Starting phenix.real_space_refine on Fri May 16 09:21:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufi_42208/05_2025/8ufi_42208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufi_42208/05_2025/8ufi_42208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ufi_42208/05_2025/8ufi_42208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufi_42208/05_2025/8ufi_42208.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufi_42208/05_2025/8ufi_42208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufi_42208/05_2025/8ufi_42208.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.045 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 2 5.49 5 Mg 2 5.21 5 S 99 5.16 5 C 9035 2.51 5 N 2381 2.21 5 O 2636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14157 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: 6678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 821, 6678 Classifications: {'peptide': 821} Link IDs: {'PTRANS': 32, 'TRANS': 788} Chain: "C" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 368 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 5, 'TRANS': 42} Chain breaks: 2 Chain: "D" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 379 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 5, 'TRANS': 43} Chain breaks: 2 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.12, per 1000 atoms: 0.57 Number of scatterers: 14157 At special positions: 0 Unit cell: (94.094, 118.91, 165.44, 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 99 16.00 P 2 15.00 Mg 2 11.99 O 2636 8.00 N 2381 7.00 C 9035 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: 3.23 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 902 " - pdb=" NE2 HIS A 599 " pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" ND1 HIS B 597 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 561 " 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3296 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 4 sheets defined 59.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 removed outlier: 3.970A pdb=" N PHE A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.994A pdb=" N ALA A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.769A pdb=" N ASP A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 89 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 138 through 148 removed outlier: 3.585A pdb=" N GLY A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 204 through 249 removed outlier: 4.303A pdb=" N ASN A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.560A pdb=" N VAL A 266 " --> pdb=" O ALA A 262 " (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 464 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 Processing helix chain 'A' and resid 530 through 536 removed outlier: 3.954A pdb=" N LYS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.649A pdb=" N GLY A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 removed outlier: 3.914A pdb=" N ARG A 582 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 583 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 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: 3.671A pdb=" N ASP A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 668 Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.503A pdb=" N TYR A 674 " --> pdb=" O ASP A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 691 removed outlier: 3.535A pdb=" N TYR A 691 " --> pdb=" O GLN A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 704 removed outlier: 3.744A pdb=" N LEU A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 Processing helix chain 'A' and resid 721 through 726 removed outlier: 4.261A pdb=" N THR A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 752 removed outlier: 4.592A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.763A 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: 3.882A pdb=" N VAL A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 821 removed outlier: 3.570A pdb=" N LEU A 799 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 15 Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 47 through 68 removed outlier: 3.703A pdb=" N GLU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.611A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 4.024A 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 removed outlier: 3.503A pdb=" N LEU B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 247 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.520A pdb=" N VAL B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 removed outlier: 3.611A pdb=" N LEU B 268 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 264 through 