Starting phenix.real_space_refine on Sat Oct 11 11:32:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufi_42208/10_2025/8ufi_42208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufi_42208/10_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_42208/10_2025/8ufi_42208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufi_42208/10_2025/8ufi_42208.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufi_42208/10_2025/8ufi_42208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufi_42208/10_2025/8ufi_42208.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.33, per 1000 atoms: 0.24 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: 0.98 Conformation dependent library (CDL) restraints added in 597.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.59 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: 2.33 Time building geometry restraints manager: 1.35 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: 2.900 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.250 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- 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 : 7.94 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (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 ARG 0.011 0.000 ARG A 652 TYR 0.014 0.001 TYR B 783 PHE 0.009 0.001 PHE B 588 TRP 0.018 0.001 TRP A 561 HIS 0.004 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00828 (14473) covalent geometry : angle 0.63486 (19561) hydrogen bonds : bond 0.15714 ( 772) hydrogen bonds : angle 5.71282 ( 2247) metal coordination : bond 0.29953 ( 4) *********************** 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 : 0.525 Fit side-chains 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: 0.1463 time to fit residues: 25.0991 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 : 0.514 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 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 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 = 0.3151 r_free = 0.3151 target = 0.050728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.038148 restraints weight = 56233.492| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.57 r_work: 0.2590 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14477 Z= 0.170 Angle : 0.541 7.125 19561 Z= 0.285 Chirality : 0.040 0.141 2125 Planarity : 0.004 0.040 2526 Dihedral : 4.742 39.921 1939 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.55 % Favored : 96.27 % Rotamer: Outliers : 1.55 % Allowed : 17.81 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.21), residues: 1718 helix: 1.86 (0.17), residues: 975 sheet: -0.07 (0.43), residues: 142 loop : 0.34 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 15 TYR 0.014 0.001 TYR B 273 PHE 0.011 0.001 PHE B 588 TRP 0.016 0.001 TRP A 561 HIS 0.007 0.001 HIS B 561 Details of bonding type rmsd covalent geometry : bond 0.00384 (14473) covalent geometry : angle 0.54110 (19561) hydrogen bonds : bond 0.04477 ( 772) hydrogen bonds : angle 4.70125 ( 2247) metal coordination : bond 0.01213 ( 4) *********************** 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 144 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8898 (mtp) cc_final: 0.8274 (mtt) REVERT: A 94 MET cc_start: 0.8845 (mtp) cc_final: 0.8286 (mtp) REVERT: A 440 MET cc_start: 0.9133 (mmm) cc_final: 0.8806 (mmm) REVERT: A 444 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8635 (tm-30) REVERT: A 652 ARG cc_start: 0.8353 (tmm-80) cc_final: 0.8144 (tmm-80) REVERT: A 661 MET cc_start: 0.9097 (mmt) cc_final: 0.8868 (mmt) REVERT: B 72 MET cc_start: 0.8834 (tmm) cc_final: 0.8490 (tmm) REVERT: B 688 ASN cc_start: 0.9374 (m-40) cc_final: 0.9079 (m110) REVERT: C 15 ARG cc_start: 0.9277 (mmt-90) cc_final: 0.9039 (mmt-90) REVERT: C 29 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8405 (mptt) REVERT: D 11 ARG cc_start: 0.8491 (tmm-80) cc_final: 0.8035 (ptm-80) outliers start: 24 outliers final: 17 residues processed: 132 average time/residue: 0.1296 time to fit residues: 24.9032 Evaluate side-chains 133 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 550 SER 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 165 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 121 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 611 GLN A 631 HIS A 660 HIS A 731 GLN B 9 HIS B 174 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.050771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.038289 restraints weight = 55499.981| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.54 r_work: 0.2617 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1009 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= 0.117 Angle : 0.494 6.821 19561 Z= 0.259 Chirality : 0.039 0.150 2125 Planarity : 0.004 0.043 2526 Dihedral : 4.631 38.900 1935 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.43 % Favored : 96.39 % Rotamer: Outliers : 1.94 % Allowed : 17.94 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.21), residues: 1718 helix: 1.94 (0.17), residues: 975 sheet: -0.02 (0.43), residues: 