Starting phenix.real_space_refine on Sat Aug 23 01:51:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snm_40629/08_2025/8snm_40629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snm_40629/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8snm_40629/08_2025/8snm_40629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snm_40629/08_2025/8snm_40629.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8snm_40629/08_2025/8snm_40629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snm_40629/08_2025/8snm_40629.map" } 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-2.0-5787/lib/python3.9/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, 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: 1.90, per 1000 atoms: 0.21 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: 0.80 Conformation dependent library (CDL) restraints added in 257.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.29 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: 1.14 Time building geometry restraints manager: 1.03 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.100 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.570 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00414 ( 9199) covalent geometry : angle 0.74325 (12463) SS BOND : bond 0.00318 ( 22) SS BOND : angle 1.72893 ( 44) hydrogen bonds : bond 0.14106 ( 344) hydrogen bonds : angle 6.41998 ( 984) metal coordination : bond 0.08411 ( 4) metal coordination : angle 9.45740 ( 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 : 0.251 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: 0.7870 (p) REVERT: C 515 THR cc_start: 0.8782 (p) cc_final: 0.8225 (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: 0.8548 (p) REVERT: C 728 LEU cc_start: 0.7914 (tp) cc_final: 0.7713 (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: 0.5909 (t0) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1011 time to fit residues: 34.8603 Evaluate side-chains 109 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.7394 ------------------------------------------------------------------------------- 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 B 444 HIS B 621 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.115038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.092687 restraints weight = 18378.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095837 restraints weight = 10398.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097939 restraints weight = 7263.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099347 restraints weight = 5767.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.100089 restraints weight = 4955.367| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9225 Z= 0.159 Angle : 0.644 9.655 12510 Z= 0.333 Chirality : 0.044 0.196 1366 Planarity : 0.005 0.084 1602 Dihedral : 4.651 23.501 1221 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.82 % Allowed : 10.51 % 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 aren not related in a simple way. whole: -0.33 (0.24), residues: 1126 helix: 1.54 (0.27), residues: 362 sheet: -0.25 (0.46), residues: 124 loop : -1.32 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 412 TYR 0.023 0.001 TYR C 685 PHE 0.015 0.001 PHE B 655 TRP 0.016 0.001 TRP B 312 HIS 0.006 0.001 HIS B 692 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9199) covalent geometry : angle 0.63200 (12463) SS BOND : bond 0.00451 ( 22) SS BOND : angle 1.77236 ( 44) hydrogen bonds : bond 0.03957 ( 344) hydrogen bonds : angle 5.17133 ( 984) metal coordination : bond 0.03077 ( 4) metal coordination : angle 5.10396 ( 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 143 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.326 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 412 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.7970 (mmm-85) REVERT: C 515 THR cc_start: 0.8331 (p) cc_final: 0.7998 (t) REVERT: C 555 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7959 (t0) REVERT: C 618 ASN cc_start: 0.8738 (t0) cc_final: 0.8452 (t0) REVERT: C 740 ASP cc_start: 0.6119 (p0) cc_final: 0.5588 (p0) REVERT: A 61 GLN cc_start: 0.8365 (tt0) cc_final: 0.8015 (tm-30) REVERT: B 232 ASP cc_start: 0.8441 (t0) cc_final: 0.8174 (t0) REVERT: B 267 TRP cc_start: 0.7625 (m100) cc_final: 0.7288 (m100) REVERT: B 564 ASP cc_start: 0.6563 (m-30) cc_final: 0.5512 (t0) REVERT: B 652 PHE cc_start: 0.8601 (t80) cc_final: 0.8344 (t80) REVERT: B 693 CYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7694 (t) outliers start: 18 outliers final: 6 residues processed: 135 average time/residue: 0.0807 time to fit residues: 15.1559 Evaluate side-chains 95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 537 ILE 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: 0.0570 chunk 84 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 403 GLN C 556 HIS A 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.115169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.092591 restraints weight = 18473.