269' Processing helix chain 'B' and resid 285 through 294 Proline residue: B 291 - end of helix Processing helix chain 'B' and resid 337 through 342 removed outlier: 4.149A 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: 3.525A pdb=" N THR B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 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: 3.833A 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: 5.900A 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 583 through 596 Processing helix chain 'B' and resid 605 through 612 removed outlier: 3.568A pdb=" N GLN B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 623 through 639 Processing helix chain 'B' and resid 640 through 643 Processing helix chain 'B' and resid 649 through 666 Processing helix chain 'B' and resid 668 through 689 removed outlier: 3.534A pdb=" N LYS B 675 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N MET B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 687 " --> pdb=" O VAL B 683 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN B 688 " --> pdb=" O ASP B 684 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 689 " --> pdb=" O GLU B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 702 removed outlier: 3.917A pdb=" N LEU B 701 " --> pdb=" O GLU B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 719 removed outlier: 3.795A pdb=" N LEU B 719 " --> pdb=" O THR B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 751 removed outlier: 4.276A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.892A pdb=" N VAL B 782 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 824 removed outlier: 3.634A pdb=" N PHE B 797 " --> pdb=" O ILE B 793 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 800 " --> pdb=" O MET B 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 78 through 84 Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.505A pdb=" N GLY D 59 " --> pdb=" O GLY D 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 60 " --> pdb=" O MET D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 78 through 84 Processing sheet with id=AA1, first strand: chain 'A' and resid 134 through 135 removed outlier: 6.656A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE A 113 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET A 94 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N ALA A 101 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 14.050A pdb=" N ASP A 187 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASN A 184 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 333 removed outlier: 3.884A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU A 355 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133 removed outlier: 6.422A pdb=" N LEU B 94 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE B 111 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS B 92 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL B 113 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 90 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA B 89 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS B 195 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 91 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL B 187 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N GLN B 99 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 13.909A pdb=" N ASP B 185 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN B 182 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.702A 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: 3.924A pdb=" N LYS B 315 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N CYS B 270 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG B 404 " --> pdb=" O CYS B 270 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B 382 " --> pdb=" O ASN B 403 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2247 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: 4.39 Time building geometry restraints manager: 3.79 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: 2416 1.31 - 1.44: 3763 1.44 - 1.56: 8116 1.56 - 1.69: 6 1.69 - 1.82: 172 Bond restraints: 14473 Sorted by residual: bond pdb=" C2' PCG B 901 " pdb=" C3' PCG B 901 " ideal model delta sigma weight residual 1.514 1.190 0.324 2.00e-02 2.50e+03 2.62e+02 bond pdb=" C2' PCG A 901 " pdb=" C3' PCG A 901 " ideal model delta sigma weight residual 1.514 1.194 0.320 2.00e-02 2.50e+03 2.57e+02 bond pdb=" C3' PCG B 901 " pdb=" C4' PCG B 901 " ideal model delta sigma weight residual 1.519 1.812 -0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C3' PCG A 901 " pdb=" C4' PCG A 901 " ideal model delta sigma