140 loop : 0.32 (0.27), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 36 TYR 0.015 0.001 TYR B 273 PHE 0.013 0.001 PHE A 19 TRP 0.016 0.001 TRP A 561 HIS 0.005 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00260 (14473) covalent geometry : angle 0.49407 (19561) hydrogen bonds : bond 0.03953 ( 772) hydrogen bonds : angle 4.42909 ( 2247) metal coordination : bond 0.00232 ( 4) *********************** 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 149 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9281 (t80) cc_final: 0.9042 (t80) REVERT: A 176 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8395 (m-40) REVERT: A 440 MET cc_start: 0.9120 (mmm) cc_final: 0.8749 (mmm) REVERT: A 444 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 652 ARG cc_start: 0.8403 (tmm-80) cc_final: 0.8133 (tmm-80) REVERT: B 72 MET cc_start: 0.8898 (tmm) cc_final: 0.8660 (tmm) REVERT: B 174 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8850 (m-40) REVERT: B 569 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8515 (ttm) REVERT: B 688 ASN cc_start: 0.9334 (m-40) cc_final: 0.9095 (m110) REVERT: C 15 ARG cc_start: 0.9322 (mmt-90) cc_final: 0.9018 (mmt-90) REVERT: C 17 MET cc_start: 0.7920 (mmt) cc_final: 0.7603 (mmm) REVERT: C 29 LYS cc_start: 0.8917 (mmmm) cc_final: 0.8361 (mptt) REVERT: D 11 ARG cc_start: 0.8548 (tmm-80) cc_final: 0.8010 (ptm-80) REVERT: D 24 ARG cc_start: 0.8673 (ttp80) cc_final: 0.8451 (ttp80) outliers start: 30 outliers final: 11 residues processed: 137 average time/residue: 0.1334 time to fit residues: 26.6960 Evaluate side-chains 125 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain B residue 174 ASN 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 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 C residue 22 THR 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 67 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.037962 restraints weight = 55940.454| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.56 r_work: 0.2572 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14477 Z= 0.121 Angle : 0.498 7.345 19561 Z= 0.258 Chirality : 0.039 0.197 2125 Planarity : 0.003 0.042 2526 Dihedral : 4.571 38.582 1935 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.43 % Favored : 96.39 % Rotamer: Outliers : 1.81 % Allowed : 18.39 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.21), residues: 1718 helix: 1.98 (0.17), residues: 978 sheet: -0.02 (0.43), residues: 140 loop : 0.36 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 36 TYR 0.016 0.001 TYR B 273 PHE 0.009 0.001 PHE B 588 TRP 0.014 0.001 TRP A 561 HIS 0.006 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00275 (14473) covalent geometry : angle 0.49809 (19561) hydrogen bonds : bond 0.03741 ( 772) hydrogen bonds : angle 4.29347 ( 2247) metal coordination : bond 0.00137 ( 4) *********************** 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 145 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9323 (t80) cc_final: 0.9032 (t80) REVERT: A 176 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8646 (p0) REVERT: A 444 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8554 (tm-30) REVERT: A 652 ARG cc_start: 0.8414 (tmm-80) cc_final: 0.8142 (tmm-80) REVERT: B 72 MET cc_start: 0.8853 (tmm) cc_final: 0.8565 (tmm) REVERT: C 15 ARG cc_start: 0.9345 (mmt-90) cc_final: 0.9044 (mmt-90) REVERT: C 17 MET cc_start: 0.7893 (mmt) cc_final: 0.7591 (mmm) outliers start: 28 outliers final: 16 residues processed: 134 average time/residue: 0.1424 time to fit residues: 27.3945 Evaluate side-chains 133 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain A residue 550 SER 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 chunk 43 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 131 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 729 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 = 0.3190 r_free = 0.3190 target = 0.051469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.038803 restraints weight = 55881.358| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.62 r_work: 0.2635 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14477 Z= 0.107 Angle : 0.494 7.536 19561 Z= 0.254 Chirality : 0.039 0.151 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.503 37.480 1935 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 1.48 % Allowed : 18.45 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.21), residues: 1718 helix: 2.04 (0.17), residues: 977 sheet: 0.00 (0.43), residues: 140 loop : 0.38 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 36 TYR 0.016 0.001 TYR B 273 PHE 0.010 0.001 PHE B 588 TRP 0.014 0.001 TRP A 561 HIS 0.007 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00242 (14473) covalent geometry : angle 0.49378 (19561) hydrogen bonds : bond 0.03522 ( 772) hydrogen bonds : angle 4.17229 ( 2247) metal coordination : bond 0.00101 ( 4) *********************** 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 141 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9375 (t80) cc_final: 