7958.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.093222 restraints weight = 6425.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.094216 restraints weight = 5642.062| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9225 Z= 0.120 Angle : 0.597 10.936 12510 Z= 0.300 Chirality : 0.042 0.141 1366 Planarity : 0.004 0.050 1602 Dihedral : 4.327 23.815 1221 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.73 % Allowed : 19.09 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.24), residues: 1126 helix: 1.97 (0.28), residues: 356 sheet: -0.08 (0.49), residues: 106 loop : -1.17 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 412 TYR 0.009 0.001 TYR C 593 PHE 0.013 0.001 PHE C 668 TRP 0.036 0.001 TRP C 738 HIS 0.015 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9199) covalent geometry : angle 0.59316 / 0.30 (12463) SS BOND : bond 0.00190 / 0.13 ( 22) SS BOND : angle 1.17866 / 0.91 ( 44) hydrogen bonds : bond 0.03363 / 2.28 ( 344) hydrogen bonds : angle 4.61135 / 3.26 ( 984) metal coordination : bond 0.01318 / 0.66 ( 4) metal coordination : angle 1.85560 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8388 (t0) cc_final: 0.7876 (p0) REVERT: C 515 THR cc_start: 0.8076 (p) cc_final: 0.7755 (t) REVERT: C 562 MET cc_start: 0.8650 (mmm) cc_final: 0.8335 (ttm) REVERT: A 30 GLN cc_start: 0.6497 (mm110) cc_final: 0.6121 (mp10) REVERT: A 61 GLN cc_start: 0.8127 (tt0) cc_final: 0.7437 (tm-30) REVERT: A 64 THR cc_start: 0.7257 (m) cc_final: 0.7053 (m) REVERT: A 170 GLU cc_start: 0.8273 (mp0) cc_final: 0.8033 (mp0) REVERT: B 583 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7645 (mm-30) outliers start: 27 outliers final: 17 residues processed: 124 average time/residue: 0.1078 time to fit residues: 18.5637 Evaluate side-chains 113 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 800 ASN Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 668 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.109960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087249 restraints weight = 19043.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.090063 restraints weight = 11196.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.091933 restraints weight = 8035.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093147 restraints weight = 6520.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093838 restraints weight = 5699.426| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9225 Z= 0.135 Angle : 0.598 11.222 12510 Z= 0.303 Chirality : 0.043 0.266 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.296 23.425 1221 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.03 % Allowed : 19.09 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1126 helix: 1.98 (0.28), residues: 356 sheet: -0.12 (0.49), residues: 106 loop : -1.13 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 412 TYR 0.027 0.001 TYR B 340 PHE 0.024 0.001 PHE B 652 TRP 0.034 0.001 TRP C 738 HIS 0.005 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 9199) covalent geometry : angle 0.59542 / 0.30 (12463) SS BOND : bond 0.00201 / 0.14 ( 22) SS BOND : angle 1.11140 / 0.87 ( 44) hydrogen bonds : bond 0.03427 / 2.32 ( 344) hydrogen bonds : angle 4.60317 / 3.25 ( 984) metal coordination : bond 0.01594 / 0.79 ( 4) metal coordination : angle 1.56719 / 0.83 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8374 (t0) cc_final: 0.7892 (p0) REVERT: C 515 THR cc_start: 0.8146 (p) cc_final: 0.7843 (t) REVERT: C 562 MET cc_start: 0.8667 (mmm) cc_final: 0.8349 (ttm) REVERT: C 736 LEU cc_start: 0.8562 (tt) cc_final: 0.8017 (pp) REVERT: A 30 GLN cc_start: 0.6560 (mm110) cc_final: 0.6092 (mp10) REVERT: A 61 GLN cc_start: 0.8103 (tt0) cc_final: 0.7618 (tm-30) REVERT: A 64 THR cc_start: 0.7399 (m) cc_final: 0.7128 (m) REVERT: A 170 GLU cc_start: 0.8287 (mp0) cc_final: 0.8071 (mp0) REVERT: B 583 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7663 (mm-30) outliers start: 30 outliers final: 21 residues processed: 117 average time/residue: 0.1006 time to fit residues: 16.6112 Evaluate side-chains 115 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 721 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 555 ASN C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.109208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.086393 restraints weight = 18904.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089315 restraints weight = 10928.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.091263 restraints weight = 7785.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092507 restraints weight = 6275.