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095666 restraints weight = 10586.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097744 restraints weight = 7432.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098969 restraints weight = 5921.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.100013 restraints weight = 5127.573| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9225 Z= 0.131 Angle : 0.574 9.921 12510 Z= 0.299 Chirality : 0.042 0.152 1366 Planarity : 0.005 0.067 1602 Dihedral : 4.585 23.867 1221 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.12 % Allowed : 12.42 % Favored : 85.45 % 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 aren not related in a simple way. whole: -0.17 (0.24), residues: 1126 helix: 1.80 (0.27), residues: 362 sheet: -0.10 (0.47), residues: 120 loop : -1.31 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 412 TYR 0.015 0.001 TYR C 685 PHE 0.011 0.001 PHE C 668 TRP 0.013 0.001 TRP C 738 HIS 0.005 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9199) covalent geometry : angle 0.56822 (12463) SS BOND : bond 0.00235 ( 22) SS BOND : angle 1.15787 ( 44) hydrogen bonds : bond 0.03580 ( 344) hydrogen bonds : angle 4.81555 ( 984) metal coordination : bond 0.02285 ( 4) metal coordination : angle 3.69285 ( 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 126 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.350 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: 0.7923 (t0) cc_final: 0.7049 (p0) REVERT: C 515 THR cc_start: 0.8267 (p) cc_final: 0.7929 (t) REVERT: C 618 ASN cc_start: 0.8657 (t0) cc_final: 0.8440 (t0) REVERT: C 770 TYR cc_start: 0.6542 (OUTLIER) cc_final: 0.6000 (m-80) REVERT: B 435 MET cc_start: 0.8982 (mmm) cc_final: 0.8238 (mmm) REVERT: B 693 CYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7682 (t) outliers start: 21 outliers final: 11 residues processed: 116 average time/residue: 0.0771 time to fit residues: 12.9890 Evaluate side-chains 97 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 C residue 770 TYR 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 92 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 GLN C 555 ASN C 635 HIS C 648 GLN A 49 ASN A 92 GLN B 497 ASN B 535 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085275 restraints weight = 19172.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.088062 restraints weight = 11260.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.089935 restraints weight = 8062.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.091156 restraints weight = 6509.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.091798 restraints weight = 5669.854| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 9225 Z= 0.271 Angle : 0.694 11.375 12510 Z= 0.359 Chirality : 0.046 0.164 1366 Planarity : 0.005 0.053 1602 Dihedral : 4.832 23.641 1221 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.03 % Allowed : 13.94 % Favored : 83.03 % 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 aren not related in a simple way. whole: -0.34 (0.24), residues: 1126 helix: 1.65 (0.27), residues: 355 sheet: -0.00 (0.47), residues: 114 loop : -1.41 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 412 TYR 0.013 0.002 TYR C 685 PHE 0.020 0.002 PHE C 812 TRP 0.031 0.002 TRP B 267 HIS 0.004 0.001 HIS C 536 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 9199) covalent geometry : angle 0.68652 (12463) SS BOND : bond 0.00413 ( 22) SS BOND : angle 1.46709 ( 44) hydrogen bonds : bond 0.04415 ( 344) hydrogen bonds : angle 4.99609 ( 984) metal coordination : bond 0.04427 ( 4) metal coordination : angle 4.40266 ( 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 131 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8398 (t0) cc_final: 0.7449 (p0) REVERT: C 480 ILE cc_start: 0.8823 (tp) cc_final: 0.8384 (tt) REVERT: C 515 THR cc_start: 0.8309 (p) cc_final: 0.8008 (t) REVERT: B 435 MET cc_start: 0.8992 (mmm) cc_final: 0.8350 (mmm) REVERT: B 689 ILE cc_start: 0.8924 (mm) cc_final: 0.8684 (mt) REVERT: B 693 CYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7667 (t) outliers start: 30 outliers final: 13 residues processed: 124 average time/residue: 0.0883 time to fit residues: 15.1860 Evaluate side-chains 100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 463 ASP 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 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 95 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 0.0030 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 648 GLN ** 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 = 0.3640 r_free = 0.3640 target = 0.114851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092225 restraints weight = 18422.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.095090 restraints weight = 11030.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.097020 restraints weight = 8028.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.098228 restraints weight = 6524.