0.9124 (t80) REVERT: A 326 LYS cc_start: 0.8994 (tppt) cc_final: 0.8760 (tptp) REVERT: A 360 MET cc_start: 0.9334 (ptm) cc_final: 0.8978 (ptp) REVERT: A 377 GLU cc_start: 0.8850 (mp0) cc_final: 0.8555 (pm20) REVERT: A 444 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8570 (tm-30) REVERT: A 652 ARG cc_start: 0.8477 (tmm-80) cc_final: 0.8152 (tmm-80) REVERT: B 72 MET cc_start: 0.8844 (tmm) cc_final: 0.8553 (tmm) REVERT: B 438 MET cc_start: 0.9420 (mmm) cc_final: 0.9181 (mmm) REVERT: B 710 MET cc_start: 0.9462 (ttp) cc_final: 0.9251 (ttp) REVERT: C 15 ARG cc_start: 0.9343 (mmt-90) cc_final: 0.9041 (mmt-90) REVERT: C 17 MET cc_start: 0.7932 (mmt) cc_final: 0.7625 (mmm) REVERT: D 24 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8441 (ttp80) outliers start: 23 outliers final: 15 residues processed: 132 average time/residue: 0.1346 time to fit residues: 26.0749 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 : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 715 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 0.0970 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.051285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.038563 restraints weight = 55963.580| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 3.56 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: 0.8900 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.896 14477 Z= 0.275 Angle : 0.500 9.242 19561 Z= 0.256 Chirality : 0.039 0.139 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.462 37.137 1935 Min Nonbonded Distance : 1.166 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.38 % Favored : 96.45 % Rotamer: Outliers : 1.55 % Allowed : 18.77 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.21), residues: 1718 helix: 2.11 (0.17), residues: 978 sheet: 0.12 (0.43), residues: 140 loop : 0.38 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 36 TYR 0.016 0.001 TYR B 273 PHE 0.010 0.001 PHE B 588 TRP 0.012 0.001 TRP A 561 HIS 0.007 0.001 HIS B 658 Details of bonding type rmsd covalent geometry : bond 0.00274 (14473) covalent geometry : angle 0.49997 (19561) hydrogen bonds : bond 0.03497 ( 772) hydrogen bonds : angle 4.12297 ( 2247) metal coordination : bond 0.44776 ( 4) *********************** 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 141 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9401 (t80) cc_final: 0.9132 (t80) REVERT: A 19 PHE cc_start: 0.9012 (t80) cc_final: 0.8646 (t80) REVERT: A 326 LYS cc_start: 0.9087 (tppt) cc_final: 0.8834 (tptp) REVERT: A 360 MET cc_start: 0.9342 (ptm) cc_final: 0.8999 (ptp) REVERT: A 444 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8431 (tm-30) REVERT: A 652 ARG cc_start: 0.8413 (tmm-80) cc_final: 0.8088 (tmm-80) REVERT: B 72 MET cc_start: 0.8834 (tmm) cc_final: 0.8542 (tmm) REVERT: B 174 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.8447 (m-40) REVERT: C 15 ARG cc_start: 0.9340 (mmt-90) cc_final: 0.9041 (mmt-90) REVERT: C 17 MET cc_start: 0.8048 (mmt) cc_final: 0.7750 (mmm) REVERT: D 24 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8463 (ttp80) outliers start: 24 outliers final: 13 residues processed: 132 average time/residue: 0.1386 time to fit residues: 26.5662 Evaluate side-chains 126 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 D residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 79 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 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 25 ASN 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 = 0.050571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.037761 restraints weight = 54832.709| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.59 r_work: 0.2550 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14477 Z= 0.137 Angle : 0.518 8.649 19561 Z= 0.265 Chirality : 0.039 0.140 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.490 37.417 1935 Min Nonbonded Distance : 1.372 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.61 % Favored : 96.27 % Rotamer: Outliers : 1.55 % Allowed : 19.23 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.21), residues: 1718 helix: 2.16 (0.17), residues: 978 sheet: 0.09 (0.43), residues: 140 loop : 0.39 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 36 TYR 0.017 0.001 TYR B 783 PHE 0.011 0.001 PHE A 565 TRP 0.012 0.001 TRP A 561 HIS 0.020 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00313 (14473) covalent geometry : angle 0.51817 (19561) hydrogen bonds : bond 0.03515 ( 772) hydrogen bonds : angle 4.10915 ( 2247) metal coordination : bond 0.03606 ( 4) *********************** 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 142 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9423 (t80) cc_final: 0.9149 (t80) REVERT: A 19 PHE cc_start: 0.8999 (t80) cc_final: 0.8589 (t80) REVERT: A 326 LYS cc_start: 0.9090 (tppt) cc_final: 0.8814 (tptp) REVERT: A 360 MET cc_start: 0.9382 (ptm) cc_final: 0.9007 (ptp) REVERT: A 377 GLU cc_start: 0.8906 (mp0) cc_final: 0.8669 (pm20) REVERT: A 444 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8403 (tm-30) REVERT: A 652 ARG cc_start: 0.8454 (tmm-80) cc_final: 0.8112 (tmm-80) REVERT: B 174 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8463 (m-40) REVERT: B 418 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8741 (mtt) REVERT: C 15 ARG cc_start: 0.9326 (mmt-90) cc_final: 0.9021 (mmt-90) REVERT: C 17 MET cc_start: 0.8045 (mmt) cc_final: 0.7751 (mmm) REVERT: D 24 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8494 (ttp80) outliers start: 24 outliers final: 16 residues processed: 132 average time/residue: 0.1354 time to fit residues: 26.3192 Evaluate side-chains 133 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 SER 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 90 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 4 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 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 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 = 0.3129 r_free = 0.3129 target = 0.050866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.038065 restraints weight = 54485.946| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.59 r_work: 0.2560 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14477 Z= 0.122 Angle : 0.512 8.565 19561 Z= 0.262 Chirality : 0.039 0.142 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.476 37.276 1935 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % Rotamer: Outliers : 1.87 % Allowed : 19.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.21), residues: 1718 helix: 2.16 (0.17), residues: 978 sheet: 0.13 (0.43), residues: 140 loop : 0.39 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 36 TYR 0.015 0.001 TYR B 273 PHE 0.010 0.001 PHE B 588 TRP 0.012 0.001 TRP A 561 HIS 0.014 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00278 (14473) covalent geometry : angle 0.51192 (19561) hydrogen bonds : bond 0.03437 ( 772) hydrogen bonds : angle 4.09477 ( 2247) metal coordination : bond 0.03619 ( 4) *********************** 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 145 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9431 (t80) cc_final: 0.9151 (t80) REVERT: A 19 PHE cc_start: 0.8976 (t80) cc_final: 0.8557 (t80) REVERT: A 176 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8182 (p0) REVERT: A 326 LYS cc_start: 0.9111 (tppt) cc_final: 0.8824 (tptp) REVERT: A 360 MET cc_start: 0.9387 (ptm) cc_final: 0.9018 (ptp) REVERT: A 377 GLU cc_start: 0.8823 (mp0) cc_final: 0.8555 (pm20) REVERT: A 415 MET cc_start: 0.9606 (mmm) cc_final: 0.9268 (mmm) REVERT: A 444 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8413 (tm-30) REVERT: A 652 ARG cc_start: 0.8482 (tmm-80) cc_final: 0.8122 (tmm-80) REVERT: B 174 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8456 (m-40) REVERT: B 191 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8396 (ttp) REVERT: B 418 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8711 (mtt) REVERT: B 476 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8810 (mm-30) REVERT: C 15 ARG cc_start: 0.9329 (mmt-90) cc_final: 0.9028 (mmt-90) REVERT: C 17 MET cc_start: 0.8049 (mmt) cc_final: 0.7760 (mmm) REVERT: D 24 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8494 (ttp80) outliers start: 29 outliers final: 17 residues processed: 133 average time/residue: 0.1344 time to fit residues: 26.1034 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 : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ASN 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 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 36 ARG 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 60 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 108 optimal weight: 0.0670 chunk 141 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 0.0010 chunk 111 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 overall best weight: 0.4526 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.038413 restraints weight = 54640.455| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.56 r_work: 0.2576 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14477 Z= 0.112 Angle : 0.521 9.446 19561 Z= 0.266 Chirality : 0.039 0.140 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.464 36.887 1935 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.51 % Rotamer: Outliers : 1.29 % Allowed : 19.81 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.21), residues: 1718 helix: 2.17 (0.17), residues: 978 sheet: 0.15 (0.44), residues: 140 loop : 0.40 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 36 TYR 0.015 0.001 TYR B 273 PHE 0.010 0.001 PHE B 588 TRP 0.013 0.001 TRP A 561 HIS 0.014 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00257 (14473) covalent geometry : angle 0.52144 (19561) hydrogen bonds : bond 0.03375 ( 772) hydrogen bonds : angle 4.05868 ( 2247) metal coordination : bond 0.03411 ( 4) *********************** 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 138 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9434 (t80) cc_final: 0.9154 (t80) REVERT: A 19 PHE cc_start: 0.8980 (t80) cc_final: 