weight residual 1.519 1.812 -0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C1' PCG A 901 " pdb=" N9 PCG A 901 " ideal model delta sigma weight residual 1.448 1.220 0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 14468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 19251 2.00 - 4.00: 228 4.00 - 6.00: 43 6.00 - 8.00: 26 8.00 - 10.00: 13 Bond angle restraints: 19561 Sorted by residual: angle pdb=" N ILE A 795 " pdb=" CA ILE A 795 " pdb=" C ILE A 795 " ideal model delta sigma weight residual 112.29 108.61 3.68 9.40e-01 1.13e+00 1.53e+01 angle pdb=" C ASP B 824 " pdb=" N GLN B 825 " pdb=" CA GLN B 825 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.50e+01 angle pdb=" CA GLN A 285 " pdb=" CB GLN A 285 " pdb=" CG GLN A 285 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CB LYS A 186 " pdb=" CG LYS A 186 " pdb=" CD LYS A 186 " ideal model delta sigma weight residual 111.30 119.13 -7.83 2.30e+00 1.89e-01 1.16e+01 angle pdb=" CB GLN C 34 " pdb=" CG GLN C 34 " pdb=" CD GLN C 34 " ideal model delta sigma weight residual 112.60 118.27 -5.67 1.70e+00 3.46e-01 1.11e+01 ... (remaining 19556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7408 17.83 - 35.66: 1045 35.66 - 53.50: 268 53.50 - 71.33: 48 71.33 - 89.16: 20 Dihedral angle restraints: 8789 sinusoidal: 3704 harmonic: 5085 Sorted by residual: dihedral pdb=" CA GLY B 562 " pdb=" C GLY B 562 " pdb=" N PHE B 563 " pdb=" CA PHE B 563 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 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 180.00 161.12 18.88 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ALA A 303 " pdb=" C ALA A 303 " pdb=" N GLY A 304 " pdb=" CA GLY A 304 " ideal model delta harmonic sigma weight residual 180.00 -161.71 -18.29 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2092 0.105 - 0.211: 27 0.211 - 0.316: 0 0.316 - 0.421: 4 0.421 - 0.527: 2 Chirality restraints: 2125 Sorted by residual: chirality pdb=" PA PCG B 901 " pdb=" O2A PCG B 901 " pdb=" O3' PCG B 901 " pdb=" O5' PCG B 901 " both_signs ideal model delta sigma weight residual True 2.70 3.23 -0.53 2.00e-01 2.50e+01 6.93e+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 3.22 -0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" C3' PCG A 901 " pdb=" C2' PCG A 901 " pdb=" C4' PCG A 901 " pdb=" O3' PCG A 901 " both_signs ideal model delta sigma weight residual False -2.45 -2.07 -0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 2122 not shown) Planarity restraints: 2526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 752 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ASP B 752 " 0.055 2.00e-02 2.50e+03 pdb=" O ASP B 752 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 753 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 433 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO A 434 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 444 " -0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" CD GLU A 444 " 0.030 2.00e-02 2.50e+03 pdb=" OE1 GLU A 444 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 444 " -0.010 2.00e-02 2.50e+03 ... (remaining 2523 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 106 2.54 - 3.13: 10917 3.13 - 3.72: 23484 3.72 - 4.31: 31872 4.31 - 4.90: 54315 Nonbonded interactions: 120694 Sorted by model distance: nonbonded pdb=" OD2 ASP A 600 " pdb="ZN ZN A 902 " model vdw 1.947 2.230 nonbonded pdb=" OD1 ASP A 720 " pdb="ZN ZN A 902 " model vdw 1.957 2.230 nonbonded pdb=" OD1 ASP A 600 " pdb="MG MG A 903 " model vdw 2.062 2.170 nonbonded pdb=" OG SER A 246 " pdb=" O PHE D 38 " model vdw 2.164 3.040 nonbonded pdb=" O ASN A 504 " pdb=" OG1 THR A 577 " model vdw 2.200 3.040 ... (remaining 120689 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: 0.010 Normalize map: mean=0, sd=1: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.800 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 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 : 0.010 0.599 14477 Z= 0.444 Angle : 0.635 9.995 19561 Z= 0.318 Chirality : 0.045 0.527 2125 Planarity : 0.004 0.043 2526 Dihedral : 17.796 89.162 5493 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.49 % Favored : 96.33 % Rotamer: Outliers : 0.19 % Allowed : 18.97 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.21), residues: 1718 helix: 1.89 (0.17), residues: 950 sheet: 0.21 (0.46), residues: 142 loop : 0.30 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 561 HIS 0.004 0.001 HIS A 660 PHE 0.009 0.001 PHE B 588 TYR 0.014 0.001 TYR B 783 ARG 0.011 0.000 ARG A 652 Details of bonding type rmsd hydrogen bonds : bond 0.15714 ( 772) hydrogen bonds : angle 5.71282 ( 2247) metal coordination : bond 0.29953 ( 4) covalent geometry : bond 0.00828 (14473) covalent geometry : angle 0.63486 (19561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.8857 (mtp) cc_final: 0.8509 (mtp) REVERT: B 72 MET cc_start: 0.8940 (tmm) cc_final: 0.8667 (tmm) REVERT: B 307 ASP cc_start: 0.8468 (t0) cc_final: 0.8238 (t0) REVERT: D 11 ARG cc_start: 0.8377 (tmm-80) cc_final: 0.8010 (ptm-80) outliers start: 3 outliers final: 2 residues processed: 120 average time/residue: 0.2990 time to fit residues: 51.1509 Evaluate side-chains 118 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain D residue 53 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 GLN A 611 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.050848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.038497 restraints weight = 55352.489| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.51 r_work: 0.2610 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14477 Z= 0.143 Angle : 0.526 7.122 19561 Z= 0.276 Chirality : 0.040 0.141 2125 Planarity : 0.004 0.041 2526 Dihedral : 4.711 39.485 1939 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.43 % Favored : 96.39 % Rotamer: Outliers : 1.48 % Allowed : 17.42 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.21), residues: 1718 helix: 1.85 (0.17), residues: 975 sheet: -0.04 (0.43), residues: 142 loop : 0.33 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 561 HIS 0.005 0.001 HIS B 658 PHE 0.010 0.001 PHE A 19 TYR 0.013 0.001 TYR B 273 ARG 0.004 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 772) hydrogen bonds : angle 4.67238 ( 2247) metal coordination : bond 0.00412 ( 4) covalent geometry : bond 0.00323 (14473) covalent geometry : angle 0.52641 (19561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8896 (mtp) cc_final: 0.8261 (mtt) REVERT: A 94 MET cc_start: 0.8849 (mtp) cc_final: 0.8293 (mtp) REVERT: A 440 MET cc_start: 0.9128 (mmm) cc_final: 0.8805 (mmm) REVERT: A 652 ARG cc_start: 0.8351 (tmm-80) cc_final: 0.8136 (tmm-80) REVERT: B 72 MET cc_start: 0.8809 (tmm) cc_final: 0.8532 (tmm) REVERT: B 688 ASN cc_start: 0.9367 (m-40) cc_final: 0.9072 (m110) REVERT: C 15 ARG cc_start: 0.9284 (mmt-90) cc_final: 0.9043 (mmt-90) REVERT: C 29 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8374 (mptt) REVERT: D 11 ARG cc_start: 0.8474 (tmm-80) cc_final: 0.8000 (ptm-80) outliers start: 23 outliers final: 14 residues processed: 133 average time/residue: 0.3057 time to fit residues: 58.9884 Evaluate side-chains 129 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 5 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 660 HIS A 731 GLN B 9 HIS B 174 ASN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.037221 restraints weight = 55749.910| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.58 r_work: 0.2583 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14477 Z= 0.174 Angle : 0.522 6.831 19561 Z= 0.273 Chirality : 0.040 0.142 2125 Planarity : 0.004 0.041 2526 Dihedral : 4.696 39.827 1935 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.51 % Rotamer: Outliers : 2.39 % Allowed : 17.35 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.21), residues: 1718 helix: 1.92 (0.17), residues: 977 sheet: -0.10 (0.43), residues: 139 loop : 0.31 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 561 HIS 0.006 0.001 HIS B 658 PHE 0.014 0.001 PHE A 19 TYR 0.016 0.001 TYR B 273 ARG 0.005 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 772) hydrogen bonds : angle 4.48555 ( 2247) metal coordination : bond 0.00328 ( 4) covalent geometry : bond 0.00395 (14473) covalent geometry : angle 0.52179 (19561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9302 (t80) cc_final: 0.9067 (t80) REVERT: A 82 MET cc_start: 0.8976 (mtp) cc_final: 0.8758 (mtt) REVERT: A 176 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8325 (p0) REVERT: A 440 MET cc_start: 0.9150 (mmm) cc_final: 0.8794 (mmm) REVERT: A 652 ARG cc_start: 0.8411 (tmm-80) cc_final: 0.8131 (tmm-80) REVERT: B 72 MET cc_start: 0.8898 (tmm) cc_final: 0.8576 (tmm) REVERT: C 15 ARG cc_start: 0.9363 (mmt-90) cc_final: 0.9074 (mmt-90) REVERT: C 17 MET cc_start: 0.7952 (mmt) cc_final: 0.7636 (mmm) REVERT: C 29 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8444 (mptt) REVERT: D 11 ARG cc_start: 0.8552 (tmm-80) cc_final: 0.8030 (ptm-80) REVERT: D 24 ARG cc_start: 0.8665 (ttp80) cc_final: 0.8444 (ttp80) outliers start: 37 outliers final: 19 residues processed: 138 average time/residue: 0.2924 time to fit residues: 59.2468 Evaluate side-chains 130 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 72 