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098930 restraints weight = 5709.486| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9225 Z= 0.134 Angle : 0.597 14.247 12510 Z= 0.305 Chirality : 0.042 0.159 1366 Planarity : 0.004 0.056 1602 Dihedral : 4.515 23.684 1221 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.32 % Allowed : 14.95 % Favored : 82.73 % 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 aren not related in a simple way. whole: -0.26 (0.24), residues: 1126 helix: 1.64 (0.28), residues: 364 sheet: -0.02 (0.48), residues: 112 loop : -1.34 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 412 TYR 0.013 0.001 TYR C 820 PHE 0.014 0.001 PHE C 668 TRP 0.015 0.001 TRP C 661 HIS 0.005 0.001 HIS C 635 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9199) covalent geometry : angle 0.59362 (12463) SS BOND : bond 0.00175 ( 22) SS BOND : angle 1.07341 ( 44) hydrogen bonds : bond 0.03588 ( 344) hydrogen bonds : angle 4.72780 ( 984) metal coordination : bond 0.01929 ( 4) metal coordination : angle 2.35572 ( 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 123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8223 (t0) cc_final: 0.7706 (p0) REVERT: C 515 THR cc_start: 0.8233 (p) cc_final: 0.7896 (t) REVERT: B 435 MET cc_start: 0.8865 (mmm) cc_final: 0.8116 (mmm) REVERT: B 583 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: B 588 LEU cc_start: 0.8109 (mt) cc_final: 0.7419 (mt) outliers start: 23 outliers final: 15 residues processed: 113 average time/residue: 0.0779 time to fit residues: 12.4391 Evaluate side-chains 102 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 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 A residue 78 HIS Chi-restraints excluded: chain A residue 81 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** 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 = 0.3589 r_free = 0.3589 target = 0.112263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088909 restraints weight = 18878.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091605 restraints weight = 11472.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093300 restraints weight = 8443.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.094602 restraints weight = 7000.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.095171 restraints weight = 6131.076| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9225 Z= 0.221 Angle : 0.657 12.323 12510 Z= 0.334 Chirality : 0.044 0.158 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.621 23.823 1221 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.73 % Allowed : 16.77 % Favored : 80.51 % 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 aren not related in a simple way. whole: -0.30 (0.24), residues: 1126 helix: 1.63 (0.28), residues: 358 sheet: -0.13 (0.48), residues: 112 loop : -1.33 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 31 TYR 0.011 0.001 TYR B 298 PHE 0.022 0.002 PHE B 652 TRP 0.060 0.002 TRP C 738 HIS 0.017 0.001 HIS C 556 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 9199) covalent geometry : angle 0.65163 (12463) SS BOND : bond 0.00335 ( 22) SS BOND : angle 1.40825 ( 44) hydrogen bonds : bond 0.04027 ( 344) hydrogen bonds : angle 4.85421 ( 984) metal coordination : bond 0.03351 ( 4) metal coordination : angle 2.96483 ( 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 116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8396 (t0) cc_final: 0.7716 (p0) REVERT: C 515 THR cc_start: 0.8254 (p) cc_final: 0.7952 (t) REVERT: A 61 GLN cc_start: 0.8189 (tt0) cc_final: 0.7605 (tm-30) REVERT: B 583 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7550 (mm-30) outliers start: 27 outliers final: 18 residues processed: 106 average time/residue: 0.0755 time to fit residues: 11.2414 Evaluate side-chains 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 664 ILE 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 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 583 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 670 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.0020 chunk 17 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** 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 = 0.3626 r_free = 0.3626 target = 0.113819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.091488 restraints weight = 18675.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094330 restraints weight = 11217.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.096063 restraints weight = 8105.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.097452 restraints weight = 6629.