Starting phenix.real_space_refine on Mon May 12 14:00:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snm_40629/05_2025/8snm_40629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snm_40629/05_2025/8snm_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_40629/05_2025/8snm_40629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snm_40629/05_2025/8snm_40629.map" model { file = "/net/cci-nas-00/data/ceres_data/8snm_40629/05_2025/8snm_40629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snm_40629/05_2025/8snm_40629.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN: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: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 6.12, per 1000 atoms: 0.68 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: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.04 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: 2.62 Time building geometry restraints manager: 2.95 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: 2.220 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.570 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (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 TRP 0.050 0.002 TRP B 312 HIS 0.009 0.001 HIS B 405 PHE 0.015 0.001 PHE B 323 TYR 0.012 0.001 TYR C 797 ARG 0.008 0.001 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.14106 ( 344) hydrogen bonds : angle 6.41998 ( 984) metal coordination : bond 0.08411 ( 4) metal coordination : angle 9.45740 ( 3) SS BOND : bond 0.00318 ( 22) SS BOND : angle 1.72893 ( 44) covalent geometry : bond 0.00414 ( 9199) covalent geometry : angle 0.74325 (12463) *********************** 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 : 1.084 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: 0.7222 (tt0) cc_final: 0.6675 (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: 0.5906 (t0) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2635 time to fit residues: 90.3149 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 : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0010 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.0470 chunk 28 optimal weight: 0.0570 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 overall best weight: 0.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN C 695 GLN A 52 GLN A 92 GLN B 320 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.118029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096079 restraints weight = 18025.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099282 restraints weight = 10191.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.101457 restraints weight = 7097.901| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9225 Z= 0.128 Angle : 0.633 8.899 12510 Z= 0.326 Chirality : 0.043 0.161 1366 Planarity : 0.005 0.084 1602 Dihedral : 4.635 24.038 1221 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.92 % Allowed : 10.00 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1126 helix: 1.56 (0.27), residues: 362 sheet: -0.18 (0.47), residues: 120 loop : -1.27 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 312 HIS 0.006 0.001 HIS B 692 PHE 0.018 0.001 PHE B 655 TYR 0.023 0.001 TYR C 685 ARG 0.005 0.001 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 344) hydrogen bonds : angle 5.16815 ( 984) metal coordination : bond 0.02422 ( 4) metal coordination : angle 5.36017 ( 3) SS BOND : bond 0.00396 ( 22) SS BOND : angle 1.86948 ( 44) covalent geometry : bond 0.00292 ( 9199) covalent geometry : angle 0.61923 (12463) *********************** 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 151 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 412 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.7976 (mmm-85) REVERT: C 515 THR cc_start: 0.8328 (p) cc_final: 0.7964 (t) REVERT: C 529 GLU cc_start: 0.7607 (tt0) cc_final: 0.7154 (tt0) REVERT: C 555 ASN cc_start: 0.8356 (OUTLIER) cc_final: 0.7962 (t0) REVERT: C 618 ASN cc_start: 0.8724 (t0) cc_final: 0.8311 (t0) REVERT: C 694 SER cc_start: 0.8832 (m) cc_final: 0.8425 (p) REVERT: C 740 ASP cc_start: 0.6142 (p0) cc_final: 0.5621 (p0) REVERT: C 816 PHE cc_start: 0.7764 (t80) cc_final: 0.7561 (t80) REVERT: A 61 GLN cc_start: 0.8325 (tt0) cc_final: 0.7985 (tm-30) REVERT: B 267 TRP cc_start: 0.7629 (m100) cc_final: 0.7251 (m100) REVERT: B 345 MET cc_start: 0.7875 (mmp) cc_final: 0.7599 (mmm) REVERT: B 564 ASP cc_start: 0.6420 (m-30) cc_final: 0.5390 (t0) REVERT: B 693 CYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7746 (t) outliers start: 19 outliers final: 8 residues processed: 143 average time/residue: 0.2246 time to fit residues: 44.2035 Evaluate side-chains 100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 463 ASP Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain B residue 365 CYS Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 668 LEU 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 107 optimal weight: 5.9990 chunk 86 optimal weight: 0.0010 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 GLN C 425 GLN ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 HIS C 800 ASN A 65 HIS A 92 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091080 restraints weight = 18835.