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 HIS B 174 ASN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.050377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.037491 restraints weight = 55620.544| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.55 r_work: 0.2554 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14477 Z= 0.126 Angle : 0.501 7.284 19561 Z= 0.260 Chirality : 0.040 0.213 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.631 39.450 1935 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.51 % Rotamer: Outliers : 2.32 % Allowed : 17.81 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.21), residues: 1718 helix: 1.99 (0.17), residues: 974 sheet: -0.01 (0.43), residues: 138 loop : 0.32 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 561 HIS 0.005 0.001 HIS B 658 PHE 0.010 0.001 PHE B 588 TYR 0.016 0.001 TYR B 273 ARG 0.002 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 772) hydrogen bonds : angle 4.34230 ( 2247) metal coordination : bond 0.00157 ( 4) covalent geometry : bond 0.00286 (14473) covalent geometry : angle 0.50123 (19561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9328 (t80) cc_final: 0.9046 (t80) REVERT: A 82 MET cc_start: 0.8963 (mtp) cc_final: 0.8696 (mtp) REVERT: A 94 MET cc_start: 0.8903 (mtp) cc_final: 0.8362 (mtp) REVERT: A 176 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8574 (p0) REVERT: A 652 ARG cc_start: 0.8427 (tmm-80) cc_final: 0.8135 (tmm-80) REVERT: B 72 MET cc_start: 0.8864 (tmm) cc_final: 0.8564 (tmm) REVERT: B 418 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8754 (mtt) REVERT: C 15 ARG cc_start: 0.9348 (mmt-90) cc_final: 0.9043 (mmt-90) REVERT: C 17 MET cc_start: 0.7873 (mmt) cc_final: 0.7583 (mmm) REVERT: C 29 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8425 (mptt) REVERT: D 24 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8480 (ttp80) outliers start: 36 outliers final: 22 residues processed: 140 average time/residue: 0.2925 time to fit residues: 58.4996 Evaluate side-chains 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 569 MET Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 81 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 170 optimal weight: 0.0470 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 HIS ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.038067 restraints weight = 56026.478| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.60 r_work: 0.2609 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.820 14477 Z= 0.256 Angle : 0.497 7.435 19561 Z= 0.257 Chirality : 0.039 0.148 2125 Planarity : 0.003 0.043 2526 Dihedral : 4.559 38.635 1935 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 1.68 % Allowed : 18.39 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.21), residues: 1718 helix: 2.04 (0.17), residues: 977 sheet: 0.12 (0.44), residues: 138 loop : 0.35 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 561 HIS 0.007 0.001 HIS B 658 PHE 0.010 0.001 PHE B 588 TYR 0.016 0.001 TYR B 273 ARG 0.006 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 772) hydrogen bonds : angle 4.22423 ( 2247) metal coordination : bond 0.41018 ( 4) covalent geometry : bond 0.00270 (14473) covalent geometry : angle 0.49737 (19561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9377 (t80) cc_final: 0.9122 (t80) REVERT: A 82 MET cc_start: 0.9019 (mtp) cc_final: 0.8472 (mtm) REVERT: A 94 MET cc_start: 0.8868 (mtp) cc_final: 0.8185 (mtp) REVERT: A 326 LYS cc_start: 0.9008 (tppt) cc_final: 0.8793 (tptp) REVERT: A 377 GLU cc_start: 0.8841 (mp0) cc_final: 0.8575 (pm20) REVERT: A 652 ARG cc_start: 0.8447 (tmm-80) cc_final: 0.8139 (tmm-80) REVERT: B 72 MET cc_start: 0.8857 (tmm) cc_final: 0.8569 (tmm) REVERT: B 174 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8840 (m110) REVERT: B 181 MET cc_start: 0.9347 (mmm) cc_final: 0.9116 (mmm) REVERT: B 438 MET cc_start: 0.9419 (mmm) cc_final: 0.9188 (mmm) REVERT: B 710 MET cc_start: 0.9460 (ttp) cc_final: 0.9237 (ttp) REVERT: C 15 ARG cc_start: 0.9357 (mmt-90) cc_final: 0.9045 (mmt-90) REVERT: C 17 MET cc_start: 0.7947 (mmt) cc_final: 0.7642 (mmm) REVERT: C 34 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8418 (tm-30) REVERT: D 11 ARG cc_start: 0.8550 (tmm-80) cc_final: 0.7977 (ptm-80) REVERT: D 24 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8492 (ttp80) outliers start: 26 outliers final: 17 residues processed: 134 average time/residue: 0.2878 time to fit residues: 56.2183 Evaluate side-chains 130 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 660 HIS B 9 HIS ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.050167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.037428 