Starting phenix.real_space_refine on Sat Oct 11 10:50:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ugs_42234/10_2025/8ugs_42234.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ugs_42234/10_2025/8ugs_42234.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ugs_42234/10_2025/8ugs_42234.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ugs_42234/10_2025/8ugs_42234.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ugs_42234/10_2025/8ugs_42234.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ugs_42234/10_2025/8ugs_42234.map" } resolution = 3.2 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= 0.000 sd= 0.036 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4 5.49 5 Mg 2 5.21 5 S 97 5.16 5 C 8909 2.51 5 N 2351 2.21 5 O 2596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13961 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6682 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 31, 'TRANS': 784} Chain: "B" Number of atoms: 6634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6634 Classifications: {'peptide': 816} Link IDs: {'PTRANS': 32, 'TRANS': 783} Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 269 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 4, 'TRANS': 29} Chain breaks: 1 Chain: "D" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 280 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 4, 'TRANS': 30} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.06, per 1000 atoms: 0.22 Number of scatterers: 13961 At special positions: 0 Unit cell: (95.63, 125.76, 170.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 97 16.00 P 4 15.00 Mg 2 11.99 O 2596 8.00 N 2351 7.00 C 8909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.17 Conformation dependent library (CDL) restraints added in 594.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 599 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 563 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 597 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 561 " 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3246 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 4 sheets defined 61.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.656A pdb=" N PHE A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN A 16 " --> pdb=" O PHE A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.627A pdb=" N ALA A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.661A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 90 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.761A pdb=" N GLU A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 204 through 250 removed outlier: 4.144A pdb=" N ASN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.037A pdb=" N ASN A 271 " --> pdb=" O ARG A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 413 through 430 Processing helix chain 'A' and resid 431 through 459 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.607A pdb=" N ILE A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 removed outlier: 3.983A pdb=" N LYS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 560 through 578 Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.908A pdb=" N ARG A 582 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 599 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 625 through 641 removed outlier: 3.602A pdb=" N ASP A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 669 Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.604A pdb=" N TYR A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 691 Processing helix chain 'A' and resid 693 through 704 removed outlier: 3.674A pdb=" N TRP A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 3.768A pdb=" N LEU A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 753 removed outlier: 4.095A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 767 No H-bonds generated for 'chain 'A' and resid 765 through 767' Processing helix chain 'A' and resid 768 through 780 Processing helix chain 'A' and resid 780 through 792 removed outlier: 3.656A pdb=" N VAL A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 821 Processing helix chain 'B' and resid 8 through 15 Processing helix chain 'B' and resid 15 through 24 Processing helix chain 'B' and resid 47 through 68 removed outlier: 3.808A pdb=" N GLU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.738A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.782A