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.094153 restraints weight = 10787.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.096228 restraints weight = 7578.231| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9225 Z= 0.163 Angle : 0.604 9.249 12510 Z= 0.312 Chirality : 0.043 0.145 1366 Planarity : 0.005 0.066 1602 Dihedral : 4.536 23.848 1221 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.22 % Allowed : 12.22 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.24), residues: 1126 helix: 1.81 (0.27), residues: 356 sheet: -0.06 (0.47), residues: 120 loop : -1.27 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 738 HIS 0.006 0.001 HIS C 556 PHE 0.013 0.001 PHE B 321 TYR 0.016 0.001 TYR C 685 ARG 0.006 0.001 ARG B 610 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 344) hydrogen bonds : angle 4.85402 ( 984) metal coordination : bond 0.02958 ( 4) metal coordination : angle 4.17494 ( 3) SS BOND : bond 0.00458 ( 22) SS BOND : angle 1.62599 ( 44) covalent geometry : bond 0.00373 ( 9199) covalent geometry : angle 0.59432 (12463) *********************** 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 128 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.069 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: 0.8040 (t0) cc_final: 0.6945 (p0) REVERT: C 515 THR cc_start: 0.8239 (p) cc_final: 0.7924 (t) REVERT: C 562 MET cc_start: 0.8392 (mmm) cc_final: 0.8167 (ttm) REVERT: C 618 ASN cc_start: 0.8657 (t0) cc_final: 0.8406 (t0) REVERT: C 694 SER cc_start: 0.8972 (m) cc_final: 0.8560 (p) REVERT: A 64 THR cc_start: 0.7415 (m) cc_final: 0.7164 (m) REVERT: B 435 MET cc_start: 0.9012 (mmm) cc_final: 0.8257 (mmm) REVERT: B 693 CYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7716 (t) outliers start: 22 outliers final: 10 residues processed: 119 average time/residue: 0.1989 time to fit residues: 33.8443 Evaluate side-chains 94 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 265 THR 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 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN C 635 HIS C 800 ASN A 92 GLN B 535 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088997 restraints weight = 18396.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.091961 restraints weight = 10507.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.093990 restraints weight = 7436.418| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9225 Z= 0.137 Angle : 0.559 8.140 12510 Z= 0.290 Chirality : 0.042 0.154 1366 Planarity : 0.004 0.059 1602 Dihedral : 4.397 23.519 1221 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.42 % Allowed : 14.14 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.24), residues: 1126 helix: 1.88 (0.28), residues: 359 sheet: -0.05 (0.48), residues: 120 loop : -1.20 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 267 HIS 0.004 0.001 HIS C 556 PHE 0.023 0.001 PHE B 655 TYR 0.010 0.001 TYR C 685 ARG 0.006 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 344) hydrogen bonds : angle 4.67303 ( 984) metal coordination : bond 0.02084 ( 4) metal coordination : angle 2.71496 ( 3) SS BOND : bond 0.00216 ( 22) SS BOND : angle 1.52324 ( 44) covalent geometry : bond 0.00320 ( 9199) covalent geometry : angle 0.55125 (12463) *********************** 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 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8105 (t0) cc_final: 0.7367 (p0) REVERT: C 515 THR cc_start: 0.8246 (p) cc_final: 0.7912 (t) REVERT: C 562 MET cc_start: 0.8434 (mmm) cc_final: 0.7914 (ttt) REVERT: C 618 ASN cc_start: 0.8579 (t0) cc_final: 0.8366 (t0) REVERT: C 694 SER cc_start: 0.8928 (m) cc_final: 0.8493 (p) REVERT: B 693 CYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7712 (t) outliers start: 24 outliers final: 10 residues processed: 119 average time/residue: 0.1959 time to fit residues: 33.6010 Evaluate side-chains 99 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 463 ASP 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 A residue 69 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 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 61 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 A 92 GLN B 497 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089109 restraints weight = 18595.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.091791 restraints weight = 11326.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.093631 restraints weight = 8367.006| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9225 Z= 0.248 Angle : 0.685 15.042 12510 Z= 0.345 Chirality : 0.045 0.145 1366 Planarity : 0.005 0.055 1602 Dihedral : 4.670 23.698 1221 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.03 % Allowed : 14.