Starting phenix.real_space_refine on Thu Jun 12 20:07:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufi_42208/06_2025/8ufi_42208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufi_42208/06_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_42208/06_2025/8ufi_42208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufi_42208/06_2025/8ufi_42208.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufi_42208/06_2025/8ufi_42208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufi_42208/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.55, per 1000 atoms: 0.60 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: 3.48 Conformation dependent library (CDL) restraints added in 1.8 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: 1.54 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: 4.54 Time building geometry restraints manager: 4.13 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: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.090 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- 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 : 1.588 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: 0.3142 time to fit residues: 53.5350 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 : 1.604 ------------------------------------------------------------------------------- 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 = 55352.483| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.51 r_work: 0.2610 rms_B_bonded: 4.01 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 : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8894 (mtp) cc_final: 0.8257 (mtt) REVERT: A 94 MET cc_start: 0.8847 (mtp) cc_final: 0.8291 (mtp) REVERT: A 440 MET cc_start: 0.9128 (mmm) cc_final: 0.8804 (mmm) REVERT: A 652 ARG cc_start: 0.8347 (tmm-80) cc_final: 0.8132 (tmm-80) REVERT: B 72 MET cc_start: 0.8812 (tmm) cc_final: 0.8535 (tmm) REVERT: B 688 ASN cc_start: 0.9367 (m-40) cc_final: 0.9073 (m110) REVERT: C 15 ARG cc_start: 0.9283 (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: 0.8001 (ptm-80) outliers start: 23 outliers final: 14 residues processed: 133 average time/residue: 0.2951 time to fit residues: 57.0857 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 : 1.601 ------------------------------------------------------------------------------- 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: 0.9990 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.049960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.037040 restraints weight = 55869.553| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.58 r_work: 0.2576 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14477 Z= 0.192 Angle : 0.531 6.829 19561 Z= 0.278 Chirality : 0.041 0.143 2125 Planarity : 0.004 0.041 2526 Dihedral : 4.718 40.132 1935 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 2.32 % Allowed : 17.42 % 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: -0.12 (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 0.013 0.001 PHE A 19 TYR 0.016 0.001 TYR B 273 ARG 0.004 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 772) hydrogen bonds : angle 4.50431 ( 2247) metal coordination : bond 0.00457 ( 4) covalent geometry : bond 0.00435 (14473) covalent geometry : angle 0.53074 (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 151 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 115 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9291 (t80) cc_final: 0.9056 (t80) REVERT: A 440 MET cc_start: 0.9152 (mmm) cc_final: 0.8794 (mmm) REVERT: A 652 ARG cc_start: 0.8395 (tmm-80) cc_final: 0.8119 (tmm-80) REVERT: B 72 MET cc_start: 0.8911 (tmm) cc_final: 0.8588 (tmm) REVERT: C 15 ARG cc_start: 0.9360 (mmt-90) cc_final: 0.9072 (mmt-90) REVERT: C 17 MET cc_start: 0.7959 (mmt) cc_final: 0.7645 (mmm) REVERT: C 29 LYS cc_start: 0.8967 (mmmm) cc_final: 0.8449 (mptt) REVERT: D 11 ARG cc_start: 0.8548 (tmm-80) cc_final: 0.8035 (ptm-80) REVERT: D 24 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8440 (ttp80) outliers start: 36 outliers final: 20 residues processed: 135 average time/residue: 0.3455 time to fit residues: 68.6775 Evaluate side-chains 132 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 35 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: 0.5980 chunk 4 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.050382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.037530 restraints weight = 55625.070| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.54 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: 0.8900 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14477 Z= 0.120 