restraints weight = 56448.999| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.61 r_work: 0.2587 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14477 Z= 0.174 Angle : 0.526 8.882 19561 Z= 0.271 Chirality : 0.040 0.145 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.581 39.316 1935 Min Nonbonded Distance : 1.319 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.55 % Favored : 96.27 % Rotamer: Outliers : 2.00 % Allowed : 18.65 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.21), residues: 1718 helix: 2.09 (0.17), residues: 978 sheet: -0.01 (0.43), residues: 141 loop : 0.39 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 561 HIS 0.012 0.001 HIS B 597 PHE 0.012 0.001 PHE B 588 TYR 0.015 0.001 TYR B 273 ARG 0.004 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 772) hydrogen bonds : angle 4.23434 ( 2247) metal coordination : bond 0.03156 ( 4) covalent geometry : bond 0.00396 (14473) covalent geometry : angle 0.52601 (19561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9401 (t80) cc_final: 0.9102 (t80) REVERT: A 19 PHE cc_start: 0.9035 (t80) cc_final: 0.8619 (t80) REVERT: A 134 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8550 (t80) REVERT: A 326 LYS cc_start: 0.9095 (tppt) cc_final: 0.8836 (tptp) REVERT: A 377 GLU cc_start: 0.8847 (mp0) cc_final: 0.8597 (pm20) REVERT: A 652 ARG cc_start: 0.8436 (tmm-80) cc_final: 0.8114 (tmm-80) REVERT: B 72 MET cc_start: 0.8865 (tmm) cc_final: 0.8596 (tmm) REVERT: B 174 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8820 (m-40) REVERT: B 476 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8797 (mm-30) REVERT: C 15 ARG cc_start: 0.9326 (mmt-90) cc_final: 0.9007 (mmt-90) REVERT: C 17 MET cc_start: 0.7940 (mmt) cc_final: 0.7640 (mmm) REVERT: C 29 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8307 (mptt) REVERT: C 34 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8464 (tm-30) REVERT: D 24 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8484 (ttp80) outliers start: 31 outliers final: 22 residues processed: 135 average time/residue: 0.2852 time to fit residues: 56.3985 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 5 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 169 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 152 optimal weight: 0.0370 chunk 19 optimal weight: 4.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 HIS B 9 HIS ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.036909 restraints weight = 54959.953| |-----------------------------------------------------------------------------| r_work (start): 0.2666 rms_B_bonded: 3.61 r_work: 0.2499 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14477 Z= 0.140 Angle : 0.517 8.954 19561 Z= 0.265 Chirality : 0.039 0.140 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.571 38.859 1935 Min Nonbonded Distance : 1.321 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.49 % Favored : 96.39 % Rotamer: Outliers : 2.32 % Allowed : 18.71 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.21), residues: 1718 helix: 2.12 (0.17), residues: 977 sheet: 0.04 (0.43), residues: 140 loop : 0.42 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 561 HIS 0.009 0.001 HIS B 597 PHE 0.011 0.001 PHE A 565 TYR 0.016 0.001 TYR B 783 ARG 0.005 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 772) hydrogen bonds : angle 4.17884 ( 2247) metal coordination : bond 0.03002 ( 4) covalent geometry : bond 0.00320 (14473) covalent geometry : angle 0.51693 (19561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9419 (t80) cc_final: 0.9119 (t80) REVERT: A 19 PHE cc_start: 0.8995 (t80) cc_final: 0.8525 (t80) REVERT: A 82 MET cc_start: 0.8948 (mtt) cc_final: 0.8717 (mtp) REVERT: A 94 MET cc_start: 0.8731 (mtm) cc_final: 0.8317 (mtp) REVERT: A 114 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.9021 (m-40) REVERT: A 134 PHE cc_start: 0.9234 (OUTLIER) cc_final: 0.8397 (t80) REVERT: A 326 LYS cc_start: 0.9058 (tppt) cc_final: 0.8748 (tptp) REVERT: A 377 GLU cc_start: 0.8874 (mp0) cc_final: 0.8589 (pm20) REVERT: A 652 ARG cc_start: 0.8456 (tmm-80) cc_final: 0.8123 (tmm-80) REVERT: B 72 MET cc_start: 0.8844 (tmm) cc_final: 0.8600 (tmm) REVERT: B 174 ASN cc_start: 0.9123 (OUTLIER) cc_final: 0.8827 (m-40) REVERT: B 181 MET cc_start: 0.9371 (mmm) cc_final: 0.9139 (mmm) REVERT: C 15 ARG cc_start: 0.9253 (mmt-90) cc_final: 0.8904 (mmt-90) REVERT: C 17 MET cc_start: 0.7911 (mmt) cc_final: 0.7624 (mmm) REVERT: D 24 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8500 (ttp80) outliers start: 36 outliers final: 25 residues