pdb=" N GLU B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 202 through 213 Processing helix chain 'B' and resid 213 through 247 Processing helix chain 'B' and resid 252 through 264 Processing helix chain 'B' and resid 264 through 269 removed outlier: 4.373A pdb=" N ASN B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.314A pdb=" N SER B 342 " --> pdb=" O TRP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 360 through 363 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 428 through 457 removed outlier: 3.708A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 481 through 493 Processing helix chain 'B' and resid 512 through 527 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.673A pdb=" N LYS B 532 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 Processing helix chain 'B' and resid 559 through 575 removed outlier: 6.258A pdb=" N VAL B 565 " --> pdb=" O HIS B 561 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 566 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 582 removed outlier: 3.958A pdb=" N SER B 580 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'B' and resid 605 through 613 removed outlier: 3.500A pdb=" N GLN B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 621 Processing helix chain 'B' and resid 623 through 639 removed outlier: 3.619A pdb=" N GLU B 639 " --> pdb=" O PHE B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 643 Processing helix chain 'B' and resid 649 through 667 removed outlier: 3.548A pdb=" N THR B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 689 removed outlier: 3.574A pdb=" N LYS B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N MET B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 700 Processing helix chain 'B' and resid 702 through 719 Processing helix chain 'B' and resid 719 through 724 removed outlier: 4.351A pdb=" N THR B 723 " --> pdb=" O LEU B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 750 removed outlier: 4.562A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 734 " --> pdb=" O SER B 730 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 765 No H-bonds generated for 'chain 'B' and resid 763 through 765' Processing helix chain 'B' and resid 766 through 778 Processing helix chain 'B' and resid 778 through 790 removed outlier: 3.672A pdb=" N VAL B 782 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 822 Processing helix chain 'D' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.721A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE A 113 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET A 94 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 11.427A pdb=" N ALA A 101 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 14.236A pdb=" N ASP A 187 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASN A 184 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA A 190 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 333 removed outlier: 4.077A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133 removed outlier: 6.810A pdb=" N LEU B 94 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE B 111 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N CYS B 92 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 113 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP B 90 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 89 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYS B 195 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 91 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 187 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N GLN B 99 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 14.321A pdb=" N ASP B 185 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASN B 182 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 188 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 331 removed outlier: 3.986A pdb=" N LYS B 315 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS B 270 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 404 " --> pdb=" O CYS B 270 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 397 " --> pdb=" O ILE B 388 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN B 382 " --> pdb=" O ASN B 403 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2259 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2370 1.31 - 1.44: 3734 1.44 - 