Angle : 0.501 7.330 19561 Z= 0.260 Chirality : 0.039 0.210 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.634 39.510 1935 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.51 % Rotamer: Outliers : 2.19 % Allowed : 17.81 % Favored : 80.00 % 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: 1.80 (0.21), residues: 1718 helix: 1.99 (0.17), residues: 974 sheet: -0.02 (0.43), residues: 138 loop : 0.30 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 561 HIS 0.006 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 0.03788 ( 772) hydrogen bonds : angle 4.34591 ( 2247) metal coordination : bond 0.00149 ( 4) covalent geometry : bond 0.00270 (14473) covalent geometry : angle 0.50067 (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 151 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 117 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9297 (t80) cc_final: 0.9040 (t80) REVERT: A 94 MET cc_start: 0.8838 (mtp) cc_final: 0.8261 (mtp) REVERT: A 176 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8379 (m-40) REVERT: A 652 ARG cc_start: 0.8431 (tmm-80) cc_final: 0.8153 (tmm-80) REVERT: A 701 MET cc_start: 0.9272 (tpt) cc_final: 0.8702 (tpp) REVERT: B 72 MET cc_start: 0.8846 (tmm) cc_final: 0.8544 (tmm) REVERT: C 15 ARG cc_start: 0.9348 (mmt-90) cc_final: 0.9044 (mmt-90) REVERT: C 17 MET cc_start: 0.7880 (mmt) cc_final: 0.7590 (mmm) REVERT: C 29 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8428 (mptt) REVERT: D 24 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8480 (ttp80) REVERT: D 38 PHE cc_start: 0.7176 (t80) cc_final: 0.6972 (t80) outliers start: 34 outliers final: 20 residues processed: 139 average time/residue: 0.2963 time to fit residues: 59.5695 Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 318 ASP Chi-restraints excluded: chain B residue 417 LEU 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 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: 0.9980 chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 170 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 chunk 135 optimal weight: 3.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.051208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.038643 restraints weight = 55486.006| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.55 r_work: 0.2622 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14477 Z= 0.108 Angle : 0.496 7.130 19561 Z= 0.256 Chirality : 0.039 0.148 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.556 38.581 1935 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 1.48 % Allowed : 18.65 % 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: 1.89 (0.21), residues: 1718 helix: 2.03 (0.17), residues: 975 sheet: 0.07 (0.44), residues: 138 loop : 0.35 (0.27), residues: 605 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 0.010 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 0.03630 ( 772) hydrogen bonds : angle 4.24030 ( 2247) metal coordination : bond 0.00107 ( 4) covalent geometry : bond 0.00244 (14473) covalent geometry : angle 0.49649 (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 142 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9354 (t80) cc_final: 0.9097 (t80) REVERT: A 326 LYS cc_start: 0.9008 (tppt) cc_final: 0.8784 (tptp) REVERT: A 652 ARG cc_start: 0.8442 (tmm-80) cc_final: 0.8133 (tmm-80) REVERT: A 701 MET cc_start: 0.9285 (tpt) cc_final: 0.8672 (tpp) REVERT: B 72 MET cc_start: 0.8865 (tmm) cc_final: 0.8576 (tmm) REVERT: B 438 MET cc_start: 0.9405 (mmm) cc_final: 0.9170 (mmm) REVERT: C 15 ARG cc_start: 0.9337 (mmt-90) cc_final: 0.9021 (mmt-90) REVERT: C 17 MET cc_start: 0.7944 (mmt) cc_final: 0.7639 (mmm) REVERT: C 34 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8359 (tm-30) REVERT: D 11 ARG cc_start: 0.8483 (tmm-80) cc_final: 0.7857 (ptm-80) REVERT: D 24 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8480 (ttp80) outliers start: 23 outliers final: 15 residues processed: 133 average time/residue: 0.2936 time to fit residues: 57.0445 Evaluate side-chains 128 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 285 GLU 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 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 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: 0.7980 chunk 9 optimal weight: 2.9990 chunk 148 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 597 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.050785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.038292 restraints weight = 55811.175| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.53 r_work: 0.2607 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.799 