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1126 helix: 1.64 (0.27), residues: 358 sheet: 0.06 (0.48), residues: 112 loop : -1.31 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 153 HIS 0.005 0.001 HIS C 635 PHE 0.020 0.002 PHE B 652 TYR 0.012 0.002 TYR B 304 ARG 0.005 0.001 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 344) hydrogen bonds : angle 4.83640 ( 984) metal coordination : bond 0.03816 ( 4) metal coordination : angle 3.74851 ( 3) SS BOND : bond 0.00356 ( 22) SS BOND : angle 1.67809 ( 44) covalent geometry : bond 0.00579 ( 9199) covalent geometry : angle 0.67677 (12463) *********************** 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 124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8457 (t0) cc_final: 0.7663 (p0) REVERT: C 515 THR cc_start: 0.8242 (p) cc_final: 0.7943 (t) REVERT: C 562 MET cc_start: 0.8609 (mmm) cc_final: 0.8332 (ttm) REVERT: C 694 SER cc_start: 0.9020 (m) cc_final: 0.8634 (p) REVERT: A 170 GLU cc_start: 0.8120 (mp0) cc_final: 0.7902 (mp0) REVERT: B 435 MET cc_start: 0.8892 (mmm) cc_final: 0.8314 (mmm) REVERT: B 693 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7626 (t) outliers start: 30 outliers final: 16 residues processed: 114 average time/residue: 0.2040 time to fit residues: 32.7818 Evaluate side-chains 104 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 689 VAL 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 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 602 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 670 ASP Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.092124 restraints weight = 18553.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.094945 restraints weight = 11071.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.096775 restraints weight = 8029.402| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9225 Z= 0.132 Angle : 0.591 11.816 12510 Z= 0.298 Chirality : 0.042 0.147 1366 Planarity : 0.004 0.050 1602 Dihedral : 4.477 23.933 1221 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.42 % Allowed : 15.86 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.24), residues: 1126 helix: 1.85 (0.28), residues: 360 sheet: -0.02 (0.48), residues: 112 loop : -1.23 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 738 HIS 0.014 0.001 HIS C 556 PHE 0.019 0.001 PHE C 812 TYR 0.008 0.001 TYR C 593 ARG 0.006 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 344) hydrogen bonds : angle 4.64350 ( 984) metal coordination : bond 0.01865 ( 4) metal coordination : angle 2.33464 ( 3) SS BOND : bond 0.00219 ( 22) SS BOND : angle 1.33818 ( 44) covalent geometry : bond 0.00307 ( 9199) covalent geometry : angle 0.58529 (12463) *********************** 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 118 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 1.398 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: 0.7775 (p0) REVERT: C 515 THR cc_start: 0.8139 (p) cc_final: 0.7828 (t) REVERT: C 555 ASN cc_start: 0.8309 (OUTLIER) cc_final: 0.8095 (t0) REVERT: C 562 MET cc_start: 0.8578 (mmm) cc_final: 0.8290 (ttm) REVERT: C 694 SER cc_start: 0.8910 (m) cc_final: 0.8464 (p) REVERT: B 435 MET cc_start: 0.8802 (mmm) cc_final: 0.8101 (mmm) outliers start: 24 outliers final: 17 residues processed: 110 average time/residue: 0.2430 time to fit residues: 37.2288 Evaluate side-chains 102 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE 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 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 400 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 0.0000 chunk 88 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092151 restraints weight = 18713.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095020 restraints weight = 11148.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096944 restraints weight = 8056.126| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9225 Z= 0.126 Angle : 0.575 10.747 12510 Z= 0.289 Chirality : 0.042 0.144 1366 Planarity : 0.004 0.050 1602 Dihedral : 4.326 23.874 1221 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.53 % Allowed : 17.17 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1126 helix: 2.03 (0.28), residues: 357 sheet: 0.04 (0.49), residues: 108 loop : -1.22 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 738 HIS 0.005 0.001 HIS C 635 PHE 0.022 0.001 PHE B 652 TYR 0.008 0.001 TYR C 626 ARG 0.007 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03375 ( 344) hydrogen bonds : angle 4.57047 ( 984) metal coordination : bond 0.01295 ( 4) metal coordination : angle 1.87292 ( 3) SS BOND : bond 0.00239 ( 22) SS BOND : angle 1.20596 ( 44) covalent geometry : bond 0.00292 ( 9199) covalent geometry : angle 0.57120 (12463) *********************** 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 122 