1.57: 7991 1.57 - 1.69: 12 1.69 - 1.82: 174 Bond restraints: 14281 Sorted by residual: bond pdb=" C2' PCG B 904 " pdb=" C3' PCG B 904 " ideal model delta sigma weight residual 1.514 1.187 0.327 2.00e-02 2.50e+03 2.67e+02 bond pdb=" C2' PCG A 901 " pdb=" C3' PCG A 901 " ideal model delta sigma weight residual 1.514 1.191 0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C2' PCG B 901 " pdb=" C3' PCG B 901 " ideal model delta sigma weight residual 1.514 1.192 0.322 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C2' PCG A 904 " pdb=" C3' PCG A 904 " ideal model delta sigma weight residual 1.514 1.192 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C3' PCG A 904 " pdb=" C4' PCG A 904 " ideal model delta sigma weight residual 1.519 1.812 -0.293 2.00e-02 2.50e+03 2.15e+02 ... (remaining 14276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 19087 2.53 - 5.06: 162 5.06 - 7.59: 40 7.59 - 10.12: 29 10.12 - 12.65: 2 Bond angle restraints: 19320 Sorted by residual: angle pdb=" C ARG A 40 " pdb=" CA ARG A 40 " pdb=" CB ARG A 40 " ideal model delta sigma weight residual 115.79 109.81 5.98 1.19e+00 7.06e-01 2.53e+01 angle pdb=" CB MET B 155 " pdb=" CG MET B 155 " pdb=" SD MET B 155 " ideal model delta sigma weight residual 112.70 125.35 -12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CA GLN A 285 " pdb=" CB GLN A 285 " pdb=" CG GLN A 285 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 angle pdb=" C5' PCG A 904 " pdb=" O5' PCG A 904 " pdb=" PA PCG A 904 " ideal model delta sigma weight residual 121.82 111.33 10.49 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C5' PCG A 901 " pdb=" O5' PCG A 901 " pdb=" PA PCG A 901 " ideal model delta sigma weight residual 121.82 111.78 10.04 3.00e+00 1.11e-01 1.12e+01 ... (remaining 19315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.23: 7542 20.23 - 40.45: 921 40.45 - 60.68: 197 60.68 - 80.90: 35 80.90 - 101.13: 11 Dihedral angle restraints: 8706 sinusoidal: 3702 harmonic: 5004 Sorted by residual: dihedral pdb=" CA TYR B 402 " pdb=" C TYR B 402 " pdb=" N ASN B 403 " pdb=" CA ASN B 403 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA PRO B 41 " pdb=" C PRO B 41 " pdb=" N GLU B 42 " pdb=" CA GLU B 42 " ideal model delta harmonic sigma weight residual 180.00 -162.12 -17.88 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" C4' PCG B 904 " pdb=" C5' PCG B 904 " pdb=" O5' PCG B 904 " pdb=" PA PCG B 904 " ideal model delta sinusoidal sigma weight residual 53.73 -47.40 101.13 1 3.00e+01 1.11e-03 1.27e+01 ... (remaining 8703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2064 0.107 - 0.214: 28 0.214 - 0.321: 1 0.321 - 0.428: 7 0.428 - 0.535: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" PA PCG B 904 " pdb=" O2A PCG B 904 " pdb=" O3' PCG B 904 " pdb=" O5' PCG B 904 " both_signs ideal model delta sigma weight residual True 2.70 3.23 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" PA PCG A 904 " pdb=" O2A PCG A 904 " pdb=" O3' PCG A 904 " pdb=" O5' PCG A 904 " both_signs ideal model delta sigma weight residual True 2.70 3.22 -0.52 2.00e-01 2.50e+01 6.84e+00 chirality pdb=" PA PCG A 901 " pdb=" O2A PCG A 901 " pdb=" O3' PCG A 901 " pdb=" O5' PCG A 901 " both_signs ideal model delta sigma weight residual True 2.70 3.20 -0.51 2.00e-01 2.50e+01 6.38e+00 ... (remaining 2101 not shown) Planarity restraints: 2482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 132 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO B 133 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 597 " 0.017 2.00e-02 2.50e+03 1.66e-02 4.13e+00 pdb=" CG HIS B 597 " -0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS B 597 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 597 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 597 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 597 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 19 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO D 20 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 20 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 20 " 0.024 5.00e-02 4.00e+02 ... (remaining 2479 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 131 2.60 - 3.18: 12054 3.18 - 3.75: 22446 3.75 - 4.33: 30129 4.33 - 4.90: 50991 Nonbonded interactions: 115751 Sorted by model distance: nonbonded pdb="MG MG B 903 " pdb=" O1A PCG B 904 " model vdw 2.028 2.170 nonbonded