processed: 138 average time/residue: 0.2719 time to fit residues: 55.4687 Evaluate side-chains 141 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 134 PHE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 36 ARG Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 168 optimal weight: 0.0010 chunk 161 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 660 HIS B 9 HIS ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.037837 restraints weight = 54553.758| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.57 r_work: 0.2556 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14477 Z= 0.115 Angle : 0.511 8.385 19561 Z= 0.262 Chirality : 0.039 0.140 2125 Planarity : 0.003 0.043 2526 Dihedral : 4.505 37.759 1935 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 1.81 % Allowed : 19.23 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.21), residues: 1718 helix: 2.13 (0.17), residues: 977 sheet: 0.08 (0.44), residues: 140 loop : 0.40 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 561 HIS 0.009 0.001 HIS B 597 PHE 0.010 0.001 PHE A 565 TYR 0.016 0.001 TYR B 273 ARG 0.004 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03489 ( 772) hydrogen bonds : angle 4.11779 ( 2247) metal coordination : bond 0.02686 ( 4) covalent geometry : bond 0.00261 (14473) covalent geometry : angle 0.51148 (19561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9430 (t80) cc_final: 0.9172 (t80) REVERT: A 19 PHE cc_start: 0.8994 (t80) cc_final: 0.8593 (t80) REVERT: A 94 MET cc_start: 0.8812 (mtm) cc_final: 0.8387 (mtp) REVERT: A 176 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8287 (p0) REVERT: A 326 LYS cc_start: 0.9111 (tppt) cc_final: 0.8832 (tptp) REVERT: A 377 GLU cc_start: 0.8783 (mp0) cc_final: 0.8497 (pm20) REVERT: A 415 MET cc_start: 0.9605 (mmm) cc_final: 0.9263 (mmm) REVERT: A 652 ARG cc_start: 0.8502 (tmm-80) cc_final: 0.8185 (tmm-80) REVERT: B 174 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8715 (m-40) REVERT: B 476 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8780 (mm-30) REVERT: C 15 ARG cc_start: 0.9329 (mmt-90) cc_final: 0.9022 (mmt-90) REVERT: C 17 MET cc_start: 0.8010 (mmt) cc_final: 0.7726 (mmm) REVERT: C 34 GLN cc_start: 0.8700 (tm130) cc_final: 0.8454 (tm-30) REVERT: D 24 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8508 (ttp80) outliers start: 28 outliers final: 19 residues processed: 134 average time/residue: 0.2835 time to fit residues: 56.0071 Evaluate side-chains 137 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 HIS ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** 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 = 0.3128 r_free = 0.3128 target = 0.051375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.038457 restraints weight = 54950.217| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.64 r_work: 0.2555 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14477 Z= 0.122 Angle : 0.525 9.507 19561 Z= 0.267 Chirality : 0.039 0.138 2125 Planarity : 0.003 0.043 2526 Dihedral : 4.497 37.512 1935 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.49 % Favored : 96.39 % Rotamer: Outliers : 1.55 % Allowed : 19.68 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1718 helix: 2.15 (0.17), residues: 977 sheet: 0.06 (0.43), residues: 140 loop : 0.42 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 561 HIS 0.009 0.001 HIS B 597 PHE 0.010 0.001 PHE A 565 TYR 0.016 0.001 TYR B 273 ARG 0.005 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 772) hydrogen bonds : angle 4.10958 ( 2247) metal coordination : bond 0.02705 ( 4) covalent geometry : bond 0.00280 (14473) covalent geometry : angle 0.52493 (19561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9433 (t80) cc_final: 0.9174 (t80) REVERT: A 19 PHE cc_start: 0.8964 (t80) cc_final: 0.8540 (t80) REVERT: A 94 MET cc_start: 0.8839 (mtm) cc_final: 0.8367 (mtp) REVERT: A 114 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.9055 (m-40) REVERT: A 326 LYS cc_start: 0.9123 (tppt) cc_final: 0.8834 (tptp) REVERT: A 377 GLU cc_start: 0.8771 (mp0) cc_final: 0.8489 (pm20) REVERT: A 415 MET cc_start: 0.9601 (mmm) cc_final: 0.9288 (mmm) REVERT: A 652 ARG cc_start: 0.8485 (tmm-80) cc_final: 0.8159 (tmm-80) REVERT: A 714 MET cc_start: 0.9269 (mmp) cc_final: 0.8964 (mmm) REVERT: B 174 ASN cc_start: 0.9134 (OUTLIER) cc_final: 0.8733 (m-40) REVERT: B 191 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8394 (ttp) REVERT: B 476 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8780 (mm-30) REVERT: C 15 ARG cc_start: 0.9318 (mmt-90) cc_final: 0.8985 (mmt-90) REVERT: C 17 MET cc_start: 0.8026 (mmt) cc_final: 