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098070 restraints weight = 5741.571| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5380 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= 0.124 Angle : 0.586 10.155 12510 Z= 0.297 Chirality : 0.042 0.148 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.394 23.727 1221 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.73 % Allowed : 17.68 % Favored : 79.60 % 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 aren not related in a simple way. whole: -0.17 (0.24), residues: 1126 helix: 1.76 (0.28), residues: 362 sheet: 0.03 (0.49), residues: 106 loop : -1.29 (0.22), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.009 0.001 TYR C 593 PHE 0.012 0.001 PHE C 668 TRP 0.037 0.001 TRP C 738 HIS 0.005 0.001 HIS C 635 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9199) covalent geometry : angle 0.58316 (12463) SS BOND : bond 0.00184 ( 22) SS BOND : angle 1.05905 ( 44) hydrogen bonds : bond 0.03427 ( 344) hydrogen bonds : angle 4.67038 ( 984) metal coordination : bond 0.01731 ( 4) metal coordination : angle 2.03453 ( 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 120 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8322 (t0) cc_final: 0.7933 (p0) REVERT: C 515 THR cc_start: 0.8152 (p) cc_final: 0.7829 (t) REVERT: A 61 GLN cc_start: 0.8351 (tt0) cc_final: 0.7760 (tm-30) outliers start: 27 outliers final: 15 residues processed: 110 average time/residue: 0.0857 time to fit residues: 13.2442 Evaluate side-chains 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 664 ILE 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 781 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 GLN ** B 233 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 = 0.3594 r_free = 0.3594 target = 0.112368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089415 restraints weight = 18796.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.092131 restraints weight = 11376.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093812 restraints weight = 8315.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.095113 restraints weight = 6847.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.095825 restraints weight = 5986.564| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9225 Z= 0.180 Angle : 0.620 11.659 12510 Z= 0.314 Chirality : 0.044 0.273 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.497 23.882 1221 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.12 % Allowed : 18.79 % Favored : 79.09 % 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 aren not related in a simple way. whole: -0.30 (0.24), residues: 1126 helix: 1.64 (0.28), residues: 364 sheet: -0.23 (0.48), residues: 112 loop : -1.34 (0.22), residues: 650 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 0.023 0.002 PHE B 652 TRP 0.032 0.001 TRP C 738 HIS 0.005 0.001 HIS C 635 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 9199) covalent geometry : angle 0.61462 (12463) SS BOND : bond 0.00274 ( 22) SS BOND : angle 1.10484 ( 44) hydrogen bonds : bond 0.03803 ( 344) hydrogen bonds : angle 4.74099 ( 984) metal coordination : bond 0.02424 ( 4) metal coordination : angle 3.78926 ( 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 111 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 427 ASN cc_start: 0.8423 (t0) cc_final: 0.7962 (p0) REVERT: C 515 THR cc_start: 0.8169 (p) cc_final: 0.7861 (t) REVERT: A 30 GLN cc_start: 0.6646 (mm110) cc_final: 0.6386 (mp10) REVERT: A 61 GLN cc_start: 0.8200 (tt0) cc_final: 0.7684 (tm-30) REVERT: A 170 GLU cc_start: 0.8153 (mp0) cc_final: 0.7774 (mp0) REVERT: B 583 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7538 (mm-30) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.0906 time to fit residues: 13.2795 Evaluate side-chains 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 78 HIS 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 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: 0.8980 chunk 10 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 95 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 54 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 16 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.115099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093030 restraints weight = 18564.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.095873 restraints weight = 11086.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097746 restraints weight = 8005.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098823 restraints weight = 6498.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.099726 restraints weight = 5700.823| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9225 Z= 0.105 Angle : 0.581 11.418 12510 Z= 0.292 Chirality : 0.042 0.302 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.235 22.553 1221 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.92 % Allowed : 19.49 % Favored : 78.59 % 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 aren not related in a simple way. whole: -0.13 (0.24), residues: 1126 helix: 1.83 (0.28), residues: 363 sheet: -0.05 (0.50), residues: 106 loop : -1.28 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 412 TYR 0.009 0.001 TYR C 626 PHE 0.028 0.001 PHE B 652 TRP 0.026 0.001 TRP C 738 HIS 0.004 0.001 HIS C 635 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9199) covalent geometry : angle 0.57902 (12463) SS BOND : bond 0.00130 ( 22) SS BOND : angle 0.85673 ( 44) hydrogen bonds : bond 0.03220 ( 344) hydrogen bonds : angle 4.63618 ( 984) metal coordination : bond 0.00593 ( 4) metal coordination : angle 1.61322 ( 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 112 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 515 THR cc_start: 0.8033 (p) cc_final: 0.7715 (t) REVERT: A 30 GLN cc_start: 0.6441 (mm110) cc_final: 0.6161 (mp10) REVERT: A 61 GLN cc_start: 0.8067 (tt0) cc_final: 0.7772 (tm-30) REVERT: A 153 TRP cc_start: 0.8537 (p-90) cc_final: 0.7703 (p-90) REVERT: A 170 GLU cc_start: 0.8036 (mp0) cc_final: 0.7672 (mp0) REVERT: B 583 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: B 588 LEU cc_start: 0.8208 (mt) cc_final: 0.7612 (mt) outliers start: 19 outliers final: 15 residues processed: 105 average time/residue: 0.0904 time to fit residues: 13.4107 Evaluate side-chains 100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 703 PHE 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 781 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 583 GLU Chi-restraints excluded: chain B residue 602 VAL Chi-restraints excluded: chain B residue 670 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 0.0060 chunk 1 optimal weight: 6.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.113986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.091685 restraints weight = 18634.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094469 restraints weight = 11279.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096313 restraints weight = 8226.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097565 restraints weight = 6697.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.098257 restraints weight = 5850.689| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9225 Z= 0.129 Angle : 0.598 11.762 12510 Z= 0.301 Chirality : 0.043 0.312 1366 Planarity : 0.004 0.049 1602 Dihedral : 4.202 22.866 1221 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.82 % Allowed : 19.70 % Favored : 78.48 % 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 aren not related in a simple way. whole: -0.10 (0.24), residues: 1126 helix: 1.89 (0.27), residues: 363 sheet: -0.10 (0.49), residues: 108 loop : -1.27 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 412 TYR 0.029 0.001 TYR B 340 PHE 0.031 0.001 PHE C 812 TRP 0.029 0.001 TRP C 738 HIS 0.004 0.001 HIS C 635 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9199) covalent geometry : angle 0.59608 (12463) SS BOND : bond 0.00176 ( 22) SS BOND : angle 0.87453 ( 44) hydrogen bonds : bond 0.03365 ( 344) hydrogen bonds : angle 4.61771 ( 984) metal coordination : bond 0.01407 ( 4) metal coordination : angle 1.64457 ( 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 105 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 515 THR cc_start: 0.8094 (p) cc_final: 0.7772 (t) REVERT: A 30 GLN cc_start: 0.6594 (mm110) cc_final: 0.6295 (mp10) REVERT: A 61 GLN cc_start: 0.8095 (tt0) cc_final: 0.7789 (tm-30) REVERT: A 153 TRP cc_start: 0.8569 (p-90) cc_final: 0.7718 (p-90) REVERT: A 170 GLU cc_start: 0.8102 (mp0) cc_final: 0.7766 (mp0) REVERT: B 583 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: B 588 LEU cc_start: 0.8277 (mt) cc_final: 0.7639 (mt) outliers start: 18 outliers final: 15 residues processed: 99 average time/residue: 0.0863 time to fit residues: 12.1849 Evaluate side-chains 98 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 556 HIS Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 703 PHE 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 781 LEU 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 583 GLU 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 49 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.092028 restraints weight = 18491.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094813 restraints weight = 11147.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096693 restraints weight = 8107.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097937 restraints weight = 6605.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098652 restraints weight = 5759.563| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5892 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 : 0.603 11.604 12510 Z= 0.300 Chirality : 0.043 0.319 1366 Planarity : 0.004 0.050 1602 Dihedral : 4.162 22.545 1221 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.72 % Allowed : 20.20 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.24), residues: 1126 helix: 1.93 (0.27), residues: 363 sheet: -0.03 (0.50), residues: 106 loop : -1.23 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 412 TYR 0.023 0.001 TYR B 340 PHE 0.024 0.001 PHE B 652 TRP 0.023 0.001 TRP C 738 HIS 0.004 0.001 HIS C 635 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9199) covalent geometry : angle 0.60146 (12463) SS BOND : bond 0.00174 ( 22) SS BOND : angle 0.86286 ( 44) hydrogen bonds : bond 0.03341 ( 344) hydrogen bonds : angle 4.62070 ( 984) metal coordination : bond 0.01424 ( 4) metal coordination : angle 1.66654 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.80 seconds wall clock time: 22 minutes 55.06 seconds (1375.06 seconds total)