pdb=" OD2 ASP A 600 " pdb="ZN ZN A 902 " model vdw 2.075 2.230 nonbonded pdb="MG MG A 903 " pdb=" O1A PCG A 904 " model vdw 2.088 2.170 nonbonded pdb=" CG HIS B 597 " pdb="ZN ZN B 902 " model vdw 2.198 1.960 nonbonded pdb=" OD1 ASN A 607 " pdb=" NE2 GLN A 745 " model vdw 2.257 3.120 ... (remaining 115746 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 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and resid 12 through 86) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.790 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.014 0.896 14285 Z= 0.624 Angle : 0.698 12.652 19320 Z= 0.319 Chirality : 0.049 0.535 2104 Planarity : 0.003 0.051 2482 Dihedral : 17.944 101.128 5460 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 0.20 % Allowed : 18.69 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.21), residues: 1689 helix: 1.72 (0.17), residues: 954 sheet: 0.68 (0.44), residues: 139 loop : -0.16 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 29 TYR 0.011 0.001 TYR B 273 PHE 0.018 0.001 PHE B 163 TRP 0.008 0.001 TRP A 697 HIS 0.017 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.01148 (14281) covalent geometry : angle 0.69763 (19320) hydrogen bonds : bond 0.19835 ( 780) hydrogen bonds : angle 6.21806 ( 2259) metal coordination : bond 0.44828 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 191 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8012 (pttp) cc_final: 0.7803 (mtmm) REVERT: A 193 MET cc_start: 0.8306 (ptm) cc_final: 0.7805 (ppp) REVERT: A 222 MET cc_start: 0.8470 (mmm) cc_final: 0.7910 (mmt) REVERT: A 286 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8514 (mtpp) REVERT: A 296 MET cc_start: 0.7913 (mmm) cc_final: 0.7473 (mmm) REVERT: A 652 ARG cc_start: 0.7144 (tmm160) cc_final: 0.6936 (tmm160) REVERT: A 756 ASN cc_start: 0.8657 (t0) cc_final: 0.8412 (t0) REVERT: A 761 MET cc_start: 0.8545 (mtt) cc_final: 0.8309 (mtm) REVERT: B 96 MET cc_start: 0.8842 (mmm) cc_final: 0.8611 (mmm) REVERT: B 141 HIS cc_start: 0.8119 (t-170) cc_final: 0.7862 (t-170) REVERT: B 190 ILE cc_start: 0.8738 (mt) cc_final: 0.8530 (mp) REVERT: B 209 PHE cc_start: 0.8474 (t80) cc_final: 0.8273 (t80) REVERT: B 681 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8563 (mtpt) REVERT: B 808 LYS cc_start: 0.9008 (tptm) cc_final: 0.8233 (tptm) outliers start: 3 outliers final: 0 residues processed: 191 average time/residue: 0.1289 time to fit residues: 35.2609 Evaluate side-chains 141 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 202 HIS A 611 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS B 729 GLN C 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075901 restraints weight = 35690.393| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.79 r_work: 0.3195 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14285 Z= 0.143 Angle : 0.542 6.120 19320 Z= 0.286 Chirality : 0.040 0.142 2104 Planarity : 0.004 0.055 2482 Dihedral : 4.889 40.388 1966 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.27 % Rotamer: Outliers : 2.03 % Allowed : 17.38 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.60 (0.21), residues: 1689 helix: 1.85 (0.17), residues: 969 sheet: 0.28 (0.42), residues: 140 loop : -0.01 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.015 0.001 TYR B 273 PHE 0.019 0.001 PHE B 209 TRP 0.008 0.001 TRP B 559 HIS 0.009 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00321 (14281) covalent geometry : angle 0.54199 (19320) hydrogen bonds : bond 0.04815 ( 780) hydrogen bonds : angle 4.58678 ( 2259) metal coordination : bond 0.01002 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8341 (ptm) cc_final: 0.7044 (ppp) REVERT: A 286 LYS cc_start: 0.8762 (mtmm) cc_final: 0.8514 (mtpp) REVERT: A 296 MET cc_start: 0.7750 (mmm) cc_final: 0.7483 (mmm) REVERT: A 700 TYR cc_start: 0.7224 (t80) cc_final: 0.6856 (t80) REVERT: A 756 ASN cc_start: 0.8759 (t0) cc_final: 0.8479 (t0) REVERT: B 681 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8565 (mtpp) REVERT: B 714 MET cc_start: 0.9068 (mmm) cc_final: 0.8730 (mmm) REVERT: B 759 MET cc_start: 0.8694 (mtt) cc_final: 0.8488 (mtm) REVERT: B 766 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7411 (mp0) REVERT: D 17 MET cc_start: 0.6769 (mmm) cc_final: 0.6541 (mmm) outliers start: 31 outliers final: 11 residues processed: 165 average time/residue: 0.1344 time to fit residues: 32.1432 Evaluate