14477 Z= 0.255 Angle : 0.505 9.163 19561 Z= 0.259 Chirality : 0.039 0.140 2125 Planarity : 0.003 0.043 2526 Dihedral : 4.523 38.165 1935 Min Nonbonded Distance : 1.093 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.51 % Rotamer: Outliers : 1.74 % Allowed : 18.77 % Favored : 79.48 % 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: 1.95 (0.21), residues: 1718 helix: 2.08 (0.17), residues: 977 sheet: 0.06 (0.44), residues: 140 loop : 0.38 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 561 HIS 0.007 0.001 HIS B 658 PHE 0.011 0.001 PHE B 588 TYR 0.016 0.001 TYR B 273 ARG 0.003 0.000 ARG D 11 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 772) hydrogen bonds : angle 4.18259 ( 2247) metal coordination : bond 0.39934 ( 4) covalent geometry : bond 0.00290 (14473) covalent geometry : angle 0.50466 (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 140 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9385 (t80) cc_final: 0.9145 (t80) REVERT: A 94 MET cc_start: 0.8874 (mtp) cc_final: 0.8374 (mtp) REVERT: A 326 LYS cc_start: 0.9090 (tppt) cc_final: 0.8845 (tptp) REVERT: A 377 GLU cc_start: 0.8873 (mp0) cc_final: 0.8593 (pm20) REVERT: A 652 ARG cc_start: 0.8443 (tmm-80) cc_final: 0.8115 (tmm-80) REVERT: B 72 MET cc_start: 0.8866 (tmm) cc_final: 0.8586 (tmm) REVERT: B 181 MET cc_start: 0.9355 (mmm) cc_final: 0.9118 (mmm) REVERT: B 438 MET cc_start: 0.9427 (mmm) cc_final: 0.9214 (mmm) REVERT: C 15 ARG cc_start: 0.9334 (mmt-90) cc_final: 0.9021 (mmt-90) REVERT: C 17 MET cc_start: 0.7916 (mmt) cc_final: 0.7616 (mmm) REVERT: D 24 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8489 (ttp80) outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 0.2919 time to fit residues: 55.1243 Evaluate side-chains 126 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 285 GLU 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 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 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: 3.9990 chunk 97 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 19 optimal weight: 0.0870 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.3135 r_free = 0.3135 target = 0.050777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.037789 restraints weight = 55737.183| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 3.63 r_work: 0.2563 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14477 Z= 0.128 Angle : 0.510 7.855 19561 Z= 0.261 Chirality : 0.039 0.141 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.502 37.850 1935 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 1.61 % Allowed : 19.29 % Favored : 79.10 % 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: 2.00 (0.21), residues: 1718 helix: 2.13 (0.17), residues: 978 sheet: 0.09 (0.44), residues: 140 loop : 0.40 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 561 HIS 0.021 0.001 HIS B 597 PHE 0.010 0.001 PHE B 588 TYR 0.016 0.001 TYR B 783 ARG 0.005 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 772) hydrogen bonds : angle 4.16477 ( 2247) metal coordination : bond 0.04133 ( 4) covalent geometry : bond 0.00289 (14473) covalent geometry : angle 0.50971 (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 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9417 (t80) cc_final: 0.9167 (t80) REVERT: A 94 MET cc_start: 0.8918 (mtp) cc_final: 0.8356 (mtp) REVERT: A 326 LYS cc_start: 0.9091 (tppt) cc_final: 0.8830 (tptp) REVERT: A 377 GLU cc_start: 0.8823 (mp0) cc_final: 0.8531 (pm20) REVERT: A 652 ARG cc_start: 0.8449 (tmm-80) cc_final: 0.8122 (tmm-80) REVERT: A 701 MET cc_start: 0.9244 (tpt) cc_final: 0.8710 (tpp) REVERT: B 174 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.8923 (m-40) REVERT: B 476 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8823 (mm-30) REVERT: C 15 ARG cc_start: 0.9338 (mmt-90) cc_final: 0.9013 (mmt-90) REVERT: C 17 MET cc_start: 0.7860 (mmt) cc_final: 0.7573 (mmm) REVERT: D 24 ARG cc_start: 0.8704 (ttp80) cc_final: 0.8500 (ttp80) outliers start: 25 outliers final: 18 residues processed: 128 average time/residue: 0.2980 time to fit residues: 56.2674 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 : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET 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 174 ASN Chi-restraints excluded: chain B residue 285 GLU 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 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 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: 0.9990 chunk 110 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 168 optimal weight: 0.3980 chunk 161 