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8347 (t0) cc_final: 0.7901 (p0) REVERT: C 515 THR cc_start: 0.8067 (p) cc_final: 0.7755 (t) REVERT: C 555 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.8004 (t0) REVERT: C 562 MET cc_start: 0.8515 (mmm) cc_final: 0.8248 (ttm) REVERT: C 650 THR cc_start: 0.8558 (m) cc_final: 0.8218 (m) REVERT: C 694 SER cc_start: 0.8874 (m) cc_final: 0.8436 (p) REVERT: B 435 MET cc_start: 0.8769 (mmm) cc_final: 0.8102 (mmm) outliers start: 25 outliers final: 19 residues processed: 114 average time/residue: 0.2284 time to fit residues: 36.2108 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 : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 717 TRP 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 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 88 GLU 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 Chi-restraints excluded: chain B residue 670 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 95 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN C 556 HIS ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.110823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088024 restraints weight = 18940.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.090909 restraints weight = 11024.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092819 restraints weight = 7902.564| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.5324 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= 0.116 Angle : 0.562 11.265 12510 Z= 0.283 Chirality : 0.042 0.142 1366 Planarity : 0.004 0.050 1602 Dihedral : 4.287 23.699 1221 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.73 % Allowed : 17.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1126 helix: 2.11 (0.28), residues: 357 sheet: -0.04 (0.49), residues: 108 loop : -1.16 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP C 738 HIS 0.008 0.001 HIS C 556 PHE 0.012 0.001 PHE C 668 TYR 0.027 0.001 TYR B 340 ARG 0.007 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 344) hydrogen bonds : angle 4.51510 ( 984) metal coordination : bond 0.01196 ( 4) metal coordination : angle 1.58925 ( 3) SS BOND : bond 0.00168 ( 22) SS BOND : angle 1.12845 ( 44) covalent geometry : bond 0.00271 ( 9199) covalent geometry : angle 0.55835 (12463) *********************** 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 127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8266 (t0) cc_final: 0.7868 (p0) REVERT: C 515 THR cc_start: 0.8115 (p) cc_final: 0.7794 (t) REVERT: C 562 MET cc_start: 0.8486 (mmm) cc_final: 0.8232 (ttm) REVERT: C 650 THR cc_start: 0.8331 (m) cc_final: 0.8031 (m) REVERT: C 694 SER cc_start: 0.8896 (m) cc_final: 0.8440 (p) REVERT: A 30 GLN cc_start: 0.6475 (mm110) cc_final: 0.6166 (mp10) REVERT: A 61 GLN cc_start: 0.8208 (tt0) cc_final: 0.7829 (tm-30) REVERT: A 153 TRP cc_start: 0.8567 (p-90) cc_final: 0.7685 (p-90) REVERT: B 435 MET cc_start: 0.8813 (mmm) cc_final: 0.8058 (mmm) outliers start: 27 outliers final: 20 residues processed: 118 average time/residue: 0.2252 time to fit residues: 37.2356 Evaluate side-chains 111 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 490 THR 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 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE 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 88 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0770 chunk 17 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.110582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.087622 restraints weight = 18871.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.090554 restraints weight = 10918.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092525 restraints weight = 7800.723| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9225 Z= 0.123 Angle : 0.573 10.783 12510 Z= 0.290 Chirality : 0.042 0.145 1366 Planarity : 0.004 0.048 1602 Dihedral : 4.257 23.555 1221 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.53 % Allowed : 18.08 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1126 helix: 2.11 (0.28), residues: 358 sheet: -0.05 (0.49), residues: 108 loop : -1.16 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 738 HIS 0.006 0.001 HIS B 297 PHE 0.024 0.001 PHE B 652 TYR 0.034 0.001 TYR B 340 ARG 0.007 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 344) hydrogen bonds : angle 4.54941 ( 984) metal coordination : bond 0.01362 ( 4) metal coordination : angle 1.67672 ( 3) SS BOND : bond 0.00189 ( 22) SS BOND : angle 1.06083 ( 44) covalent geometry : bond 0.00288 ( 9199) covalent geometry : angle 0.56974 (12463) *********************** 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 121 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8276 (t0) cc_final: 0.7910 (p0) REVERT: C 515 THR cc_start: 0.8116 (p) cc_final: 0.7798 (t) REVERT: C 562 MET cc_start: 0.8503 (mmm) cc_final: 0.8268 (ttm) REVERT: C 650 THR cc_start: 0.8205 (m) cc_final: 