0.8555 (t80) REVERT: A 326 LYS cc_start: 0.9125 (tppt) cc_final: 0.8836 (tptp) REVERT: A 360 MET cc_start: 0.9382 (ptm) cc_final: 0.9028 (ptp) REVERT: A 377 GLU cc_start: 0.8815 (mp0) cc_final: 0.8538 (pm20) REVERT: A 415 MET cc_start: 0.9595 (mmm) cc_final: 0.9261 (mmm) REVERT: A 444 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 652 ARG cc_start: 0.8468 (tmm-80) cc_final: 0.8139 (tmm-80) REVERT: B 174 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8457 (m-40) REVERT: B 418 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8706 (mtt) REVERT: B 476 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8818 (mm-30) REVERT: C 15 ARG cc_start: 0.9318 (mmt-90) cc_final: 0.9014 (mmt-90) REVERT: C 17 MET cc_start: 0.8071 (mmt) cc_final: 0.7784 (mmm) REVERT: D 24 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8501 (ttp80) outliers start: 20 outliers final: 15 residues processed: 129 average time/residue: 0.1394 time to fit residues: 25.9712 Evaluate side-chains 132 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 168 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.050884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.037999 restraints weight = 55077.417| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.57 r_work: 0.2566 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14477 Z= 0.136 Angle : 0.539 9.562 19561 Z= 0.273 Chirality : 0.039 0.142 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.491 37.214 1935 Min Nonbonded Distance : 1.319 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % Rotamer: Outliers : 1.55 % Allowed : 19.55 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.21), residues: 1718 helix: 2.18 (0.17), residues: 978 sheet: 0.14 (0.44), residues: 140 loop : 0.42 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 36 TYR 0.015 0.001 TYR B 273 PHE 0.011 0.001 PHE B 563 TRP 0.011 0.001 TRP A 561 HIS 0.014 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00314 (14473) covalent geometry : angle 0.53894 (19561) hydrogen bonds : bond 0.03450 ( 772) hydrogen bonds : angle 4.07290 ( 2247) metal coordination : bond 0.03399 ( 4) ********************** 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: 24 poor density : 117 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.9443 (t80) cc_final: 0.9159 (t80) REVERT: A 19 PHE cc_start: 0.8990 (t80) cc_final: 0.8561 (t80) REVERT: A 326 LYS cc_start: 0.9145 (tppt) cc_final: 0.8920 (tptp) REVERT: A 360 MET cc_start: 0.9382 (ptm) cc_final: 0.9021 (ptp) REVERT: A 377 GLU cc_start: 0.8786 (mp0) cc_final: 0.8530 (pm20) REVERT: A 415 MET cc_start: 0.9595 (mmm) cc_final: 0.9286 (mmm) REVERT: A 444 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 483 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8780 (tp30) REVERT: A 652 ARG cc_start: 0.8470 (tmm-80) cc_final: 0.8149 (tmm-80) REVERT: B 174 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8453 (m-40) REVERT: B 191 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8392 (ttp) REVERT: B 418 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8705 (mtt) REVERT: B 476 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8836 (mm-30) REVERT: C 15 ARG cc_start: 0.9323 (mmt-90) cc_final: 0.9018 (mmt-90) REVERT: C 17 MET cc_start: 0.8079 (mmt) cc_final: 0.7797 (mmm) REVERT: D 24 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8500 (ttp80) outliers start: 24 outliers final: 16 residues processed: 131 average time/residue: 0.1354 time to fit residues: 25.8162 Evaluate side-chains 134 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 GLU 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 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 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: 0.1980 chunk 89 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** 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 = 0.050834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.038040 restraints weight = 54988.214| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.55 r_work: 0.2566 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14477 Z= 0.131 Angle : 0.534 9.473 19561 Z= 0.272 Chirality : 0.039 0.139 2125 Planarity : 0.004 0.042 2526 Dihedral : 4.497 37.481 1935 Min Nonbonded Distance : 1.327 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.43 % Favored : 96.45 % Rotamer: Outliers : 1.42 % Allowed : 19.35 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.21), residues: 1718 helix: 2.19 (0.17), residues: 979 sheet: 0.08 (0.44), residues: 140 loop : 0.43 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 36 TYR 0.015 0.001 TYR B 273 PHE 0.010 0.001 PHE B 563 TRP 0.012 0.001 TRP A 561 HIS 0.015 0.001 HIS B 597 Details of bonding type rmsd covalent geometry : bond 0.00302 (14473) covalent geometry : angle 0.53393 (19561) hydrogen bonds : bond 0.03426 ( 772) hydrogen bonds : angle 4.06178 ( 2247) metal coordination : bond 0.03363 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3082.22 seconds wall clock time: 53 minutes 48.02 seconds (3228.02 seconds total)