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3123 r_free = 0.3123 target = 0.050644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.037803 restraints weight = 54560.867| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.59 r_work: 0.2557 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14477 Z= 0.122 Angle : 0.512 9.419 19561 Z= 0.262 Chirality : 0.039 0.144 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.481 37.479 1935 Min Nonbonded Distance : 1.307 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.55 % Favored : 96.33 % Rotamer: Outliers : 1.74 % Allowed : 19.16 % Favored : 79.10 % 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: 2.05 (0.21), residues: 1718 helix: 2.17 (0.17), residues: 977 sheet: 0.12 (0.44), residues: 140 loop : 0.40 (0.27), residues: 601 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 0.016 0.001 TYR B 273 ARG 0.005 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 772) hydrogen bonds : angle 4.12750 ( 2247) metal coordination : bond 0.03402 ( 4) covalent geometry : bond 0.00279 (14473) covalent geometry : angle 0.51154 (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 140 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9436 (t80) cc_final: 0.9157 (t80) REVERT: A 19 PHE cc_start: 0.9013 (t80) cc_final: 0.8594 (t80) REVERT: A 94 MET cc_start: 0.8927 (mtp) cc_final: 0.8345 (mtp) REVERT: A 326 LYS cc_start: 0.9117 (tppt) cc_final: 0.8832 (tptp) REVERT: A 377 GLU cc_start: 0.8791 (mp0) cc_final: 0.8520 (pm20) REVERT: A 652 ARG cc_start: 0.8472 (tmm-80) cc_final: 0.8162 (tmm-80) REVERT: A 701 MET cc_start: 0.9264 (tpt) cc_final: 0.8697 (tpp) REVERT: A 714 MET cc_start: 0.9322 (mmp) cc_final: 0.9034 (mmm) REVERT: B 174 ASN cc_start: 0.9290 (OUTLIER) cc_final: 0.8963 (m-40) REVERT: B 476 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8789 (mm-30) REVERT: C 15 ARG cc_start: 0.9341 (mmt-90) cc_final: 0.9032 (mmt-90) REVERT: C 17 MET cc_start: 0.8014 (mmt) cc_final: 0.7728 (mmm) outliers start: 27 outliers final: 19 residues processed: 128 average time/residue: 0.2805 time to fit residues: 52.8684 Evaluate side-chains 135 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET 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 417 LEU 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 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 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: 1.9990 chunk 109 optimal weight: 0.0020 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.050514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.037662 restraints weight = 54816.318| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 3.60 r_work: 0.2547 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14477 Z= 0.137 Angle : 0.531 8.985 19561 Z= 0.271 Chirality : 0.039 0.139 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.498 37.629 1935 Min Nonbonded Distance : 1.325 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.32 % Favored : 96.57 % 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: 2.04 (0.21), residues: 1718 helix: 2.17 (0.17), residues: 977 sheet: 0.10 (0.44), residues: 140 loop : 0.40 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 561 HIS 0.012 0.001 HIS B 597 PHE 0.013 0.001 PHE B 588 TYR 0.015 0.001 TYR B 273 ARG 0.005 0.000 ARG D 15 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 772) hydrogen bonds : angle 4.12756 ( 2247) metal coordination : bond 0.03148 ( 4) covalent geometry : bond 0.00316 (14473) covalent geometry : angle 0.53141 (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 145 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9443 (t80) cc_final: 0.9125 (t80) REVERT: A 19 PHE cc_start: 0.8999 (t80) cc_final: 0.8492 (t80) REVERT: A 326 LYS cc_start: 0.9141 (tppt) cc_final: 0.8851 (tptp) REVERT: A 377 GLU cc_start: 0.8761 (mp0) cc_final: 0.8492 (pm20) REVERT: A 415 MET cc_start: 0.9579 (mmm) cc_final: 0.9187 (mmm) REVERT: A 440 MET cc_start: 0.9129 (mmm) cc_final: 0.8552 (tpt) REVERT: A 652 ARG cc_start: 0.8489 (tmm-80) cc_final: 0.8174 (tmm-80) REVERT: A 714 MET cc_start: 0.9320 (mmp) cc_final: 0.9009 (mmm) REVERT: B 174 ASN cc_start: 0.9275 (OUTLIER) cc_final: 0.8906 (m-40) REVERT: B 476 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8800 (mm-30) REVERT: C 15 ARG cc_start: 0.9327 (mmt-90) cc_final: 0.8993 (mmt-90) REVERT: C 17 MET cc_start: 0.8024 (mmt) cc_final: 0.7736 (mmm) REVERT: C 34 GLN cc_start: 0.8691 (tm130) cc_final: 0.8433 (tm-30) outliers start: 28 outliers final: 21 residues processed: 133 average time/residue: 0.3026 time to fit residues: 58.4759 Evaluate side-chains 136 