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093382 restraints weight = 5460.057| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9225 Z= 0.139 Angle : 0.608 12.103 12510 Z= 0.306 Chirality : 0.043 0.258 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.284 23.039 1221 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.73 % Allowed : 19.60 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1126 helix: 1.98 (0.28), residues: 356 sheet: -0.13 (0.49), residues: 106 loop : -1.14 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 139 TYR 0.037 0.001 TYR B 340 PHE 0.026 0.001 PHE B 652 TRP 0.025 0.001 TRP C 738 HIS 0.009 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 9199) covalent geometry : angle 0.60544 / 0.30 (12463) SS BOND : bond 0.00222 / 0.15 ( 22) SS BOND : angle 1.12259 / 0.87 ( 44) hydrogen bonds : bond 0.03425 / 2.33 ( 344) hydrogen bonds : angle 4.59667 / 3.24 ( 984) metal coordination : bond 0.01664 / 0.83 ( 4) metal coordination : angle 1.55980 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8381 (t0) cc_final: 0.7957 (p0) REVERT: C 515 THR cc_start: 0.8141 (p) cc_final: 0.7837 (t) REVERT: C 562 MET cc_start: 0.8707 (mmm) cc_final: 0.8412 (ttm) REVERT: A 30 GLN cc_start: 0.6790 (mm110) cc_final: 0.6388 (mp10) REVERT: A 61 GLN cc_start: 0.8090 (tt0) cc_final: 0.7621 (tm-30) REVERT: A 64 THR cc_start: 0.7362 (m) cc_final: 0.7103 (m) REVERT: A 153 TRP cc_start: 0.8623 (p-90) cc_final: 0.7723 (p-90) REVERT: B 583 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7567 (mm-30) outliers start: 27 outliers final: 23 residues processed: 112 average time/residue: 0.0958 time to fit residues: 15.2441 Evaluate side-chains 117 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 790 LEU Chi-restraints excluded: chain C residue 800 ASN Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 683 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 20 optimal weight: 0.0770 chunk 80 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 555 ASN C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.087681 restraints weight = 18768.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.090506 restraints weight = 11015.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092430 restraints weight = 7917.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.093542 restraints weight = 6405.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094519 restraints weight = 5619.696| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9225 Z= 0.113 Angle : 0.596 13.067 12510 Z= 0.298 Chirality : 0.042 0.235 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.244 23.082 1221 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.53 % Allowed : 19.70 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.25), residues: 1126 helix: 2.02 (0.28), residues: 357 sheet: -0.09 (0.49), residues: 106 loop : -1.15 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 412 TYR 0.030 0.001 TYR B 340 PHE 0.025 0.001 PHE B 652 TRP 0.033 0.001 TRP C 738 HIS 0.012 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 9199) covalent geometry : angle 0.59369 / 0.30 (12463) SS BOND : bond 0.00219 / 0.15 ( 22) SS BOND : angle 1.04497 / 0.81 ( 44) hydrogen bonds : bond 0.03265 / 2.22 ( 344) hydrogen bonds : angle 4.52801 / 3.19 ( 984) metal coordination : bond 0.01093 / 0.54 ( 4) metal coordination : angle 1.43131 / 0.76 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8344 (t0) cc_final: 0.7979 (p0) REVERT: C 515 THR cc_start: 0.8078 (p) cc_final: 0.7778 (t) REVERT: C 562 MET cc_start: 0.8720 (mmm) cc_final: 0.8414 (ttm) REVERT: C 736 LEU cc_start: 0.8589 (tt) cc_final: 0.8074 (pp) REVERT: A 30 GLN cc_start: 0.6844 (mm110) cc_final: 0.6505 (mp10) REVERT: A 61 GLN cc_start: 0.8079 (tt0) cc_final: 0.7623 (tm-30) REVERT: A 64 THR cc_start: 0.7177 (m) cc_final: 0.6943 (m) REVERT: A 153 TRP cc_start: 0.8601 (p-90) cc_final: 0.7770 (p-90) REVERT: B 389 ASN cc_start: 0.8185 (t0) cc_final: 0.7843 (t0) REVERT: B 583 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: B 588 LEU cc_start: 0.8254 (mt) cc_final: 0.7625 (mt) REVERT: B 601 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7988 (mttm) outliers start: 25 outliers final: 21 residues processed: 115 average time/residue: 0.0988 time to fit residues: 16.1081 Evaluate side-chains 116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 703 PHE Chi-restraints excluded: chain C residue 717 TRP Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 800 ASN Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 683 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 800 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.110575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.087718 restraints weight = 18746.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090546 restraints weight = 11091.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.092402 restraints weight = 7998.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093723 restraints weight = 6492.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.094341 restraints weight = 5646.110| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9225 Z= 0.124 Angle : 0.603 12.902 12510 Z= 0.301 Chirality : 0.043 0.279 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.193 22.804 1221 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.42 % Allowed : 19.80 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1126 helix: 2.03 (0.28), residues: 357 sheet: -0.04 (0.49), residues: 106 loop : -1.15 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 412 TYR 0.042 0.001 TYR B 340 PHE 0.024 0.001 PHE B 652 TRP 0.024 0.001 TRP C 738 HIS 0.007 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 9199) covalent geometry : angle 0.60143 / 0.30 (12463) SS BOND : bond 0.00183 / 0.13 ( 22) SS BOND : angle 0.96536 / 0.74 ( 44) hydrogen bonds : bond 0.03302 / 2.24 ( 344) hydrogen bonds : angle 4.52770 / 3.19 ( 984) metal coordination : bond 0.01352 / 0.67 ( 4) metal coordination : angle 1.53219 / 0.81 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1618.80 seconds wall clock time: 28 minutes 55.86 seconds (1735.86 seconds total)