side-chains 136 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 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 = 0.3725 r_free = 0.3725 target = 0.096125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.075217 restraints weight = 35965.837| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.81 r_work: 0.3187 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14285 Z= 0.138 Angle : 0.517 7.348 19320 Z= 0.270 Chirality : 0.039 0.145 2104 Planarity : 0.004 0.054 2482 Dihedral : 4.895 40.968 1966 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 2.49 % Allowed : 16.33 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.21), residues: 1689 helix: 1.91 (0.17), residues: 962 sheet: 0.12 (0.41), residues: 141 loop : -0.10 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 48 TYR 0.016 0.001 TYR B 273 PHE 0.016 0.001 PHE B 209 TRP 0.007 0.001 TRP B 559 HIS 0.008 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00317 (14281) covalent geometry : angle 0.51700 (19320) hydrogen bonds : bond 0.04419 ( 780) hydrogen bonds : angle 4.35411 ( 2259) metal coordination : bond 0.00419 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.6874 (OUTLIER) cc_final: 0.6454 (m-40) REVERT: A 286 LYS cc_start: 0.8745 (mtmm) cc_final: 0.8522 (mtpp) REVERT: A 638 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8881 (mt) REVERT: A 756 ASN cc_start: 0.8758 (t0) cc_final: 0.8493 (t0) REVERT: B 174 ASN cc_start: 0.7001 (OUTLIER) cc_final: 0.6206 (p0) REVERT: B 671 LEU cc_start: 0.8268 (tt) cc_final: 0.8050 (mp) REVERT: B 681 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8382 (mtpp) REVERT: B 697 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: B 712 MET cc_start: 0.8244 (mpp) cc_final: 0.7784 (mpp) REVERT: B 759 MET cc_start: 0.8724 (mtt) cc_final: 0.8518 (mtm) outliers start: 38 outliers final: 19 residues processed: 163 average time/residue: 0.1201 time to fit residues: 29.0605 Evaluate side-chains 145 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 159 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.075903 restraints weight = 36251.025| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.86 r_work: 0.3199 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14285 Z= 0.116 Angle : 0.498 7.113 19320 Z= 0.259 Chirality : 0.039 0.129 2104 Planarity : 0.004 0.055 2482 Dihedral : 4.780 40.692 1966 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 2.36 % Allowed : 17.51 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.61 (0.21), residues: 1689 helix: 1.96 (0.17), residues: 962 sheet: 0.01 (0.41), residues: 141 loop : -0.09 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 27 TYR 0.016 0.001 TYR B 273 PHE 0.016 0.001 PHE B 209 TRP 0.007 0.001 TRP B 559 HIS 0.006 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00264 (14281) covalent geometry : angle 0.49768 (19320) hydrogen bonds : bond 0.03927 ( 780) hydrogen bonds : angle 4.25768 ( 2259) metal coordination : bond 0.00300 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.6669 (OUTLIER) cc_final: 0.6302 (m-40) REVERT: A 193 MET cc_start: 0.8385 (ptm) cc_final: 0.7196 (ppp) REVERT: A 296 MET cc_start: 0.7782 (mmm) cc_final: 0.7153 (ttt) REVERT: A 638 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8839 (mt) REVERT: B 146 LYS cc_start: 0.8156 (tptt) cc_final: 0.7937 (tptt) REVERT: B 681 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8358 (mtpp) outliers start: 36 outliers final: 16 residues processed: 158 average time/residue: 0.1175 time to fit residues: 27.8792 Evaluate side-chains 137 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.096403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.075374 restraints weight = 36238.899| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.86 r_work: 0.3200 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14285 Z= 0.125 Angle : 0.501 8.817 19320 Z= 0.259 Chirality : 0.039 0.133 2104 Planarity : 0.004 0.055 2482 Dihedral : 4.779 40.792 1966 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.14 % Favored : 96.80 % Rotamer: Outliers : 2.49 % Allowed : 17.70 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.65 (0.21), residues: 1689 helix: 2.00 (0.17), residues: 962 sheet: 0.07 (0.41), residues: 140 loop : -0.10 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 27 TYR 0.015 0.001 TYR B 273 PHE 0.014 0.001 PHE B 209 TRP 0.006 0.001 