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET 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 191 MET Chi-restraints excluded: chain B residue 285 GLU 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 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 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 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: 0.9980 chunk 17 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 170 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 38 optimal weight: 0.0000 chunk 77 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 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 = 0.3102 r_free = 0.3102 target = 0.050662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.037686 restraints weight = 54659.903| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.66 r_work: 0.2522 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14477 Z= 0.124 Angle : 0.537 9.428 19561 Z= 0.274 Chirality : 0.039 0.140 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.471 37.352 1935 Min Nonbonded Distance : 1.334 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 1.55 % Allowed : 19.29 % Favored : 79.16 % 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: 2.01 (0.21), residues: 1718 helix: 2.14 (0.17), residues: 977 sheet: 0.09 (0.44), residues: 140 loop : 0.41 (0.27), residues: 601 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 0.011 0.001 PHE B 563 TYR 0.016 0.001 TYR B 273 ARG 0.010 0.000 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 772) hydrogen bonds : angle 4.11572 ( 2247) metal coordination : bond 0.03134 ( 4) covalent geometry : bond 0.00286 (14473) covalent geometry : angle 0.53722 (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 139 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9447 (t80) cc_final: 0.9175 (t80) REVERT: A 19 PHE cc_start: 0.8998 (t80) cc_final: 0.8583 (t80) REVERT: A 94 MET cc_start: 0.8842 (mtm) cc_final: 0.8410 (mtp) REVERT: A 176 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8190 (p0) REVERT: A 326 LYS cc_start: 0.9145 (tppt) cc_final: 0.8886 (tptp) REVERT: A 377 GLU cc_start: 0.8859 (mp0) cc_final: 0.8569 (pm20) REVERT: A 415 MET cc_start: 0.9487 (mmm) cc_final: 0.9104 (mmm) REVERT: A 440 MET cc_start: 0.9008 (mmm) cc_final: 0.8369 (tpt) REVERT: A 652 ARG cc_start: 0.8453 (tmm-80) cc_final: 0.8078 (tmm-80) REVERT: A 701 MET cc_start: 0.9071 (tpt) cc_final: 0.8542 (tpp) REVERT: B 174 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.8994 (m-40) REVERT: B 476 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8701 (mm-30) REVERT: C 15 ARG cc_start: 0.9212 (mmt-90) cc_final: 0.8885 (mmt-90) REVERT: C 17 MET cc_start: 0.8048 (mmt) cc_final: 0.7772 (mmm) REVERT: C 34 GLN cc_start: 0.8591 (tm130) cc_final: 0.8316 (tm-30) REVERT: C 57 MET cc_start: 0.8198 (mmm) cc_final: 0.7962 (tpp) outliers start: 24 outliers final: 19 residues processed: 129 average time/residue: 0.3039 time to fit residues: 57.7535 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 : 1.665 ------------------------------------------------------------------------------- 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 417 LEU 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 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 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: 0.0870 chunk 38 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN ** A 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 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 = 0.3104 r_free = 0.3104 target = 0.050701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.037631 restraints weight = 54825.872| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.66 r_work: 0.2524 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14477 Z= 0.127 Angle : 0.537 9.529 19561 Z= 0.273 Chirality : 0.039 0.141 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.466 37.291 1935 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 1.48 % Allowed : 19.35 % Favored : 79.16 % 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: 2.01 (0.21), residues: 1718 helix: 2.13 (0.17), residues: 978 sheet: 0.05 (0.44), residues: 140 loop : 0.42 (0.27), residues: 600 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 0.011 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 0.03452 ( 772) hydrogen bonds : angle 4.11468 ( 2247) metal coordination : bond 0.03109 ( 4) covalent geometry : bond 0.00293 (14473) covalent geometry : angle 0.53695 (19561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6682.03 seconds wall clock time: 115 minutes 46.04 seconds (6946.04 seconds total)