0.7935 (m) REVERT: C 694 SER cc_start: 0.8867 (m) cc_final: 0.8411 (p) REVERT: A 30 GLN cc_start: 0.6623 (mm110) cc_final: 0.5998 (mp10) REVERT: A 61 GLN cc_start: 0.8185 (tt0) cc_final: 0.7866 (tm-30) REVERT: A 153 TRP cc_start: 0.8603 (p-90) cc_final: 0.7738 (p-90) REVERT: B 435 MET cc_start: 0.8832 (mmm) cc_final: 0.8077 (mmm) outliers start: 25 outliers final: 19 residues processed: 113 average time/residue: 0.2310 time to fit residues: 36.2216 Evaluate side-chains 107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 537 ILE 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 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 781 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 88 GLU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 602 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 111 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 74 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 350 ASN C 555 ASN ** C 595 HIS ** 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 = 0.3632 r_free = 0.3632 target = 0.115022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092505 restraints weight = 18661.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095349 restraints weight = 11100.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097252 restraints weight = 7980.956| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9225 Z= 0.123 Angle : 0.593 11.492 12510 Z= 0.299 Chirality : 0.042 0.236 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.221 22.571 1221 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.22 % Allowed : 18.48 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1126 helix: 2.12 (0.28), residues: 360 sheet: -0.03 (0.48), residues: 108 loop : -1.13 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 738 HIS 0.004 0.001 HIS C 635 PHE 0.032 0.001 PHE C 812 TYR 0.027 0.001 TYR B 340 ARG 0.009 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 344) hydrogen bonds : angle 4.52591 ( 984) metal coordination : bond 0.01321 ( 4) metal coordination : angle 1.66320 ( 3) SS BOND : bond 0.00176 ( 22) SS BOND : angle 0.93565 ( 44) covalent geometry : bond 0.00291 ( 9199) covalent geometry : angle 0.59137 (12463) ********************** 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 116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8279 (t0) cc_final: 0.8052 (p0) REVERT: C 515 THR cc_start: 0.8019 (p) cc_final: 0.7715 (t) REVERT: C 562 MET cc_start: 0.8487 (mmm) cc_final: 0.8232 (ttm) REVERT: C 650 THR cc_start: 0.8193 (m) cc_final: 0.7948 (m) REVERT: C 694 SER cc_start: 0.8824 (m) cc_final: 0.8413 (p) REVERT: A 30 GLN cc_start: 0.6470 (mm110) cc_final: 0.6153 (mp10) REVERT: A 61 GLN cc_start: 0.8184 (tt0) cc_final: 0.7900 (tm-30) REVERT: A 153 TRP cc_start: 0.8546 (p-90) cc_final: 0.7713 (p-90) REVERT: B 389 ASN cc_start: 0.8288 (t0) cc_final: 0.7837 (t0) REVERT: B 435 MET cc_start: 0.8789 (mmm) cc_final: 0.8069 (mmm) REVERT: B 693 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7197 (m) outliers start: 22 outliers final: 16 residues processed: 108 average time/residue: 0.2120 time to fit residues: 31.8520 Evaluate side-chains 105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 537 ILE 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 728 LEU Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 88 GLU 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 400 ASP Chi-restraints excluded: chain B residue 570 LEU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 693 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.0050 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 555 ASN ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.090789 restraints weight = 18533.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093553 restraints weight = 11139.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.095421 restraints weight = 8090.051| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9225 Z= 0.145 Angle : 0.615 11.802 12510 Z= 0.308 Chirality : 0.042 0.197 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.258 22.531 1221 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.92 % Allowed : 19.39 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1126 helix: 2.15 (0.28), residues: 358 sheet: -0.13 (0.47), residues: 112 loop : -1.12 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 738 HIS 0.004 0.001 HIS C 635 PHE 0.012 0.001 PHE C 668 TYR 0.035 0.001 TYR B 340 ARG 0.008 0.000 ARG C 412 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 344) hydrogen bonds : angle 4.57703 ( 984) metal coordination : bond 0.01759 ( 4) metal coordination : angle 2.02923 ( 3) SS BOND : bond 0.00195 ( 22) SS BOND : angle 0.99376 ( 44) covalent geometry : bond 0.00343 ( 9199) covalent geometry : angle 0.61279 (12463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2866.15 seconds wall clock time: 51 minutes 7.03 seconds (3067.03 seconds total)