TRP B 559 HIS 0.004 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00289 (14281) covalent geometry : angle 0.50122 (19320) hydrogen bonds : bond 0.03879 ( 780) hydrogen bonds : angle 4.20733 ( 2259) metal coordination : bond 0.00311 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.6638 (OUTLIER) cc_final: 0.6299 (m-40) REVERT: A 285 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7265 (tm-30) REVERT: A 296 MET cc_start: 0.7885 (mmm) cc_final: 0.7374 (ttt) REVERT: A 638 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8882 (mt) REVERT: A 793 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7488 (tm-30) REVERT: B 146 LYS cc_start: 0.8269 (tptt) cc_final: 0.7893 (tptt) REVERT: B 174 ASN cc_start: 0.6761 (OUTLIER) cc_final: 0.6007 (p0) REVERT: B 185 ASP cc_start: 0.7687 (m-30) cc_final: 0.6798 (m-30) REVERT: B 293 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7994 (tt) REVERT: B 681 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8420 (mtpt) REVERT: B 697 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8075 (mp0) outliers start: 38 outliers final: 18 residues processed: 156 average time/residue: 0.1140 time to fit residues: 26.8478 Evaluate side-chains 144 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.095961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.075059 restraints weight = 36093.158| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.84 r_work: 0.3178 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14285 Z= 0.134 Angle : 0.510 8.911 19320 Z= 0.262 Chirality : 0.039 0.143 2104 Planarity : 0.004 0.054 2482 Dihedral : 4.765 40.676 1966 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.03 % Allowed : 18.69 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.21), residues: 1689 helix: 2.03 (0.17), residues: 962 sheet: 0.07 (0.40), residues: 140 loop : -0.13 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 27 TYR 0.016 0.001 TYR B 783 PHE 0.013 0.001 PHE B 209 TRP 0.006 0.001 TRP B 559 HIS 0.004 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00313 (14281) covalent geometry : angle 0.50976 (19320) hydrogen bonds : bond 0.03868 ( 780) hydrogen bonds : angle 4.20312 ( 2259) metal coordination : bond 0.00307 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ASN cc_start: 0.6645 (OUTLIER) cc_final: 0.6296 (m-40) REVERT: A 193 MET cc_start: 0.8298 (ptm) cc_final: 0.7049 (ppp) REVERT: A 285 GLN cc_start: 0.7329 (tm-30) cc_final: 0.7041 (tm-30) REVERT: A 638 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8872 (mt) REVERT: A 712 MET cc_start: 0.8561 (ttm) cc_final: 0.8350 (ttp) REVERT: A 793 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 26 LYS cc_start: 0.7907 (tmtt) cc_final: 0.7550 (tmtt) REVERT: B 146 LYS cc_start: 0.8080 (tptt) cc_final: 0.7873 (tptt) REVERT: B 174 ASN cc_start: 0.6759 (OUTLIER) cc_final: 0.6051 (p0) REVERT: B 185 ASP cc_start: 0.7595 (m-30) cc_final: 0.6920 (m-30) REVERT: B 293 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7963 (tt) REVERT: B 681 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8365 (mtpp) REVERT: B 697 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: C 83 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6492 (tp-100) outliers start: 31 outliers final: 19 residues processed: 149 average time/residue: 0.1175 time to fit residues: 26.5768 Evaluate side-chains 141 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 9 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 15 optimal weight: 0.0470 chunk 84 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 162 optimal weight: 0.0030 chunk 119 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 overall best weight: 0.2288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 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 = 0.3759 r_free = 0.3759 target = 0.098225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.077752 restraints weight = 35934.773| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.84 r_work: 0.3233 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14285 Z= 0.098 Angle : 0.484 9.398 19320 Z= 0.248 Chirality : 0.038 0.170 2104 Planarity : 0.003 0.053 2482 Dihedral : 4.570 39.112 1966 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.10 % Allowed : 18.82 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.80 (0.21), residues: 1689 helix: 2.14 (0.17), residues: 961 sheet: 