0.7741 (mmm) REVERT: C 34 GLN cc_start: 0.8696 (tm130) cc_final: 0.8442 (tm-30) REVERT: D 24 ARG cc_start: 0.8717 (ttp80) cc_final: 0.8514 (ttp80) outliers start: 24 outliers final: 18 residues processed: 130 average time/residue: 0.2930 time to fit residues: 55.5950 Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 134 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 HIS ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** 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 = 0.3092 r_free = 0.3092 target = 0.050372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.037247 restraints weight = 54718.843| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.68 r_work: 0.2508 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14477 Z= 0.142 Angle : 0.545 9.462 19561 Z= 0.278 Chirality : 0.040 0.143 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.514 37.754 1935 Min Nonbonded Distance : 1.351 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 1.74 % Allowed : 19.61 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1718 helix: 2.12 (0.17), residues: 980 sheet: 0.04 (0.44), residues: 140 loop : 0.46 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 561 HIS 0.008 0.001 HIS B 597 PHE 0.011 0.001 PHE A 565 TYR 0.016 0.001 TYR B 273 ARG 0.005 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 772) hydrogen bonds : angle 4.11971 ( 2247) metal coordination : bond 0.02626 ( 4) covalent geometry : bond 0.00329 (14473) covalent geometry : angle 0.54549 (19561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3436 Ramachandran restraints generated. 1718 Oldfield, 0 Emsley, 1718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9439 (t80) cc_final: 0.9127 (t80) REVERT: A 19 PHE cc_start: 0.8979 (t80) cc_final: 0.8479 (t80) REVERT: A 94 MET cc_start: 0.8819 (mtm) cc_final: 0.8265 (mtp) REVERT: A 114 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.9017 (m-40) REVERT: A 326 LYS cc_start: 0.9160 (tppt) cc_final: 0.8882 (tptp) REVERT: A 377 GLU cc_start: 0.8864 (mp0) cc_final: 0.8587 (pm20) REVERT: A 415 MET cc_start: 0.9526 (mmm) cc_final: 0.9218 (mmm) REVERT: A 652 ARG cc_start: 0.8448 (tmm-80) cc_final: 0.8082 (tmm-80) REVERT: B 174 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8825 (m-40) REVERT: B 476 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8693 (mm-30) REVERT: C 15 ARG cc_start: 0.9237 (mmt-90) cc_final: 0.8906 (mmt-90) REVERT: C 17 MET cc_start: 0.8072 (mmt) cc_final: 0.7794 (mmm) REVERT: C 34 GLN cc_start: 0.8614 (tm130) cc_final: 0.8345 (tm-30) REVERT: D 24 ARG cc_start: 0.8723 (ttp80) cc_final: 0.8513 (ttp80) outliers start: 27 outliers final: 19 residues processed: 130 average time/residue: 0.2898 time to fit residues: 54.7039 Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 174 ASN Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 476 GLU Chi-restraints excluded: chain B residue 597 HIS Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 660 MET Chi-restraints excluded: chain B residue 672 TYR Chi-restraints excluded: chain B residue 722 ILE Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 35 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 117 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 116 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 HIS ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 743 GLN ** 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 = 0.3097 r_free = 0.3097 target = 0.050473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.037523 restraints weight = 55088.810| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.63 r_work: 0.2519 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14477 Z= 0.128 Angle : 0.540 9.493 19561 Z= 0.275 Chirality : 0.039 0.138 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.515 37.628 1935 Min Nonbonded Distance : 1.360 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.49 % Favored : 96.39 % Rotamer: Outliers : 1.48 % Allowed : 19.68 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.21), residues: 1718 helix: 2.14 (0.17), residues: 979 sheet: 0.02 (0.44), residues: 140 loop : 0.46 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 561 HIS 0.008 0.001 HIS B 597 PHE 0.010 0.001 PHE B 588 TYR 0.016 0.001 TYR B 273 ARG 0.005 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 772) hydrogen bonds : angle 4.10286 ( 2247) metal coordination : bond 0.02606 ( 4) covalent geometry : bond 0.00296 (14473) covalent geometry : angle 0.53992 (19561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6017.58 seconds wall clock time: 105 minutes 22.80 seconds (6322.80 seconds total)