0.13 (0.41), residues: 140 loop : -0.08 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.019 0.001 TYR B 783 PHE 0.015 0.001 PHE B 209 TRP 0.007 0.001 TRP B 559 HIS 0.003 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00216 (14281) covalent geometry : angle 0.48413 (19320) hydrogen bonds : bond 0.03402 ( 780) hydrogen bonds : angle 4.08318 ( 2259) metal coordination : bond 0.00084 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8112 (ptm) cc_final: 0.6930 (ppp) REVERT: A 638 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8854 (mt) REVERT: B 26 LYS cc_start: 0.7807 (tmtt) cc_final: 0.7517 (tmtt) REVERT: B 174 ASN cc_start: 0.6839 (OUTLIER) cc_final: 0.6127 (p0) REVERT: B 185 ASP cc_start: 0.7404 (m-30) cc_final: 0.6569 (m-30) REVERT: B 209 PHE cc_start: 0.8245 (t80) cc_final: 0.7976 (t80) REVERT: B 293 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7866 (tt) REVERT: B 681 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8425 (mtpt) REVERT: B 714 MET cc_start: 0.8877 (mmm) cc_final: 0.8522 (mmm) outliers start: 32 outliers final: 19 residues processed: 152 average time/residue: 0.1225 time to fit residues: 28.1961 Evaluate side-chains 141 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 163 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 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 = 0.3722 r_free = 0.3722 target = 0.096077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.075046 restraints weight = 35938.091| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.83 r_work: 0.3177 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14285 Z= 0.148 Angle : 0.526 9.939 19320 Z= 0.267 Chirality : 0.039 0.196 2104 Planarity : 0.004 0.056 2482 Dihedral : 4.692 39.740 1966 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.90 % Allowed : 19.28 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.21), residues: 1689 helix: 2.10 (0.17), residues: 962 sheet: 0.03 (0.40), residues: 141 loop : -0.11 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.014 0.001 TYR B 97 PHE 0.017 0.001 PHE B 588 TRP 0.005 0.001 TRP B 559 HIS 0.004 0.001 HIS A 630 Details of bonding type rmsd covalent geometry : bond 0.00343 (14281) covalent geometry : angle 0.52552 (19320) hydrogen bonds : bond 0.03823 ( 780) hydrogen bonds : angle 4.12114 ( 2259) metal coordination : bond 0.00350 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.8412 (ptm) cc_final: 0.7287 (ppp) REVERT: A 360 MET cc_start: 0.8509 (ttm) cc_final: 0.8268 (ttm) REVERT: A 638 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8877 (mt) REVERT: B 26 LYS cc_start: 0.7920 (tmtt) cc_final: 0.7664 (tmtt) REVERT: B 66 MET cc_start: 0.8504 (mtm) cc_final: 0.8151 (ttm) REVERT: B 174 ASN cc_start: 0.6711 (OUTLIER) cc_final: 0.6017 (p0) REVERT: B 185 ASP cc_start: 0.7377 (m-30) cc_final: 0.6809 (m-30) REVERT: B 209 PHE cc_start: 0.8222 (t80) cc_final: 0.7949 (t80) REVERT: B 293 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7829 (tt) REVERT: B 681 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8364 (mtpp) REVERT: B 697 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: B 714 MET cc_start: 0.8951 (mmm) cc_final: 0.8616 (mmm) outliers start: 29 outliers final: 20 residues processed: 144 average time/residue: 0.1048 time to fit residues: 23.3306 Evaluate side-chains 139 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 42 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 162 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 144 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 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 = 0.3735 r_free = 0.3735 target = 0.096777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.075790 restraints weight = 36199.962| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.86 r_work: 0.3191 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14285 Z= 0.113 Angle : 0.507 10.400 19320 Z= 0.257 Chirality : 0.038 0.189 2104 Planarity : 0.004 0.054 2482 Dihedral : 4.621 38.919 1966 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.90 % Allowed : 19.21 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.21), residues: 1689 helix: 2.14 (0.17), residues: 961 sheet: 0.11 (0.40), residues: 140 loop : -0.09 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.016 0.001 TYR B 783 PHE 0.020 0.001 PHE B 588 TRP 0.006 0.001 TRP B 559 HIS 0.003 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00263 (14281) covalent geometry : angle 0.50663 (19320) hydrogen bonds : bond 0.03602 ( 780) hydrogen bonds : angle 4.08810 ( 2259) metal coordination : bond 0.00218 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8457 (ptm) cc_final: 0.7332 (ppp) REVERT: A 296 MET cc_start: 0.7873 (mmm) cc_final: 0.7640 (ttt) REVERT: A 638 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8832 (mt) REVERT: B 66 MET cc_start: 0.8483 (mtm) cc_final: 0.8144 (ttm) REVERT: B 174 ASN cc_start: 0.6897 (OUTLIER) cc_final: 0.6246 (p0) REVERT: B 185 ASP cc_start: 0.7355 (m-30) cc_final: 0.6818 (m-30) REVERT: B 293 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7725 (tt) REVERT: B 681 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8430 (mtpt) REVERT: B 714 MET cc_start: 0.8893 (mmm) cc_final: 0.8535 (mmm) REVERT: C 83 GLN cc_start: 0.7360 (OUTLIER) cc_final: 0.6515 (tp-100) outliers start: 29 outliers final: 22 residues processed: 139 average time/residue: 0.1164 time to fit residues: 24.5837 Evaluate side-chains 142 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 9 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 133 optimal weight: 0.0980 chunk 110 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 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 = 0.3731 r_free = 0.3731 target = 0.096579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.075660 restraints weight = 36201.351| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.86 r_work: 0.3191 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14285 Z= 0.117 Angle : 0.517 10.115 19320 Z= 0.264 Chirality : 0.039 0.188 2104 Planarity : 0.004 0.054 2482 Dihedral : 4.574 38.674 1966 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.84 % Allowed : 19.61 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.80 (0.21), residues: 1689 helix: 2.15 (0.17), residues: 961 sheet: 0.14 (0.40), residues: 140 loop : -0.09 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 27 TYR 0.016 0.001 TYR B 783 PHE 0.018 0.001 PHE B 588 TRP 0.005 0.001 TRP B 559 HIS 0.003 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00271 (14281) covalent geometry : angle 0.51706 (19320) hydrogen bonds : bond 0.03636 ( 780) hydrogen bonds : angle 4.08497 ( 2259) metal coordination : bond 0.00235 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 MET cc_start: 0.8405 (ptm) cc_final: 0.7384 (ppp) REVERT: A 638 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8841 (mt) REVERT: B 66 MET cc_start: 0.8470 (mtm) cc_final: 0.8159 (ttm) REVERT: B 174 ASN cc_start: 0.6891 (OUTLIER) cc_final: 0.6287 (p0) REVERT: B 293 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7703 (tt) REVERT: B 681 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8366 (mtpp) outliers start: 28 outliers final: 22 residues processed: 137 average time/residue: 0.1183 time to fit residues: 24.7422 Evaluate side-chains 137 residues out of total 1525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 674 TYR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 796 MET Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 90 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 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 = 0.3732 r_free = 0.3732 target = 0.096614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075715 restraints weight = 35967.159| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.85 r_work: 0.3192 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14285 Z= 0.119 Angle : 0.526 10.223 19320 Z= 0.267 Chirality : 0.039 0.185 2104 Planarity : 0.004 0.054 2482 Dihedral : 4.569 38.424 1966 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.84 % Allowed : 19.54 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.78 (0.21), residues: 1689 helix: 2.13 (0.17), residues: 961 sheet: 0.06 (0.40), residues: 141 loop : -0.07 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 604 TYR 0.015 0.001 TYR B 783 PHE 0.015 0.001 PHE B 588 TRP 0.006 0.001 TRP B 559 HIS 0.003 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00279 (14281) covalent geometry : angle 0.52567 (19320) hydrogen bonds : bond 0.03651 ( 780) hydrogen bonds : angle 4.10037 ( 2259) metal coordination : bond 0.00239 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3150.15 seconds wall clock time: 54 minutes 57.24 seconds (3297.24 seconds total)